From 96c9a1a4c3d92fe5e42eb7d5f81431e154f58f71 Mon Sep 17 00:00:00 2001
From: rahul799 <rahulagrawal799110@gmail.com>
Date: Wed, 5 Feb 2020 21:57:11 +0530
Subject: [PATCH 1/2] adding-prettierignore

---
 .prettierignore | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 .prettierignore

diff --git a/.prettierignore b/.prettierignore
new file mode 100644
index 0000000..d331b78
--- /dev/null
+++ b/.prettierignore
@@ -0,0 +1,22 @@
+**/leaflet/**
+**/sugarcane/**
+**/vignettes/**
+*min.js
+*min.css
+*png
+*eps
+*pdf
+*ai
+*svg
+*map
+*sh
+*yml
+*json
+*md
+*bak
+*txt
+*gif
+*pegjs
+*.template
+*.ejs
+.prettierignore
\ No newline at end of file

From 59ccb42be0dbd933f497414ac5ee7932dee1b5f8 Mon Sep 17 00:00:00 2001
From: rahul799 <rahulagrawal799110@gmail.com>
Date: Wed, 5 Feb 2020 22:03:18 +0530
Subject: [PATCH 2/2] running-prettier

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-    <link rel="stylesheet" href="owl-carousel/owl.theme.css">     
-    <link rel="stylesheet" href="css/template-style.css">
-    <link href='https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
-    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
+    <link rel="stylesheet" href="css/components.css" />
+    <link rel="stylesheet" href="css/icons.css" />
+    <link rel="stylesheet" href="css/responsee.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.carousel.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.theme.css" />
+    <link rel="stylesheet" href="css/template-style.css" />
+    <link
+      href="https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
+    <link
+      href="https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
     <script type="text/javascript" src="js/jquery-1.8.3.min.js"></script>
-    <script type="text/javascript" src="js/jquery-ui.min.js"></script>      
+    <script type="text/javascript" src="js/jquery-ui.min.js"></script>
   </head>
-  
+
   <body class="size-1140">
-  	<a target="_blank" class="hide-s" href="https://github.com/PecanProject" style="position:fixed;top:120px;right:-14px;z-index:10;"><img src="images/view-on-github.png" alt="" style="width: 200px; padding-right: 10px;"></a>
-    
+    <a
+      target="_blank"
+      class="hide-s"
+      href="https://github.com/PecanProject"
+      style="position:fixed;top:120px;right:-14px;z-index:10;"
+      ><img
+        src="images/view-on-github.png"
+        alt=""
+        style="width: 200px; padding-right: 10px;"
+    /></a>
+
     <!-- HEADER -->
-    
-        <header role="banner" class="position-absolute">    
+
+    <header role="banner" class="position-absolute">
       <!-- Top Navigation -->
       <nav class="background-dark background-transparent-hightlight full-width">
         <div class="s-12 l-2">
           <a href="index.html" class="logo">
             <!-- Logo White Version -->
-            <img class="logo-white" src="images/logo.png" alt="">
+            <img class="logo-white" src="images/logo.png" alt="" />
             <!-- Logo Dark Version -->
-            <img class="logo-dark" src="images/logo.png" alt="">
+            <img class="logo-dark" src="images/logo.png" alt="" />
           </a>
         </div>
         <div class="top-nav s-12 l-10 background-dark">
-          
           <ul class="right chevron">
             <li><a href="index.html">Home</a></li>
-            <li><a>About</a>
+            <li>
+              <a>About</a>
               <ul>
-                <li><a href="people.html" style="color: black;font-weight: 800;">People</a></li>
-                <li><a href="news.html" style="color: black;font-weight: 800;">News</a></li>
-                <li><a href="pecan_workshop.html" style="color: black;font-weight: 800;">Workshop</a></li>
-                <li><a href="contact.html" style="color: black;font-weight: 800;">Contact Us</a></li>
+                <li>
+                  <a href="people.html" style="color: black;font-weight: 800;"
+                    >People</a
+                  >
+                </li>
+                <li>
+                  <a href="news.html" style="color: black;font-weight: 800;"
+                    >News</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="pecan_workshop.html"
+                    style="color: black;font-weight: 800;"
+                    >Workshop</a
+                  >
+                </li>
+                <li>
+                  <a href="contact.html" style="color: black;font-weight: 800;"
+                    >Contact Us</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a>Documentation</a>
+            <li>
+              <a>Documentation</a>
               <ul>
-                <li><a href="documentation.html" style="color: black;font-weight: 800;">Documentation</a></li>
-                <li><a href="pkgdocs.html" style="color: black;font-weight: 800;">Package Documentation</a></li>
-                <li><a href="tutorials.html" style="color: black;font-weight: 800;">Tutorials</a></li>
-                <li><a href="http://pecan.ncsa.illinois.edu/pecan" style="color: black;font-weight: 800;">Demo</a></li>
+                <li>
+                  <a
+                    href="documentation.html"
+                    style="color: black;font-weight: 800;"
+                    >Documentation</a
+                  >
+                </li>
+                <li>
+                  <a href="pkgdocs.html" style="color: black;font-weight: 800;"
+                    >Package Documentation</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="tutorials.html"
+                    style="color: black;font-weight: 800;"
+                    >Tutorials</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="http://pecan.ncsa.illinois.edu/pecan"
+                    style="color: black;font-weight: 800;"
+                    >Demo</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN">Download</a></li>
-            <li><a>Google</a>
+            <li>
+              <a
+                href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN"
+                >Download</a
+              >
+            </li>
+            <li>
+              <a>Google</a>
               <ul>
-                <li><a href="gsoc.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
-                <li><a href="gsod.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
+                <li>
+                  <a href="gsoc.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
+                <li>
+                  <a href="gsod.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
               </ul>
             </li>
             <li><a href="Report_an_issue.html">Bug Report</a></li>
@@ -69,20 +152,25 @@
       </nav>
     </header>
 
-    
     <!-- MAIN CONTENT -->
     <section class="section background-white text-center">
-    <div id="main_content_wrap" class="outer">
-      <section id="main_content" class="inner">
-
-        <iframe src="https://docs.google.com/forms/d/e/1FAIpQLSdNo42zV63L8bXo0gX5ag9-8Ut_pHwKIEmuEf7uXSOPA2JqAw/viewform?embedded=true" width="640" height="1504" frameborder="0" marginheight="0" marginwidth="0">Loading…</iframe>
-  
-      </section>
-    </div>
+      <div id="main_content_wrap" class="outer">
+        <section id="main_content" class="inner">
+          <iframe
+            src="https://docs.google.com/forms/d/e/1FAIpQLSdNo42zV63L8bXo0gX5ag9-8Ut_pHwKIEmuEf7uXSOPA2JqAw/viewform?embedded=true"
+            width="640"
+            height="1504"
+            frameborder="0"
+            marginheight="0"
+            marginwidth="0"
+            >Loading…</iframe
+          >
+        </section>
+      </div>
     </section>
-    
-    <!-- scripts -->    
-  
+
+    <!-- scripts -->
+
     <script type="text/javascript" src="js/responsee.js"></script>
     <script type="text/javascript" src="owl-carousel/owl.carousel.js"></script>
     <script type="text/javascript" src="js/template-scripts.js"></script>
@@ -90,27 +178,44 @@
     <!-- FOOTER  -->
     <div id="footer_wrap" class="outer">
       <footer class="inner">
-        <p>Published with <a href="http://pages.github.com" style="color: rgb(255, 255, 255);" >GitHub Pages</a></p>
+        <p>
+          Published with
+          <a href="http://pages.github.com" style="color: rgb(255, 255, 255);"
+            >GitHub Pages</a
+          >
+        </p>
       </footer>
     </div>
 
     <script>
-      (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-      (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-      m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-      })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-
-      ga('create', 'UA-28628282-1', 'pecanproject.github.io');
-      ga('require', 'displayfeatures');
-      ga('send', 'pageview');
+      (function(i, s, o, g, r, a, m) {
+        i["GoogleAnalyticsObject"] = r;
+        (i[r] =
+          i[r] ||
+          function() {
+            (i[r].q = i[r].q || []).push(arguments);
+          }),
+          (i[r].l = 1 * new Date());
+        (a = s.createElement(o)), (m = s.getElementsByTagName(o)[0]);
+        a.async = 1;
+        a.src = g;
+        m.parentNode.insertBefore(a, m);
+      })(
+        window,
+        document,
+        "script",
+        "//www.google-analytics.com/analytics.js",
+        "ga"
+      );
 
+      ga("create", "UA-28628282-1", "pecanproject.github.io");
+      ga("require", "displayfeatures");
+      ga("send", "pageview");
     </script>
     <script>
       ((window.gitter = {}).chat = {}).options = {
-    room: 'PecanProject/pecan'
+        room: "PecanProject/pecan"
       };
     </script>
-
-    
   </body>
-</html>
\ No newline at end of file
+</html>
diff --git a/base/all/docs/LICENSE-text.html b/base/all/docs/LICENSE-text.html
index 3037df3..0ad2322 100644
--- a/base/all/docs/LICENSE-text.html
+++ b/base/all/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>License • PEcAn.all</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="License" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>License • PEcAn.all</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.all</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.all</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/all/docs/authors.html b/base/all/docs/authors.html
index 3c3bd20..7bff9c9 100644
--- a/base/all/docs/authors.html
+++ b/base/all/docs/authors.html
@@ -2,202 +2,211 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Citation and Authors • PEcAn.all</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="pkgdown.css" rel="stylesheet">
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Citation and Authors • PEcAn.all</title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
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+    <link href="pkgdown.css" rel="stylesheet" />
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+
+    <meta property="og:title" content="Citation and Authors" />
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-citation-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Citation</h1>
-    </div>
-
-    <p>LeBauer DS, Wang D, Richter KT, Davidson CC and Dietze MC (2012).
-&ldquo;Feedbacks between measurements and models facilitated by scientific workflows: the Predictive Ecosystem Analyzer.&rdquo;
-<em>Ecological Monographs</em>.
-<a href="pecanproject.org">pecanproject.org</a>. 
-</p>
-    <pre>@Article{,
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Citation</h1>
+          </div>
+
+          <p>
+            LeBauer DS, Wang D, Richter KT, Davidson CC and Dietze MC (2012).
+            &ldquo;Feedbacks between measurements and models facilitated by
+            scientific workflows: the Predictive Ecosystem Analyzer.&rdquo;
+            <em>Ecological Monographs</em>.
+            <a href="pecanproject.org">pecanproject.org</a>.
+          </p>
+          <pre>
+@Article{,
   author = {David S. LeBauer and Dan Wang and Katherine T. Richter and Carl C. Davidson and Michael C. Dietze},
   title = {Feedbacks between measurements and models facilitated by scientific workflows: the Predictive Ecosystem Analyzer},
   journal = {Ecological Monographs},
   year = {2012},
   url = {pecanproject.org},
-}</pre>
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Ankur Desai</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>James Simkins</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Chris Black</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Istem Fer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Hamze Dookohaki</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Alexey Shiklomanov</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Elizabeth Cowdery</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Ann Raiho</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Tess McCabe</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Tony Gardella</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+}</pre
+          >
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Ankur Desai</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>James Simkins</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Chris Black</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Istem Fer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Hamze Dookohaki</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Alexey Shiklomanov</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Elizabeth Cowdery</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Ann Raiho</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Tess McCabe</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Tony Gardella</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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diff --git a/base/all/docs/docsearch.css b/base/all/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/base/all/docs/docsearch.css
+++ b/base/all/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/base/all/docs/docsearch.js b/base/all/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/base/all/docs/docsearch.js
+++ b/base/all/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/base/all/docs/index.html b/base/all/docs/index.html
index 81633fa..6a9cf3a 100644
--- a/base/all/docs/index.html
+++ b/base/all/docs/index.html
@@ -1,123 +1,177 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
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-<meta charset="utf-8">
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-<title>PEcAn functions used for ecological forecasts and
-    reanalysis • PEcAn.all</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and
-    reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis • PEcAn.all
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+    <script
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+    />
+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and
+    reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer
     (PEcAn) is a scientific workflow management tool that
     is designed to simplify the management of model
     parameterization, execution, and analysis. The goal of
     PEcAn is to streamline the interaction between data and
     models, and to improve the efficacy of scientific
-    investigation.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.all</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.all</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer
-    (PEcAn) is a scientific workflow management tool that
-    is designed to simplify the management of model
-    parameterization, execution, and analysis. The goal of
-    PEcAn is to streamline the interaction between data and
-    models, and to improve the efficacy of scientific
-    investigation.
-  </div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PEcAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="citation">
-<h2>Citation</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">Citing PEcAn.all</a></li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="citation">
+            <h2>Citation</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">Citing PEcAn.all</a></li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-  </div>
-</div>
-
-
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/base/all/docs/pkgdown.css b/base/all/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/base/all/docs/pkgdown.css
+++ b/base/all/docs/pkgdown.css
@@ -13,7 +13,8 @@
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  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/base/all/docs/pkgdown.js b/base/all/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/base/all/docs/pkgdown.js
+++ b/base/all/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/base/all/docs/reference/index.html b/base/all/docs/reference/index.html
index fa801ef..ff99a77 100644
--- a/base/all/docs/reference/index.html
+++ b/base/all/docs/reference/index.html
@@ -2,129 +2,149 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title> • PEcAn.all</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
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-<!-- clipboard.js -->
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-<!-- sticky kit -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>• PEcAn.all</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+    <link
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+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
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+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+
+    <!-- clipboard.js -->
+    <script
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+
+    <!-- sticky kit -->
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.all</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
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-
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-      
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/db/docs/LICENSE-text.html b/base/db/docs/LICENSE-text.html
index e90264f..61530ff 100644
--- a/base/db/docs/LICENSE-text.html
+++ b/base/db/docs/LICENSE-text.html
@@ -2,112 +2,149 @@
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-
-<!-- clipboard.js -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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   </head>
 
   <body>
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-        <a class="navbar-link" href="index.html">PEcAn.DB</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    <div id="navbar" class="navbar-collapse collapse">
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-  <a href="index.html">
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
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-  <ul class="dropdown-menu" role="menu">
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-      <a href="articles/betydb_access.html">BETYdb Access</a>
-    </li>
-    <li>
-      <a href="articles/create_sites.geometry.html">Create PostGIS polygon</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
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-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -136,27 +173,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
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-
+</pre
+          >
+        </div>
+      </div>
 
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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+        </div>
       </footer>
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-
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+    </div>
   </body>
 </html>
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diff --git a/base/db/docs/articles/betydb_access.html b/base/db/docs/articles/betydb_access.html
index 2adfaf1..1817d6b 100644
--- a/base/db/docs/articles/betydb_access.html
+++ b/base/db/docs/articles/betydb_access.html
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-<!-- Generated by pkgdown: do not edit by hand --><html>
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+<!-- Generated by pkgdown: do not edit by hand -->
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+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+    <!-- sticky kit -->
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+      crossorigin="anonymous"
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+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    <![endif]-->
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     <div class="container template-article">
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header toc-ignore">
+            <h1>BETYdb Access</h1>
+            <h4 class="author">David LeBauer</h4>
 
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="../articles/betydb_access.html">BETYdb Access</a>
-    </li>
-    <li>
-      <a href="../articles/create_sites.geometry.html">Create PostGIS polygon</a>
-    </li>
-  </ul>
-</li>
-      </ul>
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-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header toc-ignore">
-      <h1>BETYdb Access</h1>
-                        <h4 class="author">David LeBauer</h4>
-            
             <h4 class="date">7/30/2015</h4>
-      
-      
-      <div class="hidden name"><code>betydb_access.Rmd</code></div>
 
-    </div>
+            <div class="hidden name"><code>betydb_access.Rmd</code></div>
+          </div>
 
-    
-    
-<p>Ways to Access BETYdb from R</p>
-<div id="pecan-db-functions" class="section level3">
-<h3 class="hasAnchor">
-<a href="#pecan-db-functions" class="anchor"></a>PEcAn.DB functions</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">settings &lt;-<span class="kw">list</span>(<span class="dt">database =</span> <span class="kw">list</span>(<span class="dt">bety =</span> <span class="kw">list</span>(<span class="dt">driver =</span> <span class="st">"PostgreSQL"</span>, <span class="dt">user =</span> <span class="st">"bety"</span>, <span class="dt">dbname =</span> <span class="st">"bety"</span>, <span class="dt">password =</span> <span class="st">"bety"</span>)))
+          <p>Ways to Access BETYdb from R</p>
+          <div id="pecan-db-functions" class="section level3">
+            <h3 class="hasAnchor">
+              <a href="#pecan-db-functions" class="anchor"></a>PEcAn.DB
+              functions
+            </h3>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">settings &lt;-<span class="kw">list</span>(<span class="dt">database =</span> <span class="kw">list</span>(<span class="dt">bety =</span> <span class="kw">list</span>(<span class="dt">driver =</span> <span class="st">"PostgreSQL"</span>, <span class="dt">user =</span> <span class="st">"bety"</span>, <span class="dt">dbname =</span> <span class="st">"bety"</span>, <span class="dt">password =</span> <span class="st">"bety"</span>)))
 
 <span class="co"># equivalent to standard method to load PEcAn settings:</span>
 <span class="co"># settings &lt;- read.settings("pecan.xml")</span>
@@ -101,13 +160,25 @@ <h3 class="hasAnchor">
 
 salix_spp &lt;-<span class="st"> </span><span class="kw"><a href="../reference/query.pft_species.html">query.pft_species</a></span>(<span class="dt">pft =</span> <span class="st">"salix"</span>, <span class="dt">modeltype =</span> <span class="st">"BIOCRO"</span>, <span class="dt">con =</span> dbcon)
 
-salix_vcmax &lt;-<span class="st"> </span><span class="kw"><a href="../reference/query.trait.data.html">query.trait.data</a></span>(<span class="dt">trait =</span> <span class="st">"Vcmax"</span>, <span class="dt">spstr =</span> <span class="kw">vecpaste</span>(salix_spp<span class="op">$</span>id), <span class="dt">con =</span> dbcon)</code></pre></div>
-</div>
-<div id="r-dplyr-interface" class="section level3">
-<h3 class="hasAnchor">
-<a href="#r-dplyr-interface" class="anchor"></a>R dplyr interface</h3>
-<p>Documentation for the <code>dplyr</code> interface to databases is provided in the <a href="https://cran.r-project.org/web/packages/dplyr/vignettes/databases.html">dplyr vignette</a></p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(dplyr)
+salix_vcmax &lt;-<span class="st"> </span><span class="kw"><a href="../reference/query.trait.data.html">query.trait.data</a></span>(<span class="dt">trait =</span> <span class="st">"Vcmax"</span>, <span class="dt">spstr =</span> <span class="kw">vecpaste</span>(salix_spp<span class="op">$</span>id), <span class="dt">con =</span> dbcon)</code></pre>
+            </div>
+          </div>
+          <div id="r-dplyr-interface" class="section level3">
+            <h3 class="hasAnchor">
+              <a href="#r-dplyr-interface" class="anchor"></a>R dplyr interface
+            </h3>
+            <p>
+              Documentation for the <code>dplyr</code> interface to databases is
+              provided in the
+              <a
+                href="https://cran.r-project.org/web/packages/dplyr/vignettes/databases.html"
+                >dplyr vignette</a
+              >
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(dplyr)
 d &lt;-<span class="st"> </span>settings<span class="op">$</span>database<span class="op">$</span>bety[<span class="kw">c</span>(<span class="st">"dbname"</span>, <span class="st">"password"</span>, <span class="st">"host"</span>, <span class="st">"user"</span>)]
 bety &lt;-<span class="st"> </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/src_dbi.html">src_postgres</a></span>(<span class="dt">host =</span> d<span class="op">$</span>host, <span class="dt">user =</span> d<span class="op">$</span>user, <span class="dt">password =</span> d<span class="op">$</span>password, <span class="dt">dbname =</span> d<span class="op">$</span>dbname)
 
@@ -127,12 +198,18 @@ <h3 class="hasAnchor">
 mxgdata &lt;-<span class="st"> </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/join.html">inner_join</a></span>(species, yields, <span class="dt">by =</span> <span class="st">'specie_id'</span>) <span class="op">%&gt;%</span>
 <span class="st">  </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/join.html">left_join</a></span>(sites, <span class="dt">by =</span> <span class="st">'site_id'</span>) <span class="op">%&gt;%</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/reexports.html">ends_with</a></span>(<span class="st">".x"</span>), <span class="op">-</span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/reexports.html">ends_with</a></span>(<span class="st">".y"</span>)) <span class="op">%&gt;%</span><span class="st"> </span><span class="co"># drops duplicate rows</span>
-<span class="st">  </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/compute.html">collect</a></span>() </code></pre></div>
-</div>
-<div id="ropensci-traits-api" class="section level3">
-<h3 class="hasAnchor">
-<a href="#ropensci-traits-api" class="anchor"></a>rOpensci traits API</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># install_github("ropensci/traits")</span>
+<span class="st">  </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/compute.html">collect</a></span>() </code></pre>
+            </div>
+          </div>
+          <div id="ropensci-traits-api" class="section level3">
+            <h3 class="hasAnchor">
+              <a href="#ropensci-traits-api" class="anchor"></a>rOpensci traits
+              API
+            </h3>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="co"># install_github("ropensci/traits")</span>
 <span class="kw">library</span>(<span class="st">"traits"</span>)
 
 out &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/traits/topics/betydb_query">betydb_search</a></span>(<span class="dt">query =</span> <span class="st">"Switchgrass Yield"</span>)
@@ -142,28 +219,25 @@ <h3 class="hasAnchor">
 out <span class="op">%&gt;%</span>
 <span class="st">  </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(id) <span class="op">%&gt;%</span>
 <span class="st">  </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span>(<span class="dt">mean_result =</span> <span class="kw">mean</span>(<span class="kw">as.numeric</span>(mean), <span class="dt">na.rm =</span> <span class="ot">TRUE</span>)) <span class="op">%&gt;%</span>
-<span class="st">  </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/arrange.html">arrange</a></span>(<span class="kw"><a href="http://dplyr.tidyverse.org/reference/desc.html">desc</a></span>(mean_result))</code></pre></div>
-</div>
-  </div>
+<span class="st">  </span><span class="kw"><a href="http://dplyr.tidyverse.org/reference/arrange.html">arrange</a></span>(<span class="kw"><a href="http://dplyr.tidyverse.org/reference/desc.html">desc</a></span>(mean_result))</code></pre>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"></div>
       </div>
 
-</div>
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-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
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 </html>
diff --git a/base/db/docs/articles/create_sites.geometry.html b/base/db/docs/articles/create_sites.geometry.html
index 8ba595f..c0a1ece 100644
--- a/base/db/docs/articles/create_sites.geometry.html
+++ b/base/db/docs/articles/create_sites.geometry.html
@@ -1,112 +1,210 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
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-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+    <title>Create PostGIS polygon • PEcAn.DB</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+    <meta property="og:title" content="Create PostGIS polygon" />
+    <meta property="og:description" content="" />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-article">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-        <a class="navbar-link" href="../index.html">PEcAn.DB</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
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+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="../articles/betydb_access.html">BETYdb Access</a>
-    </li>
-    <li>
-      <a href="../articles/create_sites.geometry.html">Create PostGIS polygon</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header toc-ignore">
+            <h1>Create PostGIS polygon</h1>
+            <h4 class="author">David LeBauer</h4>
 
-      
-      </header><div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header toc-ignore">
-      <h1>Create PostGIS polygon</h1>
-                        <h4 class="author">David LeBauer</h4>
-            
             <h4 class="date">7/30/2015</h4>
-      
-      
-      <div class="hidden name"><code>create_sites.geometry.Rmd</code></div>
 
-    </div>
+            <div class="hidden name">
+              <code>create_sites.geometry.Rmd</code>
+            </div>
+          </div>
 
-    
-    
-<p>Code used to insert a polygon for Champaign County into a PostGIS geometry column.</p>
-<p>Note that the <code>sites.geometry</code> column has three dimensions. Latitude and longitude are queried using <code><a href="http://www.rdocumentation.org/packages/ggplot2/topics/map_data">ggplot2::map_data('counties')</a></code> and elevation data is queried using <code>rgbif::elevation(latidutde, longitude)</code>.</p>
-<p>This query is used to define the boundary of <a href="https://www.betydb.org/sites/1254">site 1254, Champaign County</a>, which will be used for testing and development of regional runs of PEcAn</p>
-<div id="load-libraries" class="section level3">
-<h3 class="hasAnchor">
-<a href="#load-libraries" class="anchor"></a>Load Libraries</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(ggplot2)
+          <p>
+            Code used to insert a polygon for Champaign County into a PostGIS
+            geometry column.
+          </p>
+          <p>
+            Note that the <code>sites.geometry</code> column has three
+            dimensions. Latitude and longitude are queried using
+            <code
+              ><a
+                href="http://www.rdocumentation.org/packages/ggplot2/topics/map_data"
+                >ggplot2::map_data('counties')</a
+              ></code
+            >
+            and elevation data is queried using
+            <code>rgbif::elevation(latidutde, longitude)</code>.
+          </p>
+          <p>
+            This query is used to define the boundary of
+            <a href="https://www.betydb.org/sites/1254"
+              >site 1254, Champaign County</a
+            >, which will be used for testing and development of regional runs
+            of PEcAn
+          </p>
+          <div id="load-libraries" class="section level3">
+            <h3 class="hasAnchor">
+              <a href="#load-libraries" class="anchor"></a>Load Libraries
+            </h3>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(ggplot2)
 <span class="kw">library</span>(data.table)
 <span class="kw">library</span>(rgbif)
-<span class="kw">library</span>(knitr)</code></pre></div>
-</div>
-<div id="select-lat-and-lon-points-for-champaign-county-boundary" class="section level3">
-<h3 class="hasAnchor">
-<a href="#select-lat-and-lon-points-for-champaign-county-boundary" class="anchor"></a>Select lat and lon points for Champaign County Boundary</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">d &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/data.table">data.table</a></span>(<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/map_data">map_data</a></span>(<span class="st">"county"</span>))
+<span class="kw">library</span>(knitr)</code></pre>
+            </div>
+          </div>
+          <div
+            id="select-lat-and-lon-points-for-champaign-county-boundary"
+            class="section level3"
+          >
+            <h3 class="hasAnchor">
+              <a
+                href="#select-lat-and-lon-points-for-champaign-county-boundary"
+                class="anchor"
+              ></a
+              >Select lat and lon points for Champaign County Boundary
+            </h3>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">d &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/data.table">data.table</a></span>(<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/map_data">map_data</a></span>(<span class="st">"county"</span>))
 champaign &lt;-<span class="st"> </span>d[region <span class="op">==</span><span class="st"> "illinois"</span> <span class="op">&amp;</span><span class="st"> </span>subregion <span class="op">==</span><span class="st"> "champaign"</span>]
 
-<span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(champaign)</code></pre></div>
-</div>
-<div id="query-elevation-points" class="section level3">
-<h3 class="hasAnchor">
-<a href="#query-elevation-points" class="anchor"></a>Query Elevation points</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">### for PostGIS, need polygon to return to start point
+<span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(champaign)</code></pre>
+            </div>
+          </div>
+          <div id="query-elevation-points" class="section level3">
+            <h3 class="hasAnchor">
+              <a href="#query-elevation-points" class="anchor"></a>Query
+              Elevation points
+            </h3>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">### for PostGIS, need polygon to return to start point
 champaign &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/rbindlist">rbind</a></span>(champaign, champaign[<span class="dv">1</span>])
 
 ## need to get key from Google Maps API
@@ -114,65 +212,91 @@ <h3 class="hasAnchor">
 key &lt;-<span class="st"> </span><span class="kw">readLines</span>(<span class="dt">con =</span> <span class="st">"~/.googlemapskey"</span>)
 champaign_pts &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/data.table">data.table</a></span>(champaign[,<span class="kw">elevation</span>(<span class="dt">latitude =</span> lat, <span class="dt">longitude =</span> long, <span class="dt">key =</span> key)])
 
-<span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(champaign_pts, <span class="dt">caption =</span> <span class="st">"Table with elevations"</span>)</code></pre></div>
-</div>
-<div id="define-boundary-in-postgis" class="section level3">
-<h3 class="hasAnchor">
-<a href="#define-boundary-in-postgis" class="anchor"></a>Define boundary in postGIS</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">boundary &lt;-<span class="st"> </span>champaign_pts[,<span class="kw">paste</span>(longitude, latitude, elevation, <span class="dt">collapse =</span> <span class="st">","</span>)]
+<span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(champaign_pts, <span class="dt">caption =</span> <span class="st">"Table with elevations"</span>)</code></pre>
+            </div>
+          </div>
+          <div id="define-boundary-in-postgis" class="section level3">
+            <h3 class="hasAnchor">
+              <a href="#define-boundary-in-postgis" class="anchor"></a>Define
+              boundary in postGIS
+            </h3>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">boundary &lt;-<span class="st"> </span>champaign_pts[,<span class="kw">paste</span>(longitude, latitude, elevation, <span class="dt">collapse =</span> <span class="st">","</span>)]
 
-<span class="kw">writeLines</span>(boundary)</code></pre></div>
-</div>
-<div id="define-postgis-geom" class="section level3">
-<h3 class="hasAnchor">
-<a href="#define-postgis-geom" class="anchor"></a>Define PostGIS geom</h3>
-<p>Use <code>srid = 4326</code></p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">geometry &lt;-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"ST_SetSRID(ST_MakePolygon(ST_GeomFromText('LINESTRING("</span>, boundary , <span class="st">")')), 4326)"</span>)
+<span class="kw">writeLines</span>(boundary)</code></pre>
+            </div>
+          </div>
+          <div id="define-postgis-geom" class="section level3">
+            <h3 class="hasAnchor">
+              <a href="#define-postgis-geom" class="anchor"></a>Define PostGIS
+              geom
+            </h3>
+            <p>Use <code>srid = 4326</code></p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">geometry &lt;-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"ST_SetSRID(ST_MakePolygon(ST_GeomFromText('LINESTRING("</span>, boundary , <span class="st">")')), 4326)"</span>)
 
-<span class="kw">writeLines</span>(geometry)</code></pre></div>
-<div id="insert-statement" class="section level4">
-<h4 class="hasAnchor">
-<a href="#insert-statement" class="anchor"></a>insert statement</h4>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">insert_polygon &lt;-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"INSERT into sites (sitename, geometry) VALUES ('Champaign County', "</span>, geometry, <span class="st">");"</span>)
-<span class="kw">writeLines</span>(insert_polygon)</code></pre></div>
-</div>
-<div id="update-geom-statement" class="section level4">
-<h4 class="hasAnchor">
-<a href="#update-geom-statement" class="anchor"></a>Update geom statement</h4>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">update_polygon &lt;-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"update sites set geometry = "</span>, geometry , <span class="st">" where sitename = 'Champaign County';"</span>)
-<span class="kw">writeLines</span>(update_polygon)</code></pre></div>
-</div>
-</div>
-<div id="insert-into-betydb" class="section level3">
-<h3 class="hasAnchor">
-<a href="#insert-into-betydb" class="anchor"></a>Insert into BETYdb</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAn.DB)
+<span class="kw">writeLines</span>(geometry)</code></pre>
+            </div>
+            <div id="insert-statement" class="section level4">
+              <h4 class="hasAnchor">
+                <a href="#insert-statement" class="anchor"></a>insert statement
+              </h4>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">insert_polygon &lt;-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"INSERT into sites (sitename, geometry) VALUES ('Champaign County', "</span>, geometry, <span class="st">");"</span>)
+<span class="kw">writeLines</span>(insert_polygon)</code></pre>
+              </div>
+            </div>
+            <div id="update-geom-statement" class="section level4">
+              <h4 class="hasAnchor">
+                <a href="#update-geom-statement" class="anchor"></a>Update geom
+                statement
+              </h4>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">update_polygon &lt;-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"update sites set geometry = "</span>, geometry , <span class="st">" where sitename = 'Champaign County';"</span>)
+<span class="kw">writeLines</span>(update_polygon)</code></pre>
+              </div>
+            </div>
+          </div>
+          <div id="insert-into-betydb" class="section level3">
+            <h3 class="hasAnchor">
+              <a href="#insert-into-betydb" class="anchor"></a>Insert into
+              BETYdb
+            </h3>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(PEcAn.DB)
 <span class="kw">library</span>(RPostgreSQL)
 <span class="co">#settings &lt;- read.settings('settings.xml')</span>
 settings &lt;-<span class="kw">list</span>(<span class="dt">database =</span> <span class="kw">list</span>(<span class="dt">bety =</span> <span class="kw">list</span>(<span class="dt">driver =</span> <span class="st">"PostgreSQL"</span>, <span class="dt">user =</span> <span class="st">"bety"</span>, <span class="dt">dbname =</span> <span class="st">"bety"</span>, <span class="dt">password =</span> <span class="st">"bety"</span>)))
 
-<span class="kw"><a href="../reference/db.query.html">db.query</a></span>(insert_polygon, <span class="dt">con =</span> <span class="kw"><a href="../reference/db.open.html">db.open</a></span>(settings<span class="op">$</span>database<span class="op">$</span>bety))</code></pre></div>
-</div>
-  </div>
+<span class="kw"><a href="../reference/db.query.html">db.query</a></span>(insert_polygon, <span class="dt">con =</span> <span class="kw"><a href="../reference/db.open.html">db.open</a></span>(settings<span class="op">$</span>database<span class="op">$</span>bety))</code></pre>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"></div>
       </div>
 
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-</div>
+      <footer>
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index cd0faa7..98ec1ea 100644
--- a/base/db/docs/articles/index.html
+++ b/base/db/docs/articles/index.html
@@ -2,137 +2,172 @@
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 <html>
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
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+      crossorigin="anonymous"
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-        <a class="navbar-link" href="../index.html">PEcAn.DB</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
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-</li>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
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+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-      <h1>Articles</h1>
-    </div>
-
-    <div class="section ">
-      <h3>All vignettes</h3>
-      <p class="section-desc"></p>
-
-      <ul>
-        <li><a href="betydb_access.html">BETYdb Access</a></li>
-        <li><a href="create_sites.geometry.html">Create PostGIS polygon</a></li>
-      </ul>
-    </div>
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Articles</h1>
+          </div>
+
+          <div class="section ">
+            <h3>All vignettes</h3>
+            <p class="section-desc"></p>
+
+            <ul>
+              <li><a href="betydb_access.html">BETYdb Access</a></li>
+              <li>
+                <a href="create_sites.geometry.html">Create PostGIS polygon</a>
+              </li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
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-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
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diff --git a/base/db/docs/authors.html b/base/db/docs/authors.html
index 16eb3ab..fae767c 100644
--- a/base/db/docs/authors.html
+++ b/base/db/docs/authors.html
@@ -2,161 +2,184 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
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-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
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-<![endif]-->
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.DB</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/betydb_access.html">BETYdb Access</a>
-    </li>
-    <li>
-      <a href="articles/create_sites.geometry.html">Create PostGIS polygon</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/db/docs/docsearch.css b/base/db/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/base/db/docs/docsearch.css
+++ b/base/db/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/base/db/docs/docsearch.js b/base/db/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/base/db/docs/docsearch.js
+++ b/base/db/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/base/db/docs/index.html b/base/db/docs/index.html
index 06932df..109a495 100644
--- a/base/db/docs/index.html
+++ b/base/db/docs/index.html
@@ -1,126 +1,191 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for ecological forecasts and reanalysis • PEcAn.DB</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis • PEcAn.DB
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    <!-- sticky kit -->
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+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.">
-<meta name="twitter:card" content="summary">
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+    efficacy of scientific investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <span class="icon-bar"></span>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.DB</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
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-
-    <div id="navbar" class="navbar-collapse collapse">
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-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/betydb_access.html">BETYdb Access</a>
-    </li>
-    <li>
-      <a href="articles/create_sites.geometry.html">Create PostGIS polygon</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/base/db/docs/pkgdown.css b/base/db/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/base/db/docs/pkgdown.css
+++ b/base/db/docs/pkgdown.css
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+html,
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@@ -68,7 +69,7 @@ img {
 
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+  display: inline-block;
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@@ -89,10 +90,12 @@ a.anchor {
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 }
 
-
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-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
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@@ -107,7 +110,6 @@ a.anchor {
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-
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 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
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-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
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+}
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+}
 
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+}
 
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-.ref-arguments th, .ref-arguments td {vertical-align: top;}
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-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
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+}
+.ref-arguments th,
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+}
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+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
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@@ -162,7 +186,8 @@ pre {
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+pre,
+code {
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@@ -183,7 +208,8 @@ pre .img img {
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-code a, pre a {
+code a,
+pre a {
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@@ -191,15 +217,35 @@ a.sourceLine:hover {
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-.fl      {color: #1514b5;}
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-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
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+}
+.fu {
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+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
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+} /* keyword */
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+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
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+}
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+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
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diff --git a/base/db/docs/pkgdown.js b/base/db/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/base/db/docs/pkgdown.js
+++ b/base/db/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
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-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
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@@ -23,8 +26,7 @@
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     var pos = -1;
     for (var i = 0; i < links.length; i++) {
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-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
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+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
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     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
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     }
 
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+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
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-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
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+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
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+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
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@@ -88,23 +88,23 @@
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       // Initialize tooltips:
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+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/base/db/docs/reference/PEcAn.DB.html b/base/db/docs/reference/PEcAn.DB.html
index 138d667..a16f495 100644
--- a/base/db/docs/reference/PEcAn.DB.html
+++ b/base/db/docs/reference/PEcAn.DB.html
@@ -2,149 +2,193 @@
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 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- pkgdown -->
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-
-
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-<meta name="twitter:card" content="summary" />
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-
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>
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+    <script src="../pkgdown.js"></script>
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+    <meta
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+      content="Database functions for PEcAn, the Predictive Ecosystem Analyzer — PEcAn.DB"
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+    <meta
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+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+      <div class="row">
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+            <h1>
+              Database functions for PEcAn, the Predictive Ecosystem Analyzer
+            </h1>
+
+            <div class="hidden name"><code>PEcAn.DB.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This package provides an interface between PEcAn and the BETY
+              database. For usage examples, please see
+              <code
+                ><a href="../articles/betydb_access.html"
+                  >vignette("betydb_access")</a
+                ></code
+              >
+            </p>
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index 3e82f70..77282a8 100644
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+++ b/base/db/docs/reference/append.covariate.html
@@ -2,178 +2,233 @@
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+      content="append.covariate appends a data frame of covariates as a new column in a data frame
   of trait data.
 In the event a trait has several covariates available, the first one found
-  (i.e. lowest row number) will take precedence" />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Append covariate data as a column within a table</h1>
-    
-    <div class="hidden name"><code>append.covariate.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p><code>append.covariate</code> appends a data frame of covariates as a new column in a data frame
-  of trait data.
-In the event a trait has several covariates available, the first one found
-  (i.e. lowest row number) will take precedence</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>append.covariate</span>(<span class='no'>data</span>, <span class='no'>column.name</span>, <span class='no'>covariates.data</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data</th>
-      <td><p>trait dataframe that will be appended to.</p></td>
-    </tr>
-    <tr>
-      <th>column.name</th>
-      <td><p>name of the covariate as it will appear in the appended column</p></td>
-    </tr>
-    <tr>
-      <th>covariates.data</th>
-      <td><p>one or more tables of covariate data, ordered by the precedence
-they will assume in the event a trait has covariates across multiple tables.
-All tables must contain an 'id' and 'level' column, at minimum.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Carl Davidson, Ryan Kelly
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Append covariate data as a column within a table</h1>
+
+            <div class="hidden name"><code>append.covariate.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              <code>append.covariate</code> appends a data frame of covariates
+              as a new column in a data frame of trait data. In the event a
+              trait has several covariates available, the first one found (i.e.
+              lowest row number) will take precedence
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>append.covariate</span>(<span class='no'>data</span>, <span class='no'>column.name</span>, <span class='no'>covariates.data</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data</th>
+              <td><p>trait dataframe that will be appended to.</p></td>
+            </tr>
+            <tr>
+              <th>column.name</th>
+              <td>
+                <p>
+                  name of the covariate as it will appear in the appended column
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>covariates.data</th>
+              <td>
+                <p>
+                  one or more tables of covariate data, ordered by the
+                  precedence they will assume in the event a trait has
+                  covariates across multiple tables. All tables must contain an
+                  'id' and 'level' column, at minimum.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Carl Davidson, Ryan Kelly
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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diff --git a/base/db/docs/reference/arrhenius.scaling.traits.html b/base/db/docs/reference/arrhenius.scaling.traits.html
index 7875da7..4a15e64 100644
--- a/base/db/docs/reference/arrhenius.scaling.traits.html
+++ b/base/db/docs/reference/arrhenius.scaling.traits.html
@@ -2,181 +2,253 @@
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Apply Arrhenius scaling to 25 degC for temperature-dependent traits</h1>
-    
-    <div class="hidden name"><code>arrhenius.scaling.traits.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Apply Arrhenius scaling to 25 degC for temperature-dependent traits</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>arrhenius.scaling.traits</span>(<span class='no'>data</span>, <span class='no'>covariates</span>, <span class='no'>temp.covariates</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Apply Arrhenius scaling to 25 degC for temperature-dependent
+              traits
+            </h1>
+
+            <div class="hidden name">
+              <code>arrhenius.scaling.traits.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Apply Arrhenius scaling to 25 degC for temperature-dependent
+              traits
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>arrhenius.scaling.traits</span>(<span class='no'>data</span>, <span class='no'>covariates</span>, <span class='no'>temp.covariates</span>,
   <span class='kw'>new.temp</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>missing.temp</span> <span class='kw'>=</span> <span class='fl'>25</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data</th>
-      <td><p>data frame of data to scale, as returned by query.data()</p></td>
-    </tr>
-    <tr>
-      <th>covariates</th>
-      <td><p>data frame of covariates, as returned by query.covariates().
-Note that data with no matching covariates will be unchanged.</p></td>
-    </tr>
-    <tr>
-      <th>temp.covariates</th>
-      <td><p>names of covariates used to adjust for temperature;
-if length &gt; 1, order matters (first will be used preferentially)</p></td>
-    </tr>
-    <tr>
-      <th>new.temp</th>
-      <td><p>the reference temperature for the scaled traits. Curerntly 25 degC</p></td>
-    </tr>
-    <tr>
-      <th>missing.temp</th>
-      <td><p>the temperature assumed for traits with no covariate found. Curerntly 25 degC</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Carl Davidson, David LeBauer, Ryan Kelly
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data</th>
+              <td>
+                <p>data frame of data to scale, as returned by query.data()</p>
+              </td>
+            </tr>
+            <tr>
+              <th>covariates</th>
+              <td>
+                <p>
+                  data frame of covariates, as returned by query.covariates().
+                  Note that data with no matching covariates will be unchanged.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>temp.covariates</th>
+              <td>
+                <p>
+                  names of covariates used to adjust for temperature; if length
+                  &gt; 1, order matters (first will be used preferentially)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>new.temp</th>
+              <td>
+                <p>
+                  the reference temperature for the scaled traits. Curerntly 25
+                  degC
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>missing.temp</th>
+              <td>
+                <p>
+                  the temperature assumed for traits with no covariate found.
+                  Curerntly 25 degC
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Carl Davidson, David LeBauer, Ryan Kelly
+        </div>
+      </div>
 
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+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>assign.treatments</h1>
-    
-    <div class="hidden name"><code>assign.treatments.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Change treatments to sequential integers</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>assign.treatments</span>(<span class='no'>data</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data</th>
-      <td><p>input data</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dataframe with sequential treatments</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Assigns all control treatments the same value, then assigns unique treatments
-within each site. Each site is required to have a control treatment.
-The algorithm (incorrectly) assumes that each site has a unique set of experimental
-treatments.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>assign.treatments</h1>
+
+            <div class="hidden name"><code>assign.treatments.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Change treatments to sequential integers</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>assign.treatments</span>(<span class='no'>data</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data</th>
+              <td><p>input data</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>dataframe with sequential treatments</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Assigns all control treatments the same value, then assigns unique
+            treatments within each site. Each site is required to have a control
+            treatment. The algorithm (incorrectly) assumes that each site has a
+            unique set of experimental treatments.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Carl Davidson
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/base/db/docs/reference/bety2pecan.html b/base/db/docs/reference/bety2pecan.html
index 206edb0..e9f2784 100644
--- a/base/db/docs/reference/bety2pecan.html
+++ b/base/db/docs/reference/bety2pecan.html
@@ -2,162 +2,212 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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+      Convert BETY variable names to MsTMIP and subsequently PEcAn standard
+      names — bety2pecan • PEcAn.DB
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+    />
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+      content="Convert BETY variable names to MsTMIP and subsequently PEcAn standard names"
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.DB</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
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-  <a href="../index.html">
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-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
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-    <li>
-      <a href="../articles/betydb_access.html">BETYdb Access</a>
-    </li>
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-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert BETY variable names to MsTMIP and subsequently PEcAn standard names</h1>
-    
-    <div class="hidden name"><code>bety2pecan.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert BETY variable names to MsTMIP and subsequently PEcAn standard names</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>bety2pecan</span>(<span class='no'>vars_bety</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>vars_bety</th>
-      <td><p>data frame with variable names and units</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Convert BETY variable names to MsTMIP and subsequently PEcAn
+              standard names
+            </h1>
+
+            <div class="hidden name"><code>bety2pecan.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Convert BETY variable names to MsTMIP and subsequently PEcAn
+              standard names
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>bety2pecan</span>(<span class='no'>vars_bety</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>vars_bety</th>
+              <td><p>data frame with variable names and units</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/db/docs/reference/betyConnect.html b/base/db/docs/reference/betyConnect.html
index 79c62c4..cfa963f 100644
--- a/base/db/docs/reference/betyConnect.html
+++ b/base/db/docs/reference/betyConnect.html
@@ -2,158 +2,201 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Connect to bety using current PEcAn configuration — betyConnect • PEcAn.DB</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<script src="../pkgdown.js"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Connect to bety using current PEcAn configuration — betyConnect • PEcAn.DB
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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-    </div>
-
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-    
-    <p>Connect to bety using current PEcAn configuration</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>betyConnect</span>(<span class='kw'>php.config</span> <span class='kw'>=</span> <span class='st'>"../../web/config.php"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>php.config</th>
-      <td><p>Path to `config.php`</p></td>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
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-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Connect to bety using current PEcAn configuration</h1>
+
+            <div class="hidden name"><code>betyConnect.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Connect to bety using current PEcAn configuration</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>betyConnect</span>(<span class='kw'>php.config</span> <span class='kw'>=</span> <span class='st'>"../../web/config.php"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>php.config</th>
+              <td><p>Path to `config.php`</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/build_insert_query.html b/base/db/docs/reference/build_insert_query.html
index dfb6c2f..a598e0d 100644
--- a/base/db/docs/reference/build_insert_query.html
+++ b/base/db/docs/reference/build_insert_query.html
@@ -2,166 +2,221 @@
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 <html>
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+      Build query to insert R data frame into SQL table — build_insert_query •
+      PEcAn.DB
+    </title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+    ></script>
+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <script src="../pkgdown.js"></script>
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+      content="Build query to insert R data frame into SQL table — build_insert_query"
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+    />
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+                    </li>
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+                        >Create PostGIS polygon</a
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Build query to insert R data frame into SQL table</h1>
-    
-    <div class="hidden name"><code>build_insert_query.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Build query to insert R data frame into SQL table</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>build_insert_query</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>.con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>values</th>
-      <td><p>`data.frame` of values to write to SQL database</p></td>
-    </tr>
-    <tr>
-      <th>table</th>
-      <td><p>Name of target SQL table, as character</p></td>
-    </tr>
-    <tr>
-      <th>.con</th>
-      <td><p>[<code>DBIConnection</code>]:A DBI connection object obtained from <code><a href='http://www.rdocumentation.org/packages/DBI/topics/dbConnect'>DBI::dbConnect()</a></code>.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Build query to insert R data frame into SQL table</h1>
+
+            <div class="hidden name"><code>build_insert_query.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Build query to insert R data frame into SQL table</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>build_insert_query</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>.con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>values</th>
+              <td><p>`data.frame` of values to write to SQL database</p></td>
+            </tr>
+            <tr>
+              <th>table</th>
+              <td><p>Name of target SQL table, as character</p></td>
+            </tr>
+            <tr>
+              <th>.con</th>
+              <td>
+                <p>
+                  [<code>DBIConnection</code>]:A DBI connection object obtained
+                  from
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/DBI/topics/dbConnect"
+                      >DBI::dbConnect()</a
+                    ></code
+                  >.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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+          <p>Developed by .</p>
+        </div>
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diff --git a/base/db/docs/reference/check.lists.html b/base/db/docs/reference/check.lists.html
index edb3824..2c3fe56 100644
--- a/base/db/docs/reference/check.lists.html
+++ b/base/db/docs/reference/check.lists.html
@@ -2,178 +2,220 @@
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 <html>
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      crossorigin="anonymous"
+    ></script>
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+      crossorigin="anonymous"
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+from the database and the other from a CSV file."
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+                    </li>
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+                        >Create PostGIS polygon</a
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+                </li>
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Compares two lists</h1>
-    
-    <div class="hidden name"><code>check.lists.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check two lists. Identical does not work since one can be loaded
-from the database and the other from a CSV file.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.lists</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='st'>"species.csv"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>first list</p></td>
-    </tr>
-    <tr>
-      <th>y</th>
-      <td><p>second list</p></td>
-    </tr>
-    <tr>
-      <th>filename</th>
-      <td><p>one of "species.csv" or "cultivars.csv"</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>true if two list are the same</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Compares two lists</h1>
+
+            <div class="hidden name"><code>check.lists.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Check two lists. Identical does not work since one can be loaded
+              from the database and the other from a CSV file.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.lists</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='st'>"species.csv"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>first list</p></td>
+            </tr>
+            <tr>
+              <th>y</th>
+              <td><p>second list</p></td>
+            </tr>
+            <tr>
+              <th>filename</th>
+              <td><p>one of "species.csv" or "cultivars.csv"</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>true if two list are the same</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
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diff --git a/base/db/docs/reference/clone_pft.html b/base/db/docs/reference/clone_pft.html
index ac1ddcf..4641404 100644
--- a/base/db/docs/reference/clone_pft.html
+++ b/base/db/docs/reference/clone_pft.html
@@ -2,197 +2,262 @@
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 <html>
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-<meta property="og:description" content="Creates a new pft that is a duplicate of an existing pft,
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Duplicate existing pft with associated priors, species, and cultivars —
+      clone_pft • PEcAn.DB
+    </title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Duplicate existing pft with associated priors, species, and cultivars — clone_pft"
+    />
+
+    <meta
+      property="og:description"
+      content="Creates a new pft that is a duplicate of an existing pft,
 including relationships with priors, species, and cultivars (if any) of the existing pft.
 This function mimics the 'clone pft' button in the PFTs record view page in the 
 BETYdb web interface for PFTs that aggregate &amp;gt;=1 species, but adds the ability to 
-clone the cultivar associations." />
-<meta name="twitter:card" content="summary" />
-
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-<![endif]-->
+clone the cultivar associations."
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
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+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Duplicate existing pft with associated priors, species, and cultivars</h1>
-    
-    <div class="hidden name"><code>clone_pft.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Creates a new pft that is a duplicate of an existing pft,
-including relationships with priors, species, and cultivars (if any) of the existing pft.
-This function mimics the 'clone pft' button in the PFTs record view page in the 
-BETYdb web interface for PFTs that aggregate &gt;=1 species, but adds the ability to 
-clone the cultivar associations.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>clone_pft</span>(<span class='no'>parent.pft.name</span>, <span class='no'>new.pft.name</span>, <span class='no'>new.pft.definition</span>, <span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>parent.pft.name</th>
-      <td><p>name of PFT to duplicate</p></td>
-    </tr>
-    <tr>
-      <th>new.pft.name</th>
-      <td><p>name for new PFT. Must not be the same as parent.pft.name</p></td>
-    </tr>
-    <tr>
-      <th>new.pft.definition</th>
-      <td><p>text for the new PFT's definition field.</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings list, used only for BETYdb connection parameters</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>ID of the newly created pft in database, creates new PFT as a side effect</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Duplicate existing pft with associated priors, species, and
+              cultivars
+            </h1>
+
+            <div class="hidden name"><code>clone_pft.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Creates a new pft that is a duplicate of an existing pft,
+              including relationships with priors, species, and cultivars (if
+              any) of the existing pft. This function mimics the 'clone pft'
+              button in the PFTs record view page in the BETYdb web interface
+              for PFTs that aggregate &gt;=1 species, but adds the ability to
+              clone the cultivar associations.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>clone_pft</span>(<span class='no'>parent.pft.name</span>, <span class='no'>new.pft.name</span>, <span class='no'>new.pft.definition</span>, <span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>parent.pft.name</th>
+              <td><p>name of PFT to duplicate</p></td>
+            </tr>
+            <tr>
+              <th>new.pft.name</th>
+              <td>
+                <p>name for new PFT. Must not be the same as parent.pft.name</p>
+              </td>
+            </tr>
+            <tr>
+              <th>new.pft.definition</th>
+              <td><p>text for the new PFT's definition field.</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  PEcAn settings list, used only for BETYdb connection
+                  parameters
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            ID of the newly created pft in database, creates new PFT as a side
+            effect
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>clone_pft</span>(<span class='kw'>parent.pft.name</span>    <span class='kw'>=</span> <span class='st'>"tempdecid"</span>,
           <span class='kw'>new.pft.name</span>       <span class='kw'>=</span> <span class='st'>"mytempdecid"</span>,
           <span class='kw'>new.pft.definition</span> <span class='kw'>=</span> <span class='st'>"mytempdecid is a new pft"</span>,
           <span class='kw'>settings</span> <span class='kw'>=</span> <span class='no'>pecan_settings_list</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Chris Black
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          David LeBauer, Chris Black
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/db/docs/reference/db.close.html b/base/db/docs/reference/db.close.html
index 10e70e2..e86ceb2 100644
--- a/base/db/docs/reference/db.close.html
+++ b/base/db/docs/reference/db.close.html
@@ -2,184 +2,229 @@
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Close database connection — db.close" />
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+      property="og:description"
+      content="Generic function to close a database connection"
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+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-    </div>
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-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/betydb_access.html">BETYdb Access</a>
-    </li>
-    <li>
-      <a href="../articles/create_sites.geometry.html">Create PostGIS polygon</a>
-    </li>
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-        
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Close database connection</h1>
-    
-    <div class="hidden name"><code>db.close.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generic function to close a database connection</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>db.close</span>(<span class='no'>con</span>, <span class='kw'>showWarnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>con</th>
-      <td><p>database connection to be closed</p></td>
-    </tr>
-    <tr>
-      <th>showWarnings</th>
-      <td><p>logical: report possible issues with connection?</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>connection to database</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Close a previously opened connection to a database.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Close database connection</h1>
+
+            <div class="hidden name"><code>db.close.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Generic function to close a database connection</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>db.close</span>(<span class='no'>con</span>, <span class='kw'>showWarnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>con</th>
+              <td><p>database connection to be closed</p></td>
+            </tr>
+            <tr>
+              <th>showWarnings</th>
+              <td><p>logical: report possible issues with connection?</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>connection to database</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Close a previously opened connection to a database.</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>db.close</span>(<span class='no'>con</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
+        </div>
+      </div>
+
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/db/docs/reference/db.exists.html b/base/db/docs/reference/db.exists.html
index 86d85c6..3dca512 100644
--- a/base/db/docs/reference/db.exists.html
+++ b/base/db/docs/reference/db.exists.html
@@ -2,182 +2,224 @@
 <!DOCTYPE html>
 <html>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    ></script>
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <script src="../pkgdown.js"></script>
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+                        >Create PostGIS polygon</a
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>db.exists</h1>
-    
-    <div class="hidden name"><code>db.exists.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Test connection to database</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>db.exists</span>(<span class='no'>params</span>, <span class='kw'>write</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>table</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>params</th>
-      <td><p>database connection information</p></td>
-    </tr>
-    <tr>
-      <th>write</th>
-      <td><p>logical: test whether we have write access?</p></td>
-    </tr>
-    <tr>
-      <th>table</th>
-      <td><p>name of database table to check</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>TRUE if database connection works; else FALSE</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Useful to only run tests that depend on database when a connection exists</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>db.exists</h1>
+
+            <div class="hidden name"><code>db.exists.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Test connection to database</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>db.exists</span>(<span class='no'>params</span>, <span class='kw'>write</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>table</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>params</th>
+              <td><p>database connection information</p></td>
+            </tr>
+            <tr>
+              <th>write</th>
+              <td><p>logical: test whether we have write access?</p></td>
+            </tr>
+            <tr>
+              <th>table</th>
+              <td><p>name of database table to check</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>TRUE if database connection works; else FALSE</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Useful to only run tests that depend on database when a connection
+            exists
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Rob Kooper
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/db.getShowQueries.html b/base/db/docs/reference/db.getShowQueries.html
index 74e306d..0ed1524 100644
--- a/base/db/docs/reference/db.getShowQueries.html
+++ b/base/db/docs/reference/db.getShowQueries.html
@@ -2,158 +2,192 @@
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 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>db.getShowQueries</h1>
-    
-    <div class="hidden name"><code>db.getShowQueries.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>db.getShowQueries</h1>
 
-    <div class="ref-description">
-    
-    <p>Returns if the queries should be shown that are being executed</p>
-    
-    </div>
+            <div class="hidden name"><code>db.getShowQueries.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>db.getShowQueries</span>()</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <div class="ref-description">
+            <p>
+              Returns if the queries should be shown that are being executed
+            </p>
+          </div>
 
-    <p>will return TRUE if queries are shown</p>
-    
+          <pre class="usage"><span class='fu'>db.getShowQueries</span>()</pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>will return TRUE if queries are shown</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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+    </div>
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 </html>
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diff --git a/base/db/docs/reference/db.open.html b/base/db/docs/reference/db.open.html
index 4c97f0d..0a1d830 100644
--- a/base/db/docs/reference/db.open.html
+++ b/base/db/docs/reference/db.open.html
@@ -2,181 +2,229 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- clipboard.js -->
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-<![endif]-->
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+    <meta charset="utf-8" />
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+    <title>Open database connection — db.open • PEcAn.DB</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Open database connection — db.open" />
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+      property="og:description"
+      content="Generic function to open a database connection"
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+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              </button>
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+                <a class="navbar-link" href="../index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Open database connection</h1>
-    
-    <div class="hidden name"><code>db.open.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generic function to open a database connection</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>db.open</span>(<span class='no'>params</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>params</th>
-      <td><p>database connection information</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>connection to database</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Create a connection to a database usign the specified parameters. If the paramters contain
-driver element it will be used as the database driver, otherwise it will use PostgreSQL.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Open database connection</h1>
+
+            <div class="hidden name"><code>db.open.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Generic function to open a database connection</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>db.open</span>(<span class='no'>params</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>params</th>
+              <td><p>database connection information</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>connection to database</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Create a connection to a database usign the specified parameters. If
+            the paramters contain driver element it will be used as the database
+            driver, otherwise it will use PostgreSQL.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>db.open</span>(<span class='no'>settings</span>$<span class='no'>database</span>$<span class='no'>bety</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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-
diff --git a/base/db/docs/reference/db.print.connections.html b/base/db/docs/reference/db.print.connections.html
index 7d20e09..6adfb39 100644
--- a/base/db/docs/reference/db.print.connections.html
+++ b/base/db/docs/reference/db.print.connections.html
@@ -2,165 +2,207 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
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-
-<!-- sticky kit -->
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
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+                        >Create PostGIS polygon</a
+                      >
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Debug leaked connections</h1>
-    
-    <div class="hidden name"><code>db.print.connections.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Debug leaked connections</h1>
 
-    <div class="ref-description">
-    
-    <p>Debug method for db.open and db.close</p>
-    
-    </div>
+            <div class="hidden name"><code>db.print.connections.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Debug method for db.open and db.close</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>db.print.connections</span>()</pre>
 
-    <pre class="usage"><span class='fu'>db.print.connections</span>()</pre>
-        
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
 
-    <p>Prints the number of connections opened as well as any connections
-that have never been closes.</p>
-    
+          <p>
+            Prints the number of connections opened as well as any connections
+            that have never been closes.
+          </p>
 
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>db.print.connections</span>()
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
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-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#details">Details</a></li>
 
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-  <p>Developed by .</p>
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+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
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+          <h2>Author</h2>
 
-  
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diff --git a/base/db/docs/reference/db.query.html b/base/db/docs/reference/db.query.html
index 727cfe6..068c6c8 100644
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+++ b/base/db/docs/reference/db.query.html
@@ -2,189 +2,237 @@
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+    />
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+                <li class="dropdown">
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+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Query database</h1>
-    
-    <div class="hidden name"><code>db.query.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generic function to query database</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>db.query</span>(<span class='no'>query</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>query</th>
-      <td><p>SQL query string</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>params</th>
-      <td><p>database connection information</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data frame with query results</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Given a connection and a query, will return a query as a data frame. Either con or params need
-to be specified. If both are specified it will use con.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Query database</h1>
+
+            <div class="hidden name"><code>db.query.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Generic function to query database</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>db.query</span>(<span class='no'>query</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>query</th>
+              <td><p>SQL query string</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>params</th>
+              <td><p>database connection information</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>data frame with query results</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Given a connection and a query, will return a query as a data frame.
+            Either con or params need to be specified. If both are specified it
+            will use con.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>db.query</span>(<span class='st'>'select count(id) from traits;'</span>, <span class='kw'>params</span><span class='kw'>=</span><span class='no'>settings</span>$<span class='no'>database</span>$<span class='no'>bety</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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 </html>
-
diff --git a/base/db/docs/reference/db.showQueries.html b/base/db/docs/reference/db.showQueries.html
index 3528e1d..209dd5f 100644
--- a/base/db/docs/reference/db.showQueries.html
+++ b/base/db/docs/reference/db.showQueries.html
@@ -2,168 +2,208 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="db.showQueries — db.showQueries" />
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+      property="og:description"
+      content="Sets if the queries should be shown that are being executed"
+    />
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+    <![endif]-->
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+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>db.showQueries</h1>
-    
-    <div class="hidden name"><code>db.showQueries.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Sets if the queries should be shown that are being executed</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>db.showQueries</span>(<span class='no'>show</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>show</th>
-      <td><p>set to TRUE to show the queries, FALSE by default</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Useful to print queries when debuging SQL statements</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>db.showQueries</h1>
+
+            <div class="hidden name"><code>db.showQueries.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Sets if the queries should be shown that are being executed</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>db.showQueries</span>(<span class='no'>show</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>show</th>
+              <td><p>set to TRUE to show the queries, FALSE by default</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Useful to print queries when debuging SQL statements</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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-</div>
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+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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-
diff --git a/base/db/docs/reference/dbHostInfo.html b/base/db/docs/reference/dbHostInfo.html
index 9b54a3c..d2edab2 100644
--- a/base/db/docs/reference/dbHostInfo.html
+++ b/base/db/docs/reference/dbHostInfo.html
@@ -2,158 +2,196 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-    
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-
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-    
-    <p>Database host information</p>
-    
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-
-    <pre class="usage"><span class='fu'>dbHostInfo</span>(<span class='no'>bety</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
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-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
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-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Database host information</h1>
+
+            <div class="hidden name"><code>dbHostInfo.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Database host information</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dbHostInfo</span>(<span class='no'>bety</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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index b00f2e6..7c36c06 100644
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+                        >Create PostGIS polygon</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Merge local data frame into SQL table</h1>
-    
-    <div class="hidden name"><code>db_merge_into.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Merge local data frame into SQL table</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>db_merge_into</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>con</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>values</th>
-      <td><p>`data.frame` of values to write to SQL database</p></td>
-    </tr>
-    <tr>
-      <th>table</th>
-      <td><p>Name of target SQL table, as character</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>by</th>
-      <td><p>Character vector of columns by which to perform merge. Defaults to all columns in `values`</p></td>
-    </tr>
-    <tr>
-      <th>drop</th>
-      <td><p>logical. If `TRUE` (default), drop columns not found in SQL table.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Arguments passed on to <code>insert_table</code></p><dl class='dl-horizontal'>
-  <dt>values</dt><dd><p>`data.frame` of values to write to SQL database</p></dd>
-  <dt>table</dt><dd><p>Name of target SQL table, as character</p></dd>
-  <dt>coerce_col_class</dt><dd><p>logical, whether or not to coerce local data columns 
-to SQL classes. Default = `TRUE.`</p></dd>
-  <dt>drop</dt><dd><p>logical. If `TRUE` (default), drop columns not found in SQL table.</p></dd>
-  <dt>con</dt><dd><p>database connection object</p></dd>
-</dl></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Data frame: Inner join of SQL table and input data frame (as unevaluated "lazy query" table)</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Merge local data frame into SQL table</h1>
+
+            <div class="hidden name"><code>db_merge_into.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Merge local data frame into SQL table</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>db_merge_into</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>con</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>values</th>
+              <td><p>`data.frame` of values to write to SQL database</p></td>
+            </tr>
+            <tr>
+              <th>table</th>
+              <td><p>Name of target SQL table, as character</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>by</th>
+              <td>
+                <p>
+                  Character vector of columns by which to perform merge.
+                  Defaults to all columns in `values`
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>drop</th>
+              <td>
+                <p>
+                  logical. If `TRUE` (default), drop columns not found in SQL
+                  table.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>Arguments passed on to <code>insert_table</code></p>
+                <dl class="dl-horizontal">
+                  <dt>values</dt>
+                  <dd>
+                    <p>`data.frame` of values to write to SQL database</p>
+                  </dd>
+                  <dt>table</dt>
+                  <dd><p>Name of target SQL table, as character</p></dd>
+                  <dt>coerce_col_class</dt>
+                  <dd>
+                    <p>
+                      logical, whether or not to coerce local data columns to
+                      SQL classes. Default = `TRUE.`
+                    </p>
+                  </dd>
+                  <dt>drop</dt>
+                  <dd>
+                    <p>
+                      logical. If `TRUE` (default), drop columns not found in
+                      SQL table.
+                    </p>
+                  </dd>
+                  <dt>con</dt>
+                  <dd><p>database connection object</p></dd>
+                </dl>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Data frame: Inner join of SQL table and input data frame (as
+            unevaluated "lazy query" table)
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>irisdb</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>DBI</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/DBI/topics/dbConnect'>dbConnect</a></span>(<span class='kw pkg'>RSQLite</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/RSQLite/topics/SQLite'>SQLite</a></span>(), <span class='st'>":memory:"</span>)
 <span class='kw pkg'>dplyr</span><span class='kw ns'>::</span><span class='fu'><a href='http://dplyr.tidyverse.org/reference/copy_to.html'>copy_to</a></span>(<span class='no'>irisdb</span>, <span class='no'>iris</span>[<span class='fl'>1</span>:<span class='fl'>10</span>,], <span class='kw'>name</span> <span class='kw'>=</span> <span class='st'>"iris"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='fu'>db_merge_into</span>(<span class='no'>iris</span>[<span class='fl'>1</span>:<span class='fl'>12</span>,], <span class='st'>"iris"</span>, <span class='no'>irisdb</span>)
 <span class='kw pkg'>dplyr</span><span class='kw ns'>::</span><span class='fu'><a href='http://dplyr.tidyverse.org/reference/tbl.html'>tbl</a></span>(<span class='no'>irisdb</span>, <span class='st'>"iris"</span>) <span class='kw'>%&gt;%</span> <span class='kw pkg'>dplyr</span><span class='kw ns'>::</span><span class='fu'><a href='http://dplyr.tidyverse.org/reference/tally.html'>count</a></span>()
 <span class='co'># }</span></pre>
-  </div>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
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-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
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-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
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+          <p>Developed by .</p>
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/base/db/docs/reference/dbfile.check.html b/base/db/docs/reference/dbfile.check.html
index c681aa0..e928d2c 100644
--- a/base/db/docs/reference/dbfile.check.html
+++ b/base/db/docs/reference/dbfile.check.html
@@ -2,201 +2,273 @@
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+      Check for a file in the dbfiles tables — dbfile.check • PEcAn.DB
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check for a file in the dbfiles tables</h1>
-    
-    <div class="hidden name"><code>dbfile.check.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check for a file in the dbfiles tables</h1>
 
-    <div class="ref-description">
-    
-    <p>Function to check to see if a file exists in the dbfiles table</p>
-    
-    </div>
+            <div class="hidden name"><code>dbfile.check.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>dbfile.check</span>(<span class='no'>type</span>, <span class='no'>container.id</span>, <span class='no'>con</span>, <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>(),
+          <div class="ref-description">
+            <p>
+              Function to check to see if a file exists in the dbfiles table
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dbfile.check</span>(<span class='no'>type</span>, <span class='no'>container.id</span>, <span class='no'>con</span>, <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>(),
   <span class='kw'>machine.check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>return.all</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>type</th>
-      <td><p>the type of dbfile (Input, Posterior)</p></td>
-    </tr>
-    <tr>
-      <th>container.id</th>
-      <td><p>the id of container type</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>hostname</th>
-      <td><p>the name of the host where the file is stored, this will default to the name of the current machine</p></td>
-    </tr>
-    <tr>
-      <th>machine.check</th>
-      <td><p>setting to check for file on named host, otherwise will check for any file given container id</p></td>
-    </tr>
-    <tr>
-      <th>return.all</th>
-      <td><p>logical flag, if TRUE will return all the files in the directory, not only the max(dbfiles$updated_at) subset</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data.frame with the id, filename and pathname of all the files that are associated</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This will check the dbfiles and machines to see if the file exists</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>type</th>
+              <td><p>the type of dbfile (Input, Posterior)</p></td>
+            </tr>
+            <tr>
+              <th>container.id</th>
+              <td><p>the id of container type</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>hostname</th>
+              <td>
+                <p>
+                  the name of the host where the file is stored, this will
+                  default to the name of the current machine
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>machine.check</th>
+              <td>
+                <p>
+                  setting to check for file on named host, otherwise will check
+                  for any file given container id
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>return.all</th>
+              <td>
+                <p>
+                  logical flag, if TRUE will return all the files in the
+                  directory, not only the max(dbfiles$updated_at) subset
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            data.frame with the id, filename and pathname of all the files that
+            are associated
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This will check the dbfiles and machines to see if the file exists
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>dbfile.check</span>(<span class='st'>'Input'</span>, <span class='fl'>7</span>, <span class='no'>dbcon</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
+        </div>
+      </div>
+
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+        <div class="copyright">
+          <p>Developed by .</p>
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+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/base/db/docs/reference/dbfile.file.html b/base/db/docs/reference/dbfile.file.html
index 5caef4d..45200c0 100644
--- a/base/db/docs/reference/dbfile.file.html
+++ b/base/db/docs/reference/dbfile.file.html
@@ -2,211 +2,275 @@
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 <html>
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-
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
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+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+    />
+
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+      property="og:description"
+      content="These functions check the dbfiles and machines tables to see if the file
 exists, and return the container_id (dbfile.id) or full filename
 with path (dbfile.file) to the first one found.
-If none is found, both will return NA." />
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+                        >Create PostGIS polygon</a
+                      >
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert between file paths and ids</h1>
-    
-    <div class="hidden name"><code>dbfile.file.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert between file paths and ids</h1>
 
-    <div class="ref-description">
-    
-    <p>These functions check the dbfiles and machines tables to see if the file
-exists, and return the container_id (<code>dbfile.id</code>) or full filename
-with path (<code>dbfile.file</code>) to the first one found.
-If none is found, both will return NA.</p>
-    
-    </div>
+            <div class="hidden name"><code>dbfile.file.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              These functions check the dbfiles and machines tables to see if
+              the file exists, and return the container_id
+              (<code>dbfile.id</code>) or full filename with path
+              (<code>dbfile.file</code>) to the first one found. If none is
+              found, both will return NA.
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>dbfile.file</span>(<span class='no'>type</span>, <span class='no'>id</span>, <span class='no'>con</span>, <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>())
+          <pre
+            class="usage"
+          ><span class='fu'>dbfile.file</span>(<span class='no'>type</span>, <span class='no'>id</span>, <span class='no'>con</span>, <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>())
 
 <span class='fu'>dbfile.id</span>(<span class='no'>type</span>, <span class='no'>file</span>, <span class='no'>con</span>, <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>())</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>type</th>
-      <td><p>the type of dbfile (Input, Posterior)</p></td>
-    </tr>
-    <tr>
-      <th>id</th>
-      <td><p>the id of container type</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>hostname</th>
-      <td><p>the name of the host where the file is stored, this will default to the name of the current machine</p></td>
-    </tr>
-    <tr>
-      <th>file</th>
-      <td><p>the full pathname to the file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>filename on host, or NA if none found</p>
-    
-    <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2>
-
-    <ul>
-<li><p><code>dbfile.file</code>: Return full path to file from the dbfiles table</p></li>
-<li><p><code>dbfile.id</code>: Return id to container type given a filename</p></li>
-</ul>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>type</th>
+              <td><p>the type of dbfile (Input, Posterior)</p></td>
+            </tr>
+            <tr>
+              <th>id</th>
+              <td><p>the id of container type</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>hostname</th>
+              <td>
+                <p>
+                  the name of the host where the file is stored, this will
+                  default to the name of the current machine
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>file</th>
+              <td><p>the full pathname to the file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>filename on host, or NA if none found</p>
+
+          <h2 class="hasAnchor" id="functions">
+            <a class="anchor" href="#functions"></a>Functions
+          </h2>
+
+          <ul>
+            <li>
+              <p>
+                <code>dbfile.file</code>: Return full path to file from the
+                dbfiles table
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>dbfile.id</code>: Return id to container type given a
+                filename
+              </p>
+            </li>
+          </ul>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>dbfile.file</span>(<span class='st'>'Input'</span>, <span class='fl'>7</span>, <span class='no'>dbcon</span>)
 <span class='co'># }</span><span class='co'># NOT RUN {</span>
   <span class='fu'>dbfile.id</span>(<span class='st'>'Model'</span>, <span class='st'>'/usr/local/bin/sipnet'</span>, <span class='no'>dbcon</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <li><a href="#functions">Functions</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
+            <li><a href="#value">Value</a></li>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+            <li><a href="#functions">Functions</a></li>
 
-Rob Kooper
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  </div>
-</div>
+          <h2>Author</h2>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          Rob Kooper Rob Kooper
+        </div>
+      </div>
 
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index 7e418ea..8a1c9b5 100644
--- a/base/db/docs/reference/dbfile.input.check.html
+++ b/base/db/docs/reference/dbfile.input.check.html
@@ -2,219 +2,294 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                    </li>
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+                        >Create PostGIS polygon</a
+                      >
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check for a file in the input/dbfiles tables</h1>
-    
-    <div class="hidden name"><code>dbfile.input.check.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check for a file in the input/dbfiles tables</h1>
 
-    <div class="ref-description">
-    
-    <p>Function to check to see if a file exists in the dbfiles table as an input</p>
-    
-    </div>
+            <div class="hidden name"><code>dbfile.input.check.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>dbfile.input.check</span>(<span class='no'>siteid</span>, <span class='kw'>startdate</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>enddate</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>mimetype</span>,
+          <div class="ref-description">
+            <p>
+              Function to check to see if a file exists in the dbfiles table as
+              an input
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dbfile.input.check</span>(<span class='no'>siteid</span>, <span class='kw'>startdate</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>enddate</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>mimetype</span>,
   <span class='no'>formatname</span>, <span class='kw'>parentid</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='no'>con</span>, <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>(),
   <span class='kw'>exact.dates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>pattern</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>siteid</th>
-      <td><p>the id of the site that this data is applicable to</p></td>
-    </tr>
-    <tr>
-      <th>startdate</th>
-      <td><p>the start date of the data stored in the file</p></td>
-    </tr>
-    <tr>
-      <th>enddate</th>
-      <td><p>the end date of the data stored in the file</p></td>
-    </tr>
-    <tr>
-      <th>mimetype</th>
-      <td><p>the mime-type of the file</p></td>
-    </tr>
-    <tr>
-      <th>formatname</th>
-      <td><p>the name of the format to distinguish between simmilair mime-types</p></td>
-    </tr>
-    <tr>
-      <th>parentid</th>
-      <td><p>the id of the parent of the input</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>hostname</th>
-      <td><p>the name of the host where the file is stored, this will default to the name of the current machine</p></td>
-    </tr>
-    <tr>
-      <th>exact.dates</th>
-      <td><p>setting to include start and end date in input query</p></td>
-    </tr>
-    <tr>
-      <th>pattern</th>
-      <td><p>text to seach for in the file name (default NULL = no check).</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data.frame with the id, filename and pathname of the input that is requested</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This will check the dbfiles, inputs, machines and formats tables to see if the
-file exists</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>siteid</th>
+              <td><p>the id of the site that this data is applicable to</p></td>
+            </tr>
+            <tr>
+              <th>startdate</th>
+              <td><p>the start date of the data stored in the file</p></td>
+            </tr>
+            <tr>
+              <th>enddate</th>
+              <td><p>the end date of the data stored in the file</p></td>
+            </tr>
+            <tr>
+              <th>mimetype</th>
+              <td><p>the mime-type of the file</p></td>
+            </tr>
+            <tr>
+              <th>formatname</th>
+              <td>
+                <p>
+                  the name of the format to distinguish between simmilair
+                  mime-types
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>parentid</th>
+              <td><p>the id of the parent of the input</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>hostname</th>
+              <td>
+                <p>
+                  the name of the host where the file is stored, this will
+                  default to the name of the current machine
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>exact.dates</th>
+              <td>
+                <p>setting to include start and end date in input query</p>
+              </td>
+            </tr>
+            <tr>
+              <th>pattern</th>
+              <td>
+                <p>
+                  text to seach for in the file name (default NULL = no check).
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            data.frame with the id, filename and pathname of the input that is
+            requested
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This will check the dbfiles, inputs, machines and formats tables to
+            see if the file exists
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>dbfile.input.check</span>(<span class='no'>siteid</span>, <span class='no'>startdate</span>, <span class='no'>enddate</span>, <span class='st'>'application/x-RData'</span>, <span class='st'>'traits'</span>, <span class='no'>dbcon</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper, Tony Gardella
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper, Tony Gardella
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
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index 4bb7561..fabaca8 100644
--- a/base/db/docs/reference/dbfile.input.insert.html
+++ b/base/db/docs/reference/dbfile.input.insert.html
@@ -2,223 +2,298 @@
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+    ></script>
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+                        >Create PostGIS polygon</a
+                      >
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Insert file into tables</h1>
-    
-    <div class="hidden name"><code>dbfile.input.insert.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Insert file into tables</h1>
 
-    <div class="ref-description">
-    
-    <p>Function to insert a file into the dbfiles table as an input</p>
-    
-    </div>
+            <div class="hidden name"><code>dbfile.input.insert.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>dbfile.input.insert</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>siteid</span>, <span class='no'>startdate</span>, <span class='no'>enddate</span>,
+          <div class="ref-description">
+            <p>Function to insert a file into the dbfiles table as an input</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dbfile.input.insert</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>siteid</span>, <span class='no'>startdate</span>, <span class='no'>enddate</span>,
   <span class='no'>mimetype</span>, <span class='no'>formatname</span>, <span class='kw'>parentid</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='no'>con</span>,
   <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>(), <span class='kw'>allow.conflicting.dates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>path to the directory containing the file to be inserted</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>initial portion of the filename that does not vary by date. Does not include directory; specify that as part of in.path</p></td>
-    </tr>
-    <tr>
-      <th>siteid</th>
-      <td><p>the id of the site that this data is applicable to</p></td>
-    </tr>
-    <tr>
-      <th>startdate</th>
-      <td><p>the start date of the data stored in the file</p></td>
-    </tr>
-    <tr>
-      <th>enddate</th>
-      <td><p>the end date of the data stored in the file</p></td>
-    </tr>
-    <tr>
-      <th>mimetype</th>
-      <td><p>the mime-type of the file</p></td>
-    </tr>
-    <tr>
-      <th>formatname</th>
-      <td><p>the name of the format to distinguish between simmilair mime-types</p></td>
-    </tr>
-    <tr>
-      <th>parentid</th>
-      <td><p>the id of the parent of the input</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>hostname</th>
-      <td><p>the name of the host where the file is stored, this will default to the name of the current machine</p></td>
-    </tr>
-    <tr>
-      <th>allow.conflicting.dates</th>
-      <td><p>Whether to allow a new input record with same siteid, name, and format but different start/end dates</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data.frame with the id, filename and pathname of the input that is requested</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This will write into the dbfiles, inputs, machines and formats the required
-data to store the file</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td>
+                <p>path to the directory containing the file to be inserted</p>
+              </td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td>
+                <p>
+                  initial portion of the filename that does not vary by date.
+                  Does not include directory; specify that as part of in.path
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>siteid</th>
+              <td><p>the id of the site that this data is applicable to</p></td>
+            </tr>
+            <tr>
+              <th>startdate</th>
+              <td><p>the start date of the data stored in the file</p></td>
+            </tr>
+            <tr>
+              <th>enddate</th>
+              <td><p>the end date of the data stored in the file</p></td>
+            </tr>
+            <tr>
+              <th>mimetype</th>
+              <td><p>the mime-type of the file</p></td>
+            </tr>
+            <tr>
+              <th>formatname</th>
+              <td>
+                <p>
+                  the name of the format to distinguish between simmilair
+                  mime-types
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>parentid</th>
+              <td><p>the id of the parent of the input</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>hostname</th>
+              <td>
+                <p>
+                  the name of the host where the file is stored, this will
+                  default to the name of the current machine
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>allow.conflicting.dates</th>
+              <td>
+                <p>
+                  Whether to allow a new input record with same siteid, name,
+                  and format but different start/end dates
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            data.frame with the id, filename and pathname of the input that is
+            requested
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This will write into the dbfiles, inputs, machines and formats the
+            required data to store the file
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>dbfile.input.insert</span>(<span class='st'>'trait.data.Rdata'</span>, <span class='no'>siteid</span>, <span class='no'>startdate</span>, <span class='no'>enddate</span>, <span class='st'>'application/x-RData'</span>, <span class='st'>'traits'</span>, <span class='no'>dbcon</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper, Betsy Cowdery
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper, Betsy Cowdery
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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 </html>
-
diff --git a/base/db/docs/reference/dbfile.insert.html b/base/db/docs/reference/dbfile.insert.html
index d0992e5..6c87d62 100644
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@@ -2,205 +2,266 @@
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Insert file into tables — dbfile.insert"
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+      property="og:description"
+      content="Function to insert a file into the dbfiles table"
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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+                    </li>
+                    <li>
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+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Insert file into tables</h1>
-    
-    <div class="hidden name"><code>dbfile.insert.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Insert file into tables</h1>
 
-    <div class="ref-description">
-    
-    <p>Function to insert a file into the dbfiles table</p>
-    
-    </div>
+            <div class="hidden name"><code>dbfile.insert.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>dbfile.insert</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>type</span>, <span class='no'>id</span>, <span class='no'>con</span>, <span class='kw'>reuse</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+          <div class="ref-description">
+            <p>Function to insert a file into the dbfiles table</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dbfile.insert</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>type</span>, <span class='no'>id</span>, <span class='no'>con</span>, <span class='kw'>reuse</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>())</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>Path to file directory</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>Filename prefix (not including directory)</p></td>
-    </tr>
-    <tr>
-      <th>type</th>
-      <td><p>One of "Model", "Posterior", "Input"</p></td>
-    </tr>
-    <tr>
-      <th>id</th>
-      <td><p>container_id of the input to be modified</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>reuse</th>
-      <td><p>logical: If a record already exists, use it or create a new one?</p></td>
-    </tr>
-    <tr>
-      <th>hostname</th>
-      <td><p>the name of the host where the file is stored, this will default to the name of the current machine</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>id of the file that is written</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This will write into the dbfiles and machines the required data to store the file</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>Path to file directory</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>Filename prefix (not including directory)</p></td>
+            </tr>
+            <tr>
+              <th>type</th>
+              <td><p>One of "Model", "Posterior", "Input"</p></td>
+            </tr>
+            <tr>
+              <th>id</th>
+              <td><p>container_id of the input to be modified</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>reuse</th>
+              <td>
+                <p>
+                  logical: If a record already exists, use it or create a new
+                  one?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>hostname</th>
+              <td>
+                <p>
+                  the name of the host where the file is stored, this will
+                  default to the name of the current machine
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>id of the file that is written</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This will write into the dbfiles and machines the required data to
+            store the file
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>dbfile.insert</span>(<span class='st'>'somefile.txt'</span>, <span class='st'>'Input'</span>, <span class='fl'>7</span>, <span class='no'>dbcon</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper, Ryan Kelly
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+          </ul>
 
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diff --git a/base/db/docs/reference/dbfile.posterior.check.html b/base/db/docs/reference/dbfile.posterior.check.html
index 5828b45..9c46094 100644
--- a/base/db/docs/reference/dbfile.posterior.check.html
+++ b/base/db/docs/reference/dbfile.posterior.check.html
@@ -2,198 +2,271 @@
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check for a file in the input/dbfiles tables</h1>
-    
-    <div class="hidden name"><code>dbfile.posterior.check.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to check to see if a file exists in the dbfiles table as an input</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>dbfile.posterior.check</span>(<span class='no'>pft</span>, <span class='no'>mimetype</span>, <span class='no'>formatname</span>, <span class='no'>con</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check for a file in the input/dbfiles tables</h1>
+
+            <div class="hidden name">
+              <code>dbfile.posterior.check.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to check to see if a file exists in the dbfiles table as
+              an input
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dbfile.posterior.check</span>(<span class='no'>pft</span>, <span class='no'>mimetype</span>, <span class='no'>formatname</span>, <span class='no'>con</span>,
   <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>())</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pft</th>
-      <td><p>the name of the pft that this data is applicable to</p></td>
-    </tr>
-    <tr>
-      <th>mimetype</th>
-      <td><p>the mime-type of the file</p></td>
-    </tr>
-    <tr>
-      <th>formatname</th>
-      <td><p>the name of the format to distinguish between simmilair mime-types</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>hostname</th>
-      <td><p>the name of the host where the file is stored, this will default to the name of the current machine</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data.frame with the id, filename and pathname of the posterior that is requested</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This will check the dbfiles, inputs, machines and formats tables to see if the
-file exists</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pft</th>
+              <td>
+                <p>the name of the pft that this data is applicable to</p>
+              </td>
+            </tr>
+            <tr>
+              <th>mimetype</th>
+              <td><p>the mime-type of the file</p></td>
+            </tr>
+            <tr>
+              <th>formatname</th>
+              <td>
+                <p>
+                  the name of the format to distinguish between simmilair
+                  mime-types
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>hostname</th>
+              <td>
+                <p>
+                  the name of the host where the file is stored, this will
+                  default to the name of the current machine
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            data.frame with the id, filename and pathname of the posterior that
+            is requested
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This will check the dbfiles, inputs, machines and formats tables to
+            see if the file exists
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>dbfile.posterior.check</span>(<span class='no'>pft</span>, <span class='st'>'application/x-RData'</span>, <span class='st'>'traits'</span>, <span class='no'>dbcon</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/base/db/docs/reference/dbfile.posterior.insert.html b/base/db/docs/reference/dbfile.posterior.insert.html
index b361cfb..cf9429b 100644
--- a/base/db/docs/reference/dbfile.posterior.insert.html
+++ b/base/db/docs/reference/dbfile.posterior.insert.html
@@ -2,202 +2,271 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
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+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Insert file into tables</h1>
-    
-    <div class="hidden name"><code>dbfile.posterior.insert.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to insert a file into the dbfiles table as a posterior</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>dbfile.posterior.insert</span>(<span class='no'>filename</span>, <span class='no'>pft</span>, <span class='no'>mimetype</span>, <span class='no'>formatname</span>, <span class='no'>con</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Insert file into tables</h1>
+
+            <div class="hidden name">
+              <code>dbfile.posterior.insert.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to insert a file into the dbfiles table as a posterior
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dbfile.posterior.insert</span>(<span class='no'>filename</span>, <span class='no'>pft</span>, <span class='no'>mimetype</span>, <span class='no'>formatname</span>, <span class='no'>con</span>,
   <span class='kw'>hostname</span> <span class='kw'>=</span> <span class='kw pkg'>PEcAn.remote</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.remote/topics/fqdn'>fqdn</a></span>())</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>filename</th>
-      <td><p>the name of the file to be inserted</p></td>
-    </tr>
-    <tr>
-      <th>pft</th>
-      <td><p>the name of the pft that this data is applicable to</p></td>
-    </tr>
-    <tr>
-      <th>mimetype</th>
-      <td><p>the mime-type of the file</p></td>
-    </tr>
-    <tr>
-      <th>formatname</th>
-      <td><p>the name of the format to distinguish between simmilair mime-types</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>hostname</th>
-      <td><p>the name of the host where the file is stored, this will default to the name of the current machine</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data.frame with the id, filename and pathname of the posterior that is requested</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This will write into the dbfiles, posteriors, machines and formats the require
-data to store the file</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>filename</th>
+              <td><p>the name of the file to be inserted</p></td>
+            </tr>
+            <tr>
+              <th>pft</th>
+              <td>
+                <p>the name of the pft that this data is applicable to</p>
+              </td>
+            </tr>
+            <tr>
+              <th>mimetype</th>
+              <td><p>the mime-type of the file</p></td>
+            </tr>
+            <tr>
+              <th>formatname</th>
+              <td>
+                <p>
+                  the name of the format to distinguish between simmilair
+                  mime-types
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>hostname</th>
+              <td>
+                <p>
+                  the name of the host where the file is stored, this will
+                  default to the name of the current machine
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            data.frame with the id, filename and pathname of the posterior that
+            is requested
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This will write into the dbfiles, posteriors, machines and formats
+            the require data to store the file
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>dbfile.posterior.insert</span>(<span class='st'>'trait.data.Rdata'</span>, <span class='no'>pft</span>, <span class='st'>'application/x-RData'</span>, <span class='st'>'traits'</span>, <span class='no'>dbcon</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
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+
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-
diff --git a/base/db/docs/reference/default_hostname.html b/base/db/docs/reference/default_hostname.html
index c418e3a..014fbe1 100644
--- a/base/db/docs/reference/default_hostname.html
+++ b/base/db/docs/reference/default_hostname.html
@@ -2,164 +2,204 @@
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+    <meta charset="utf-8" />
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
+    <!-- Bootstrap -->
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="default_hostname — default_hostname" />
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+      property="og:description"
+      content="Convenience function to fix hostname if localhost"
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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+                    </li>
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+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>default_hostname</h1>
-    
-    <div class="hidden name"><code>default_hostname.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convenience function to fix hostname if localhost</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>default_hostname</span>(<span class='no'>hostname</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>hostname</th>
-      <td><p>character</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>hostname</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>default_hostname</h1>
+
+            <div class="hidden name"><code>default_hostname.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convenience function to fix hostname if localhost</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>default_hostname</span>(<span class='no'>hostname</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>hostname</th>
+              <td><p>character</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>hostname</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
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 the result as a derived trait.
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait.</h1>
-    
-    <div class="hidden name"><code>derive.trait.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Performs an arithmetic function, FUN, over a series of traits and returns
-the result as a derived trait.
-Traits must be specified as either lists or single row data frames,
-and must be either single data points or normally distributed.
-In the event one or more input traits are normally distributed,
-the resulting distribution is approximated by numerical simulation.
-The output trait is effectively a copy of the first input trait with
-modified mean, stat, and n.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>derive.trait</span>(<span class='no'>FUN</span>, <span class='no'>...</span>, <span class='kw'>input</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='no'>...</span>), <span class='kw'>var.name</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Performs an arithmetic function, FUN, over a series of traits and
+              returns the result as a derived trait.
+            </h1>
+
+            <div class="hidden name"><code>derive.trait.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Performs an arithmetic function, FUN, over a series of traits and
+              returns the result as a derived trait. Traits must be specified as
+              either lists or single row data frames, and must be either single
+              data points or normally distributed. In the event one or more
+              input traits are normally distributed, the resulting distribution
+              is approximated by numerical simulation. The output trait is
+              effectively a copy of the first input trait with modified mean,
+              stat, and n.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>derive.trait</span>(<span class='no'>FUN</span>, <span class='no'>...</span>, <span class='kw'>input</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='no'>...</span>), <span class='kw'>var.name</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
   <span class='kw'>sample.size</span> <span class='kw'>=</span> <span class='fl'>10</span>^<span class='fl'>6</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>FUN</th>
-      <td><p>arithmetic function</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>traits that will be supplied to FUN as input</p></td>
-    </tr>
-    <tr>
-      <th>input</th>
-      <td><p>list of trait inputs. See examples</p></td>
-    </tr>
-    <tr>
-      <th>var.name</th>
-      <td><p>name to use in output</p></td>
-    </tr>
-    <tr>
-      <th>sample.size</th>
-      <td><p>number of random samples generated by rnorm for normally distributed trait input</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a copy of the first input trait with mean, stat, and n reflecting the derived trait</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>FUN</th>
+              <td><p>arithmetic function</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>traits that will be supplied to FUN as input</p></td>
+            </tr>
+            <tr>
+              <th>input</th>
+              <td><p>list of trait inputs. See examples</p></td>
+            </tr>
+            <tr>
+              <th>var.name</th>
+              <td><p>name to use in output</p></td>
+            </tr>
+            <tr>
+              <th>sample.size</th>
+              <td>
+                <p>
+                  number of random samples generated by rnorm for normally
+                  distributed trait input
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            a copy of the first input trait with mean, stat, and n reflecting
+            the derived trait
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>input</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>mean</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>stat</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>))
 <span class='fu'>derive.trait</span>(<span class='kw'>FUN</span> <span class='kw'>=</span> <span class='no'>identity</span>, <span class='kw'>input</span> <span class='kw'>=</span> <span class='no'>input</span>, <span class='kw'>var.name</span> <span class='kw'>=</span> <span class='st'>'x'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait.</h1>
-    
-    <div class="hidden name"><code>derive.traits.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Equivalent to derive.trait(), but operates over a series of trait datasets,
-as opposed to individual trait rows. See <code><a href='derive.trait.html'>derive.trait</a></code>; for more information.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>derive.traits</span>(<span class='no'>FUN</span>, <span class='no'>...</span>, <span class='kw'>input</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='no'>...</span>),
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Performs an arithmetic function, FUN, over a series of traits and
+              returns the result as a derived trait.
+            </h1>
+
+            <div class="hidden name"><code>derive.traits.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Equivalent to derive.trait(), but operates over a series of trait
+              datasets, as opposed to individual trait rows. See
+              <code><a href="derive.trait.html">derive.trait</a></code
+              >; for more information.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>derive.traits</span>(<span class='no'>FUN</span>, <span class='no'>...</span>, <span class='kw'>input</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='no'>...</span>),
   <span class='kw'>match.columns</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"citation_id"</span>, <span class='st'>"site_id"</span>, <span class='st'>"specie_id"</span>),
   <span class='kw'>var.name</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>sample.size</span> <span class='kw'>=</span> <span class='fl'>10</span>^<span class='fl'>6</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>FUN</th>
-      <td><p>arithmetic function</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>trait datasets that will be supplied to FUN as input</p></td>
-    </tr>
-    <tr>
-      <th>input</th>
-      <td><p>list of trait inputs. See examples in <code><a href='derive.trait.html'>derive.trait</a></code></p></td>
-    </tr>
-    <tr>
-      <th>match.columns</th>
-      <td><p>in the event more than one trait dataset is supplied,
-this specifies the columns that identify a unique data point</p></td>
-    </tr>
-    <tr>
-      <th>var.name</th>
-      <td><p>name to use in output</p></td>
-    </tr>
-    <tr>
-      <th>sample.size</th>
-      <td><p>where traits are normally distributed with a given</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a copy of the first input trait with modified mean, stat, and n</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>FUN</th>
+              <td><p>arithmetic function</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>trait datasets that will be supplied to FUN as input</p>
+              </td>
+            </tr>
+            <tr>
+              <th>input</th>
+              <td>
+                <p>
+                  list of trait inputs. See examples in
+                  <code><a href="derive.trait.html">derive.trait</a></code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>match.columns</th>
+              <td>
+                <p>
+                  in the event more than one trait dataset is supplied, this
+                  specifies the columns that identify a unique data point
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>var.name</th>
+              <td><p>name to use in output</p></td>
+            </tr>
+            <tr>
+              <th>sample.size</th>
+              <td><p>where traits are normally distributed with a given</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>a copy of the first input trait with modified mean, stat, and n</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
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+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
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+                        >Create PostGIS polygon</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Count rows of a data frame</h1>
-    
-    <div class="hidden name"><code>dplyr.count.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Count rows of a data frame</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>dplyr.count</span>(<span class='no'>df</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>df</th>
-      <td><p>Data frame of which to count length</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Count rows of a data frame</h1>
+
+            <div class="hidden name"><code>dplyr.count.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Count rows of a data frame</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dplyr.count</span>(<span class='no'>df</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>df</th>
+              <td><p>Data frame of which to count length</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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+          <p>Developed by .</p>
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diff --git a/base/db/docs/reference/fancy_scientific.html b/base/db/docs/reference/fancy_scientific.html
index 35ca1fd..0f0a6f0 100644
--- a/base/db/docs/reference/fancy_scientific.html
+++ b/base/db/docs/reference/fancy_scientific.html
@@ -2,158 +2,202 @@
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+      Convert number to scientific notation pretty expression — fancy_scientific
+      • PEcAn.DB
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert number to scientific notation pretty expression</h1>
-    
-    <div class="hidden name"><code>fancy_scientific.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert number to scientific notation pretty expression</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>fancy_scientific</span>(<span class='no'>l</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>l</th>
-      <td><p>Number to convert to scientific notation</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert number to scientific notation pretty expression</h1>
+
+            <div class="hidden name"><code>fancy_scientific.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert number to scientific notation pretty expression</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>fancy_scientific</span>(<span class='no'>l</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>l</th>
+              <td><p>Number to convert to scientific notation</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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diff --git a/base/db/docs/reference/fetch.stats2se.html b/base/db/docs/reference/fetch.stats2se.html
index 0d1b3d1..25b2d05 100644
--- a/base/db/docs/reference/fetch.stats2se.html
+++ b/base/db/docs/reference/fetch.stats2se.html
@@ -2,185 +2,246 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Fetch data and transform stats to SE — fetch.stats2se • PEcAn.DB
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
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+    ></script>
+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Fetch data and transform stats to SE</h1>
-    
-    <div class="hidden name"><code>fetch.stats2se.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Queries data from the trait database and transforms statistics to SE</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>fetch.stats2se</span>(<span class='no'>connection</span>, <span class='no'>query</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>connection</th>
-      <td><p>connection to trait database</p></td>
-    </tr>
-    <tr>
-      <th>query</th>
-      <td><p>to send to databse</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dataframe with trait data</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Performs query and then uses <code>transformstats</code> to convert miscellaneous statistical summaries
-to SE</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>used in <code><a href='query.trait.data.html'>query.trait.data</a></code>; <code>transformstats</code> performs transformation calculations</p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Fetch data and transform stats to SE</h1>
+
+            <div class="hidden name"><code>fetch.stats2se.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Queries data from the trait database and transforms statistics to
+              SE
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>fetch.stats2se</span>(<span class='no'>connection</span>, <span class='no'>query</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>connection</th>
+              <td><p>connection to trait database</p></td>
+            </tr>
+            <tr>
+              <th>query</th>
+              <td><p>to send to databse</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>dataframe with trait data</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Performs query and then uses <code>transformstats</code> to convert
+            miscellaneous statistical summaries to SE
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              used in
+              <code><a href="query.trait.data.html">query.trait.data</a></code
+              >; <code>transformstats</code> performs transformation
+              calculations
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-&lt;unknown&gt;
+          <h2>Author</h2>
 
-  </div>
-</div>
+          &lt;unknown&gt;
+        </div>
+      </div>
 
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+
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diff --git a/base/db/docs/reference/filter_sunleaf_traits.html b/base/db/docs/reference/filter_sunleaf_traits.html
index 2346be3..ffabcf8 100644
--- a/base/db/docs/reference/filter_sunleaf_traits.html
+++ b/base/db/docs/reference/filter_sunleaf_traits.html
@@ -2,166 +2,210 @@
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+    />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to filter out upper canopy leaves</h1>
-    
-    <div class="hidden name"><code>filter_sunleaf_traits.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to filter out upper canopy leaves</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>filter_sunleaf_traits</span>(<span class='no'>data</span>, <span class='no'>covariates</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data</th>
-      <td><p>input data</p></td>
-    </tr>
-    <tr>
-      <th>covariates</th>
-      <td><p>covariate data</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Function to filter out upper canopy leaves</h1>
+
+            <div class="hidden name"><code>filter_sunleaf_traits.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Function to filter out upper canopy leaves</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>filter_sunleaf_traits</span>(<span class='no'>data</span>, <span class='no'>covariates</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data</th>
+              <td><p>input data</p></td>
+            </tr>
+            <tr>
+              <th>covariates</th>
+              <td><p>covariate data</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          David LeBauer
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/get.id.html b/base/db/docs/reference/get.id.html
index e95b1b6..85971af 100644
--- a/base/db/docs/reference/get.id.html
+++ b/base/db/docs/reference/get.id.html
@@ -2,195 +2,245 @@
 <!DOCTYPE html>
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get.id</h1>
-    
-    <div class="hidden name"><code>get.id.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Retrieve id from a table matching query</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.id</span>(<span class='no'>table</span>, <span class='no'>colnames</span>, <span class='no'>values</span>, <span class='no'>con</span>, <span class='kw'>create</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>dates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>table</th>
-      <td><p>name of table</p></td>
-    </tr>
-    <tr>
-      <th>colnames</th>
-      <td><p>names of one or more columns used in where clause</p></td>
-    </tr>
-    <tr>
-      <th>values</th>
-      <td><p>values to be queried in fields corresponding to colnames</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object,</p></td>
-    </tr>
-    <tr>
-      <th>create</th>
-      <td><p>logical: make a record if none found?</p></td>
-    </tr>
-    <tr>
-      <th>dates</th>
-      <td><p>logical: update created_at and updated_at timestamps? Used only if `create` is TRUE</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>will numeric</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get.id</h1>
+
+            <div class="hidden name"><code>get.id.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Retrieve id from a table matching query</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.id</span>(<span class='no'>table</span>, <span class='no'>colnames</span>, <span class='no'>values</span>, <span class='no'>con</span>, <span class='kw'>create</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>dates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>table</th>
+              <td><p>name of table</p></td>
+            </tr>
+            <tr>
+              <th>colnames</th>
+              <td><p>names of one or more columns used in where clause</p></td>
+            </tr>
+            <tr>
+              <th>values</th>
+              <td>
+                <p>values to be queried in fields corresponding to colnames</p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object,</p></td>
+            </tr>
+            <tr>
+              <th>create</th>
+              <td><p>logical: make a record if none found?</p></td>
+            </tr>
+            <tr>
+              <th>dates</th>
+              <td>
+                <p>
+                  logical: update created_at and updated_at timestamps? Used
+                  only if `create` is TRUE
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>will numeric</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>pftid</span> <span class='kw'>&lt;-</span> <span class='fu'>get.id</span>(<span class='st'>"pfts"</span>, <span class='st'>"name"</span>, <span class='st'>"salix"</span>, <span class='no'>con</span>)
 <span class='no'>pftid</span> <span class='kw'>&lt;-</span> <span class='fu'>get.id</span>(<span class='st'>"pfts"</span>, <span class='fu'>c</span>(<span class='st'>"name"</span>, <span class='st'>"modeltype_id"</span>), <span class='fu'>c</span>(<span class='st'>"ebifarm.salix"</span>, <span class='fl'>1</span>), <span class='no'>con</span>)
 <span class='co'># }</span></pre>
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-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
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-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
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+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
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+            <li><a href="#value">Value</a></li>
 
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+            <li><a href="#examples">Examples</a></li>
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index 9ceb111..92c6b64 100644
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+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
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+                        >Create PostGIS polygon</a
+                      >
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Gets trait data from the database</h1>
-    
-    <div class="hidden name"><code>get.trait.data.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Gets trait data from the database</h1>
 
-    <div class="ref-description">
-    
-    <p>Get trait data from the database.</p>
-    
-    </div>
+            <div class="hidden name"><code>get.trait.data.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get trait data from the database.</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>get.trait.data</span>(<span class='no'>pfts</span>, <span class='no'>modeltype</span>, <span class='no'>dbfiles</span>, <span class='no'>database</span>, <span class='no'>forceupdate</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>get.trait.data</span>(<span class='no'>pfts</span>, <span class='no'>modeltype</span>, <span class='no'>dbfiles</span>, <span class='no'>database</span>, <span class='no'>forceupdate</span>,
   <span class='kw'>trait.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pfts</th>
-      <td><p>the list of pfts to get traits for</p></td>
-    </tr>
-    <tr>
-      <th>modeltype</th>
-      <td><p>type of model that is used, this is is used to distinguis between different pfts with the same name.</p></td>
-    </tr>
-    <tr>
-      <th>dbfiles</th>
-      <td><p>location where previous results are found</p></td>
-    </tr>
-    <tr>
-      <th>database</th>
-      <td><p>database connection parameters</p></td>
-    </tr>
-    <tr>
-      <th>forceupdate</th>
-      <td><p>set this to true to force an update, false to check to see if an update is needed.</p></td>
-    </tr>
-    <tr>
-      <th>trait.names</th>
-      <td><p>list of traits to query. If TRUE, uses trait.dictionary</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list of pfts with update posteriorids</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This will use the following items from setings:
-- settings$pfts
-- settings$model$type
-- settings$database$bety
-- settings$database$dbfiles
-- settings$meta.analysis$update</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pfts</th>
+              <td><p>the list of pfts to get traits for</p></td>
+            </tr>
+            <tr>
+              <th>modeltype</th>
+              <td>
+                <p>
+                  type of model that is used, this is is used to distinguis
+                  between different pfts with the same name.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>dbfiles</th>
+              <td><p>location where previous results are found</p></td>
+            </tr>
+            <tr>
+              <th>database</th>
+              <td><p>database connection parameters</p></td>
+            </tr>
+            <tr>
+              <th>forceupdate</th>
+              <td>
+                <p>
+                  set this to true to force an update, false to check to see if
+                  an update is needed.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>trait.names</th>
+              <td>
+                <p>list of traits to query. If TRUE, uses trait.dictionary</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list of pfts with update posteriorids</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This will use the following items from setings: - settings$pfts -
+            settings$model$type - settings$database$bety -
+            settings$database$dbfiles - settings$meta.analysis$update
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin
+        </div>
+      </div>
 
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index 323c70e..148a47f 100644
--- a/base/db/docs/reference/get.trait.data.pft.html
+++ b/base/db/docs/reference/get.trait.data.pft.html
@@ -2,195 +2,261 @@
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+                        >Create PostGIS polygon</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Gets trait data from the database</h1>
-    
-    <div class="hidden name"><code>get.trait.data.pft.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Gets trait data from the database</h1>
 
-    <div class="ref-description">
-    
-    <p>Get trait data from the database for a single pft</p>
-    
-    </div>
+            <div class="hidden name"><code>get.trait.data.pft.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get trait data from the database for a single pft</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>get.trait.data.pft</span>(<span class='no'>pft</span>, <span class='no'>modeltype</span>, <span class='no'>dbfiles</span>, <span class='no'>dbcon</span>, <span class='no'>trait.names</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>get.trait.data.pft</span>(<span class='no'>pft</span>, <span class='no'>modeltype</span>, <span class='no'>dbfiles</span>, <span class='no'>dbcon</span>, <span class='no'>trait.names</span>,
   <span class='kw'>forceupdate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pft</th>
-      <td><p>list of settings for the pft whos traits to retrieve. See details</p></td>
-    </tr>
-    <tr>
-      <th>modeltype</th>
-      <td><p>type of model that is used, this is used to distinguish between different pfts with the same name.</p></td>
-    </tr>
-    <tr>
-      <th>dbfiles</th>
-      <td><p>location where previous results are found</p></td>
-    </tr>
-    <tr>
-      <th>dbcon</th>
-      <td><p>database connection</p></td>
-    </tr>
-    <tr>
-      <th>trait.names</th>
-      <td><p>list of trait names to retrieve</p></td>
-    </tr>
-    <tr>
-      <th>forceupdate</th>
-      <td><p>set this to true to force an update, auto will check to see if an update is needed.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>updated pft with posteriorid</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><code>pft</code> should be a list containing at least `name` and `outdir`, and optionally `posteriorid` and `constants`. BEWARE: All existing files in <code>outir</code> will be deleted!</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pft</th>
+              <td>
+                <p>
+                  list of settings for the pft whos traits to retrieve. See
+                  details
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>modeltype</th>
+              <td>
+                <p>
+                  type of model that is used, this is used to distinguish
+                  between different pfts with the same name.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>dbfiles</th>
+              <td><p>location where previous results are found</p></td>
+            </tr>
+            <tr>
+              <th>dbcon</th>
+              <td><p>database connection</p></td>
+            </tr>
+            <tr>
+              <th>trait.names</th>
+              <td><p>list of trait names to retrieve</p></td>
+            </tr>
+            <tr>
+              <th>forceupdate</th>
+              <td>
+                <p>
+                  set this to true to force an update, auto will check to see if
+                  an update is needed.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>updated pft with posteriorid</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            <code>pft</code> should be a list containing at least `name` and
+            `outdir`, and optionally `posteriorid` and `constants`. BEWARE: All
+            existing files in <code>outir</code> will be deleted!
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin, Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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diff --git a/base/db/docs/reference/get_run_ids.html b/base/db/docs/reference/get_run_ids.html
index 99129b3..4787d30 100644
--- a/base/db/docs/reference/get_run_ids.html
+++ b/base/db/docs/reference/get_run_ids.html
@@ -2,162 +2,205 @@
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+
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+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get vector of run IDs for a given workflow ID</h1>
-    
-    <div class="hidden name"><code>get_run_ids.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get vector of run IDs for a given workflow ID</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_run_ids</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
-    </tr>
-    <tr>
-      <th>workflow_id</th>
-      <td><p>Workflow ID</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get vector of run IDs for a given workflow ID</h1>
+
+            <div class="hidden name"><code>get_run_ids.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get vector of run IDs for a given workflow ID</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_run_ids</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+            <tr>
+              <th>workflow_id</th>
+              <td><p>Workflow ID</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/get_users.html b/base/db/docs/reference/get_users.html
index 4d048ef..66df0f0 100644
--- a/base/db/docs/reference/get_users.html
+++ b/base/db/docs/reference/get_users.html
@@ -2,158 +2,196 @@
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
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+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get data frame of users and IDs</h1>
-    
-    <div class="hidden name"><code>get_users.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get data frame of users and IDs</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_users</span>(<span class='no'>bety</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get data frame of users and IDs</h1>
+
+            <div class="hidden name"><code>get_users.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get data frame of users and IDs</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_users</span>(<span class='no'>bety</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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diff --git a/base/db/docs/reference/get_var_names.html b/base/db/docs/reference/get_var_names.html
index 2a37437..c3001f4 100644
--- a/base/db/docs/reference/get_var_names.html
+++ b/base/db/docs/reference/get_var_names.html
@@ -2,170 +2,220 @@
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+                    </li>
+                    <li>
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+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
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+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get vector of variable names for a particular workflow and run ID</h1>
-    
-    <div class="hidden name"><code>get_var_names.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get vector of variable names for a particular workflow and run ID</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_var_names</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>, <span class='no'>run_id</span>, <span class='kw'>remove_pool</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
-    </tr>
-    <tr>
-      <th>workflow_id</th>
-      <td><p>Workflow ID</p></td>
-    </tr>
-    <tr>
-      <th>run_id</th>
-      <td><p>Run ID</p></td>
-    </tr>
-    <tr>
-      <th>remove_pool</th>
-      <td><p>logical: ignore variables with 'pools' in their names?</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Get vector of variable names for a particular workflow and run ID
+            </h1>
+
+            <div class="hidden name"><code>get_var_names.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Get vector of variable names for a particular workflow and run ID
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_var_names</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>, <span class='no'>run_id</span>, <span class='kw'>remove_pool</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+            <tr>
+              <th>workflow_id</th>
+              <td><p>Workflow ID</p></td>
+            </tr>
+            <tr>
+              <th>run_id</th>
+              <td><p>Run ID</p></td>
+            </tr>
+            <tr>
+              <th>remove_pool</th>
+              <td>
+                <p>logical: ignore variables with 'pools' in their names?</p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/get_workflow_ids.html b/base/db/docs/reference/get_workflow_ids.html
index 30eecb7..c71ec5c 100644
--- a/base/db/docs/reference/get_workflow_ids.html
+++ b/base/db/docs/reference/get_workflow_ids.html
@@ -2,162 +2,200 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get vector of workflow IDs</h1>
-    
-    <div class="hidden name"><code>get_workflow_ids.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get vector of workflow IDs</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_workflow_ids</span>(<span class='no'>bety</span>, <span class='no'>query</span>, <span class='kw'>all.ids</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
-    </tr>
-    <tr>
-      <th>query</th>
-      <td><p>Named vector or list of workflow IDs</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get vector of workflow IDs</h1>
+
+            <div class="hidden name"><code>get_workflow_ids.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get vector of workflow IDs</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_workflow_ids</span>(<span class='no'>bety</span>, <span class='no'>query</span>, <span class='kw'>all.ids</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+            <tr>
+              <th>query</th>
+              <td><p>Named vector or list of workflow IDs</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-        
-        <td>
-          <p><code><a href="check.lists.html">check.lists()</a></code> </p>
-        </td>
-        <td><p>Compares two lists</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="clone_pft.html">clone_pft()</a></code> </p>
-        </td>
-        <td><p>Duplicate existing pft with associated priors, species, and cultivars</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="db.close.html">db.close()</a></code> </p>
-        </td>
-        <td><p>Close database connection</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="db.exists.html">db.exists()</a></code> </p>
-        </td>
-        <td><p>db.exists</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="db.getShowQueries.html">db.getShowQueries()</a></code> </p>
-        </td>
-        <td><p>db.getShowQueries</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="db.open.html">db.open()</a></code> </p>
-        </td>
-        <td><p>Open database connection</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="db.print.connections.html">db.print.connections()</a></code> </p>
-        </td>
-        <td><p>Debug leaked connections</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="db.query.html">db.query()</a></code> </p>
-        </td>
-        <td><p>Query database</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="db.showQueries.html">db.showQueries()</a></code> </p>
-        </td>
-        <td><p>db.showQueries</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dbHostInfo.html">dbHostInfo()</a></code> </p>
-        </td>
-        <td><p>Database host information</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="db_merge_into.html">db_merge_into()</a></code> </p>
-        </td>
-        <td><p>Merge local data frame into SQL table</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dbfile.check.html">dbfile.check()</a></code> </p>
-        </td>
-        <td><p>Check for a file in the dbfiles tables</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dbfile.file.html">dbfile.file()</a></code> <code><a href="dbfile.file.html">dbfile.id()</a></code> </p>
-        </td>
-        <td><p>Convert between file paths and ids</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dbfile.input.check.html">dbfile.input.check()</a></code> </p>
-        </td>
-        <td><p>Check for a file in the input/dbfiles tables</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dbfile.input.insert.html">dbfile.input.insert()</a></code> </p>
-        </td>
-        <td><p>Insert file into tables</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dbfile.insert.html">dbfile.insert()</a></code> </p>
-        </td>
-        <td><p>Insert file into tables</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dbfile.posterior.check.html">dbfile.posterior.check()</a></code> </p>
-        </td>
-        <td><p>Check for a file in the input/dbfiles tables</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dbfile.posterior.insert.html">dbfile.posterior.insert()</a></code> </p>
-        </td>
-        <td><p>Insert file into tables</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="default_hostname.html">default_hostname()</a></code> </p>
-        </td>
-        <td><p>default_hostname</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="derive.trait.html">derive.trait()</a></code> </p>
-        </td>
-        <td><p>Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="derive.traits.html">derive.traits()</a></code> </p>
-        </td>
-        <td><p>Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dplyr.count.html">dplyr.count()</a></code> </p>
-        </td>
-        <td><p>Count rows of a data frame</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="fancy_scientific.html">fancy_scientific()</a></code> </p>
-        </td>
-        <td><p>Convert number to scientific notation pretty expression</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="fetch.stats2se.html">fetch.stats2se()</a></code> </p>
-        </td>
-        <td><p>Fetch data and transform stats to SE</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="filter_sunleaf_traits.html">filter_sunleaf_traits()</a></code> </p>
-        </td>
-        <td><p>Function to filter out upper canopy leaves</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.id.html">get.id()</a></code> </p>
-        </td>
-        <td><p>get.id</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.trait.data.html">get.trait.data()</a></code> </p>
-        </td>
-        <td><p>Gets trait data from the database</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.trait.data.pft.html">get.trait.data.pft()</a></code> </p>
-        </td>
-        <td><p>Gets trait data from the database</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_run_ids.html">get_run_ids()</a></code> </p>
-        </td>
-        <td><p>Get vector of run IDs for a given workflow ID</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_users.html">get_users()</a></code> </p>
-        </td>
-        <td><p>Get data frame of users and IDs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_var_names.html">get_var_names()</a></code> </p>
-        </td>
-        <td><p>Get vector of variable names for a particular workflow and run ID</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_workflow_ids.html">get_workflow_ids()</a></code> </p>
-        </td>
-        <td><p>Get vector of workflow IDs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="insert.format.vars.html">insert.format.vars()</a></code> </p>
-        </td>
-        <td><p>Insert Format and Format-Variable Records</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="insert_table.html">insert_table()</a></code> </p>
-        </td>
-        <td><p>Insert R data frame into SQL database</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load_data_single_run.html">load_data_single_run()</a></code> </p>
-        </td>
-        <td><p>Load data for a single run of the model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="match_colnames.html">match_colnames()</a></code> </p>
-        </td>
-        <td><p>Match names of local data frame to SQL table</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="match_dbcols.html">match_dbcols()</a></code> </p>
-        </td>
-        <td><p>Match column names and classes between local and SQL table</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ncdays2date.html">ncdays2date()</a></code> </p>
-        </td>
-        <td><p>Convert netcdf number of days to date</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.covariates.html">query.covariates()</a></code> </p>
-        </td>
-        <td><p>Queries covariates from database for a given vector of trait id's</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.data.html">query.data()</a></code> </p>
-        </td>
-        <td><p>Query data and transform stats to SE by calling <code>fetch.stats2se</code>;</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.file.path.html">query.file.path()</a></code> </p>
-        </td>
-        <td><p>Get file path given id and machine</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.format.vars.html">query.format.vars()</a></code> </p>
-        </td>
-        <td><p>Given input_id, return formats table and table of variables and units</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.pft_cultivars.html">query.pft_cultivars()</a></code> </p>
-        </td>
-        <td><p>Select cultivars associated with a PFT</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.pft_species.html">query.pft_species()</a></code> </p>
-        </td>
-        <td><p>Query species given pft name</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.priors.html">query.priors()</a></code> </p>
-        </td>
-        <td><p>Query Priors</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.site.html">query.site()</a></code> </p>
-        </td>
-        <td><p>Given site_id, return site table</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.trait.data.html">query.trait.data()</a></code> </p>
-        </td>
-        <td><p>Extract trait data from database</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.traits.html">query.traits()</a></code> </p>
-        </td>
-        <td><p>Query trait data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.yields.html">query.yields()</a></code> </p>
-        </td>
-        <td><p>Query yield data and transform stats to SE by calling <code>fetch.stats2se</code>;</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="rename_jags_columns.html">rename_jags_columns()</a></code> </p>
-        </td>
-        <td><p>renames the variables within output data frame trait.data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="runs.html">runs()</a></code> </p>
-        </td>
-        <td><p>Get table of runs corresponding to a workflow</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="search_reference_single.html">search_reference_single()</a></code> </p>
-        </td>
-        <td><p>Perform crossref search for a single reference</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="search_references.html">search_references()</a></code> </p>
-        </td>
-        <td><p>Perform crossref search for a list of references</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="take.samples.html">take.samples()</a></code> </p>
-        </td>
-        <td><p>Sample from normal distribution, given summary stats</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="try2sqlite.html">try2sqlite()</a></code> </p>
-        </td>
-        <td><p>Convert TRY text file to SQLite database</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="var_names_all.html">var_names_all()</a></code> </p>
-        </td>
-        <td><p>Get vector of variable names for a particular workflow and run ID</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="workflow.html">workflow()</a></code> </p>
-        </td>
-        <td><p>Get single workflow by workflow_id</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="workflows.html">workflows()</a></code> </p>
-        </td>
-        <td><p>list of workflows that exist</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="PEcAn.DB.html">PEcAn.DB</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Database functions for PEcAn, the Predictive Ecosystem
+                    Analyzer
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="append.covariate.html"
+                        >append.covariate()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Append covariate data as a column within a table</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="arrhenius.scaling.traits.html"
+                        >arrhenius.scaling.traits()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Apply Arrhenius scaling to 25 degC for temperature-dependent
+                    traits
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="assign.treatments.html"
+                        >assign.treatments()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>assign.treatments</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="bety2pecan.html">bety2pecan()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Convert BETY variable names to MsTMIP and subsequently PEcAn
+                    standard names
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="betyConnect.html">betyConnect()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Connect to bety using current PEcAn configuration</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="build_insert_query.html"
+                        >build_insert_query()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Build query to insert R data frame into SQL table</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="check.lists.html">check.lists()</a></code>
+                  </p>
+                </td>
+                <td><p>Compares two lists</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="clone_pft.html">clone_pft()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Duplicate existing pft with associated priors, species, and
+                    cultivars
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="db.close.html">db.close()</a></code>
+                  </p>
+                </td>
+                <td><p>Close database connection</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="db.exists.html">db.exists()</a></code>
+                  </p>
+                </td>
+                <td><p>db.exists</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="db.getShowQueries.html"
+                        >db.getShowQueries()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>db.getShowQueries</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="db.open.html">db.open()</a></code>
+                  </p>
+                </td>
+                <td><p>Open database connection</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="db.print.connections.html"
+                        >db.print.connections()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Debug leaked connections</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="db.query.html">db.query()</a></code>
+                  </p>
+                </td>
+                <td><p>Query database</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="db.showQueries.html">db.showQueries()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>db.showQueries</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="dbHostInfo.html">dbHostInfo()</a></code>
+                  </p>
+                </td>
+                <td><p>Database host information</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="db_merge_into.html">db_merge_into()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Merge local data frame into SQL table</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="dbfile.check.html">dbfile.check()</a></code>
+                  </p>
+                </td>
+                <td><p>Check for a file in the dbfiles tables</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="dbfile.file.html">dbfile.file()</a></code>
+                    <code><a href="dbfile.file.html">dbfile.id()</a></code>
+                  </p>
+                </td>
+                <td><p>Convert between file paths and ids</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="dbfile.input.check.html"
+                        >dbfile.input.check()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check for a file in the input/dbfiles tables</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="dbfile.input.insert.html"
+                        >dbfile.input.insert()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Insert file into tables</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="dbfile.insert.html">dbfile.insert()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Insert file into tables</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="dbfile.posterior.check.html"
+                        >dbfile.posterior.check()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check for a file in the input/dbfiles tables</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="dbfile.posterior.insert.html"
+                        >dbfile.posterior.insert()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Insert file into tables</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="default_hostname.html"
+                        >default_hostname()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>default_hostname</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="derive.trait.html">derive.trait()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Performs an arithmetic function, FUN, over a series of
+                    traits and returns the result as a derived trait.
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="derive.traits.html">derive.traits()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Performs an arithmetic function, FUN, over a series of
+                    traits and returns the result as a derived trait.
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="dplyr.count.html">dplyr.count()</a></code>
+                  </p>
+                </td>
+                <td><p>Count rows of a data frame</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="fancy_scientific.html"
+                        >fancy_scientific()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Convert number to scientific notation pretty expression</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="fetch.stats2se.html">fetch.stats2se()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Fetch data and transform stats to SE</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="filter_sunleaf_traits.html"
+                        >filter_sunleaf_traits()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Function to filter out upper canopy leaves</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.id.html">get.id()</a></code>
+                  </p>
+                </td>
+                <td><p>get.id</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.trait.data.html">get.trait.data()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Gets trait data from the database</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.trait.data.pft.html"
+                        >get.trait.data.pft()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Gets trait data from the database</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get_run_ids.html">get_run_ids()</a></code>
+                  </p>
+                </td>
+                <td><p>Get vector of run IDs for a given workflow ID</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get_users.html">get_users()</a></code>
+                  </p>
+                </td>
+                <td><p>Get data frame of users and IDs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_var_names.html">get_var_names()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Get vector of variable names for a particular workflow and
+                    run ID
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_workflow_ids.html"
+                        >get_workflow_ids()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get vector of workflow IDs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="insert.format.vars.html"
+                        >insert.format.vars()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Insert Format and Format-Variable Records</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="insert_table.html">insert_table()</a></code>
+                  </p>
+                </td>
+                <td><p>Insert R data frame into SQL database</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="load_data_single_run.html"
+                        >load_data_single_run()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Load data for a single run of the model</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="match_colnames.html">match_colnames()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Match names of local data frame to SQL table</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="match_dbcols.html">match_dbcols()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Match column names and classes between local and SQL table
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ncdays2date.html">ncdays2date()</a></code>
+                  </p>
+                </td>
+                <td><p>Convert netcdf number of days to date</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="query.covariates.html"
+                        >query.covariates()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Queries covariates from database for a given vector of trait
+                    id's
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="query.data.html">query.data()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Query data and transform stats to SE by calling
+                    <code>fetch.stats2se</code>;
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="query.file.path.html"
+                        >query.file.path()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get file path given id and machine</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="query.format.vars.html"
+                        >query.format.vars()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Given input_id, return formats table and table of variables
+                    and units
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="query.pft_cultivars.html"
+                        >query.pft_cultivars()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Select cultivars associated with a PFT</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="query.pft_species.html"
+                        >query.pft_species()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Query species given pft name</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="query.priors.html">query.priors()</a></code>
+                  </p>
+                </td>
+                <td><p>Query Priors</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="query.site.html">query.site()</a></code>
+                  </p>
+                </td>
+                <td><p>Given site_id, return site table</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="query.trait.data.html"
+                        >query.trait.data()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Extract trait data from database</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="query.traits.html">query.traits()</a></code>
+                  </p>
+                </td>
+                <td><p>Query trait data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="query.yields.html">query.yields()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Query yield data and transform stats to SE by calling
+                    <code>fetch.stats2se</code>;
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="rename_jags_columns.html"
+                        >rename_jags_columns()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    renames the variables within output data frame trait.data
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="runs.html">runs()</a></code>
+                  </p>
+                </td>
+                <td><p>Get table of runs corresponding to a workflow</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="search_reference_single.html"
+                        >search_reference_single()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Perform crossref search for a single reference</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="search_references.html"
+                        >search_references()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Perform crossref search for a list of references</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="take.samples.html">take.samples()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Sample from normal distribution, given summary stats</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="try2sqlite.html">try2sqlite()</a></code>
+                  </p>
+                </td>
+                <td><p>Convert TRY text file to SQLite database</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="var_names_all.html">var_names_all()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Get vector of variable names for a particular workflow and
+                    run ID
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="workflow.html">workflow()</a></code>
+                  </p>
+                </td>
+                <td><p>Get single workflow by workflow_id</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="workflows.html">workflows()</a></code>
+                  </p>
+                </td>
+                <td><p>list of workflows that exist</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
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-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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+        <div class="copyright">
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Insert Format and Format-Variable Records</h1>
-    
-    <div class="hidden name"><code>insert.format.vars.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Insert Format and Format-Variable Records</h1>
 
-    <div class="ref-description">
-    
-    <p>Insert Format and Format-Variable Records</p>
-    
-    </div>
+            <div class="hidden name"><code>insert.format.vars.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>insert.format.vars</span>(<span class='no'>con</span>, <span class='no'>format_name</span>, <span class='no'>mimetype_id</span>, <span class='kw'>notes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>Insert Format and Format-Variable Records</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>insert.format.vars</span>(<span class='no'>con</span>, <span class='no'>format_name</span>, <span class='no'>mimetype_id</span>, <span class='kw'>notes</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>formats_variables</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>suppress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>con</th>
-      <td><p>SQL connection to BETYdb</p></td>
-    </tr>
-    <tr>
-      <th>format_name</th>
-      <td><p>The name of the format. Type: character string.</p></td>
-    </tr>
-    <tr>
-      <th>mimetype_id</th>
-      <td><p>The id associated with the mimetype of the format. Type: integer.</p></td>
-    </tr>
-    <tr>
-      <th>notes</th>
-      <td><p>Additional description of the format: character string.</p></td>
-    </tr>
-    <tr>
-      <th>header</th>
-      <td><p>Boolean that indicates the presence of a header in the format. Defaults to "TRUE".</p></td>
-    </tr>
-    <tr>
-      <th>skip</th>
-      <td><p>Integer that indicates the number of lines to skip in the header. Defaults to 0.</p></td>
-    </tr>
-    <tr>
-      <th>formats_variables</th>
-      <td><p>A 'tibble' consisting of entries that correspond to columns in the formats-variables table. See Details for further information.</p></td>
-    </tr>
-    <tr>
-      <th>suppress</th>
-      <td><p>Boolean that suppresses or allows a test for an existing variable id. This test is inconvenient in applications where the variable_ids are already known.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>format_id</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>The formats_variables argument must be a 'tibble' and be structured in a specific format so that the SQL query functions properly. All arguments should be passed as vectors so that each entry will correspond with a specific row. All empty values should be specified as NA.</p><dl class='dl-horizontal'>
-<dt>variable_id</dt><dd><p>(Required) Vector of integers.</p></dd>
-<dt>name</dt><dd><p>(Optional) Vector of character strings. The variable name in the imported data need only be specified if it differs from the BETY variable name.</p></dd> 
-<dt>unit</dt><dd><p>(Optional) Vector of type character string. Should be in a format parseable by the udunits library and need only be secified if the units of the data in the file differ from the BETY standard.</p></dd>
-<dt>storage_type</dt><dd><p>(Optional) Vector of character strings. Storage type need only be specified if the variable is stored in a format other than would be expected (e.g. if numeric values are stored as quoted character strings). Additionally, storage_type stores POSIX codes that are used to store any time variables (e.g. a column with a 4-digit year would be %Y). See also <code>[base::strptime]</code></p></dd>
-<dt>column_number</dt><dd><p>Vector of integers that list the column numbers associated with variables in a dataset. Required for text files that lack headers.</p></dd></dl>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>con</th>
+              <td><p>SQL connection to BETYdb</p></td>
+            </tr>
+            <tr>
+              <th>format_name</th>
+              <td><p>The name of the format. Type: character string.</p></td>
+            </tr>
+            <tr>
+              <th>mimetype_id</th>
+              <td>
+                <p>
+                  The id associated with the mimetype of the format. Type:
+                  integer.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>notes</th>
+              <td>
+                <p>Additional description of the format: character string.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>header</th>
+              <td>
+                <p>
+                  Boolean that indicates the presence of a header in the format.
+                  Defaults to "TRUE".
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>skip</th>
+              <td>
+                <p>
+                  Integer that indicates the number of lines to skip in the
+                  header. Defaults to 0.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>formats_variables</th>
+              <td>
+                <p>
+                  A 'tibble' consisting of entries that correspond to columns in
+                  the formats-variables table. See Details for further
+                  information.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>suppress</th>
+              <td>
+                <p>
+                  Boolean that suppresses or allows a test for an existing
+                  variable id. This test is inconvenient in applications where
+                  the variable_ids are already known.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>format_id</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            The formats_variables argument must be a 'tibble' and be structured
+            in a specific format so that the SQL query functions properly. All
+            arguments should be passed as vectors so that each entry will
+            correspond with a specific row. All empty values should be specified
+            as NA.
+          </p>
+          <dl class="dl-horizontal">
+            <dt>variable_id</dt>
+            <dd><p>(Required) Vector of integers.</p></dd>
+            <dt>name</dt>
+            <dd>
+              <p>
+                (Optional) Vector of character strings. The variable name in the
+                imported data need only be specified if it differs from the BETY
+                variable name.
+              </p>
+            </dd>
+            <dt>unit</dt>
+            <dd>
+              <p>
+                (Optional) Vector of type character string. Should be in a
+                format parseable by the udunits library and need only be
+                secified if the units of the data in the file differ from the
+                BETY standard.
+              </p>
+            </dd>
+            <dt>storage_type</dt>
+            <dd>
+              <p>
+                (Optional) Vector of character strings. Storage type need only
+                be specified if the variable is stored in a format other than
+                would be expected (e.g. if numeric values are stored as quoted
+                character strings). Additionally, storage_type stores POSIX
+                codes that are used to store any time variables (e.g. a column
+                with a 4-digit year would be %Y). See also
+                <code>[base::strptime]</code>
+              </p>
+            </dd>
+            <dt>column_number</dt>
+            <dd>
+              <p>
+                Vector of integers that list the column numbers associated with
+                variables in a dataset. Required for text files that lack
+                headers.
+              </p>
+            </dd>
+          </dl>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>bety</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>PEcAn.DB</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.DB/topics/betyConnect'>betyConnect</a></span>()
 
 <span class='no'>formats_variables_tibble</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>tibble</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/tibble/topics/tibble'>tibble</a></span>(
@@ -186,40 +311,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
  )
   <span class='fu'>insert.format.vars</span>(<span class='kw'>con</span> <span class='kw'>=</span> <span class='no'>bety</span>$<span class='no'>con</span>, <span class='kw'>format_name</span> <span class='kw'>=</span> <span class='st'>"LTER-HFR-103"</span>, <span class='kw'>mimetype_id</span> <span class='kw'>=</span> <span class='fl'>1090</span>, <span class='kw'>notes</span> <span class='kw'>=</span> <span class='st'>"NPP from Harvard Forest."</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>formats_variables</span> <span class='kw'>=</span> <span class='no'>formats_variables_tibble</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Liam Burke (liam.burke24@gmail.com)
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Liam Burke (liam.burke24@gmail.com)
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/db/docs/reference/insert_table.html b/base/db/docs/reference/insert_table.html
index a7f555d..d4a5666 100644
--- a/base/db/docs/reference/insert_table.html
+++ b/base/db/docs/reference/insert_table.html
@@ -2,196 +2,255 @@
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Insert R data frame into SQL database — insert_table • PEcAn.DB
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Insert R data frame into SQL database — insert_table"
+    />
+
+    <meta
+      property="og:description"
+      content="First, subset to matching columns. Then, make sure the local and SQL column 
 classes match, coercing local to SQL as necessary (or throwing an error). 
 Then, build an SQL string for the insert statement. Finally, insert into the 
-database." />
-<meta name="twitter:card" content="summary" />
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+database."
+    />
+    <meta name="twitter:card" content="summary" />
 
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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+                  class="label label-default"
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+                        >Create PostGIS polygon</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Insert R data frame into SQL database</h1>
-    
-    <div class="hidden name"><code>insert_table.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>First, subset to matching columns. Then, make sure the local and SQL column 
-classes match, coercing local to SQL as necessary (or throwing an error). 
-Then, build an SQL string for the insert statement. Finally, insert into the 
-database.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>insert_table</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>con</span>, <span class='kw'>coerce_col_class</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>values</th>
-      <td><p>`data.frame` of values to write to SQL database</p></td>
-    </tr>
-    <tr>
-      <th>table</th>
-      <td><p>Name of target SQL table, as character</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>coerce_col_class</th>
-      <td><p>logical, whether or not to coerce local data columns 
-to SQL classes. Default = `TRUE.`</p></td>
-    </tr>
-    <tr>
-      <th>drop</th>
-      <td><p>logical. If `TRUE` (default), drop columns not found in SQL table.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data frame with query results</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Insert R data frame into SQL database</h1>
+
+            <div class="hidden name"><code>insert_table.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              First, subset to matching columns. Then, make sure the local and
+              SQL column classes match, coercing local to SQL as necessary (or
+              throwing an error). Then, build an SQL string for the insert
+              statement. Finally, insert into the database.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>insert_table</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>con</span>, <span class='kw'>coerce_col_class</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>values</th>
+              <td><p>`data.frame` of values to write to SQL database</p></td>
+            </tr>
+            <tr>
+              <th>table</th>
+              <td><p>Name of target SQL table, as character</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>coerce_col_class</th>
+              <td>
+                <p>
+                  logical, whether or not to coerce local data columns to SQL
+                  classes. Default = `TRUE.`
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>drop</th>
+              <td>
+                <p>
+                  logical. If `TRUE` (default), drop columns not found in SQL
+                  table.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>data frame with query results</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>irisdb</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>DBI</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/DBI/topics/dbConnect'>dbConnect</a></span>(<span class='kw pkg'>RSQLite</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/RSQLite/topics/SQLite'>SQLite</a></span>(), <span class='st'>":memory:"</span>)
 <span class='kw pkg'>dplyr</span><span class='kw ns'>::</span><span class='fu'><a href='http://dplyr.tidyverse.org/reference/copy_to.html'>copy_to</a></span>(<span class='no'>irisdb</span>, <span class='no'>iris</span>[<span class='fl'>1</span>,], <span class='kw'>name</span> <span class='kw'>=</span> <span class='st'>"iris"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='fu'>insert_table</span>(<span class='no'>iris</span>[-<span class='fl'>1</span>,], <span class='st'>"iris"</span>, <span class='no'>irisdb</span>)
 <span class='kw pkg'>dplyr</span><span class='kw ns'>::</span><span class='fu'><a href='http://dplyr.tidyverse.org/reference/tbl.html'>tbl</a></span>(<span class='no'>irisdb</span>, <span class='st'>"iris"</span>)
 <span class='co'># }</span></pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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diff --git a/base/db/docs/reference/load_data_single_run.html b/base/db/docs/reference/load_data_single_run.html
index 595c005..a57c2e4 100644
--- a/base/db/docs/reference/load_data_single_run.html
+++ b/base/db/docs/reference/load_data_single_run.html
@@ -2,166 +2,209 @@
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+
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+    ></script>
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+
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
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+
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+      crossorigin="anonymous"
+    ></script>
+
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+    <script
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+
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+    />
+    <meta name="twitter:card" content="summary" />
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
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+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Load data for a single run of the model</h1>
-    
-    <div class="hidden name"><code>load_data_single_run.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Load data for a single run of the model</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>load_data_single_run</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>, <span class='no'>run_id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
-    </tr>
-    <tr>
-      <th>workflow_id</th>
-      <td><p>Workflow ID</p></td>
-    </tr>
-    <tr>
-      <th>run_id</th>
-      <td><p>Run ID</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Load data for a single run of the model</h1>
+
+            <div class="hidden name"><code>load_data_single_run.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Load data for a single run of the model</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load_data_single_run</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>, <span class='no'>run_id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+            <tr>
+              <th>workflow_id</th>
+              <td><p>Workflow ID</p></td>
+            </tr>
+            <tr>
+              <th>run_id</th>
+              <td><p>Run ID</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/match_colnames.html b/base/db/docs/reference/match_colnames.html
index 949e57a..9c1cb68 100644
--- a/base/db/docs/reference/match_colnames.html
+++ b/base/db/docs/reference/match_colnames.html
@@ -2,166 +2,209 @@
 <!DOCTYPE html>
 <html>
   <head>
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+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Match names of local data frame to SQL table</h1>
-    
-    <div class="hidden name"><code>match_colnames.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Match names of local data frame to SQL table</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>match_colnames</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>values</th>
-      <td><p>`data.frame` of values to write to SQL database</p></td>
-    </tr>
-    <tr>
-      <th>table</th>
-      <td><p>Name of target SQL table, as character</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Match names of local data frame to SQL table</h1>
+
+            <div class="hidden name"><code>match_colnames.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Match names of local data frame to SQL table</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>match_colnames</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>values</th>
+              <td><p>`data.frame` of values to write to SQL database</p></td>
+            </tr>
+            <tr>
+              <th>table</th>
+              <td><p>Name of target SQL table, as character</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Match column names and classes between local and SQL table</h1>
-    
-    <div class="hidden name"><code>match_dbcols.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Match column names and classes between local and SQL table</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>match_dbcols</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>con</span>, <span class='kw'>coerce_col_class</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>values</th>
-      <td><p>`data.frame` of values to write to SQL database</p></td>
-    </tr>
-    <tr>
-      <th>table</th>
-      <td><p>Name of target SQL table, as character</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>coerce_col_class</th>
-      <td><p>logical, whether or not to coerce local data columns 
-to SQL classes. Default = `TRUE.`</p></td>
-    </tr>
-    <tr>
-      <th>drop</th>
-      <td><p>logical. If `TRUE` (default), drop columns not found in SQL table.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`values` `data.frame` with column names and classes matched to SQL</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Match column names and classes between local and SQL table</h1>
+
+            <div class="hidden name"><code>match_dbcols.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Match column names and classes between local and SQL table</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>match_dbcols</span>(<span class='no'>values</span>, <span class='no'>table</span>, <span class='no'>con</span>, <span class='kw'>coerce_col_class</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>values</th>
+              <td><p>`data.frame` of values to write to SQL database</p></td>
+            </tr>
+            <tr>
+              <th>table</th>
+              <td><p>Name of target SQL table, as character</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>coerce_col_class</th>
+              <td>
+                <p>
+                  logical, whether or not to coerce local data columns to SQL
+                  classes. Default = `TRUE.`
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>drop</th>
+              <td>
+                <p>
+                  logical. If `TRUE` (default), drop columns not found in SQL
+                  table.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            `values` `data.frame` with column names and classes matched to SQL
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
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+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/ncdays2date.html b/base/db/docs/reference/ncdays2date.html
index fb44ef1..639d0a3 100644
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+++ b/base/db/docs/reference/ncdays2date.html
@@ -2,148 +2,185 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert netcdf number of days to date</h1>
-    
-    <div class="hidden name"><code>ncdays2date.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert netcdf number of days to date</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert netcdf number of days to date</h1>
 
-    <pre class="usage"><span class='fu'>ncdays2date</span>(<span class='no'>time</span>, <span class='no'>unit</span>)</pre>
-        
+            <div class="hidden name"><code>ncdays2date.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Convert netcdf number of days to date</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>ncdays2date</span>(<span class='no'>time</span>, <span class='no'>unit</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/query.covariates.html b/base/db/docs/reference/query.covariates.html
index 0eb58a6..aeb0c4d 100644
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@@ -2,170 +2,218 @@
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+                <li class="dropdown">
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+                    href="#"
+                    class="dropdown-toggle"
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+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
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+
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Queries covariates from database for a given vector of trait id's</h1>
-    
-    <div class="hidden name"><code>query.covariates.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Queries covariates from database for a given vector of trait id's</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.covariates</span>(<span class='no'>trait.ids</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.ids</th>
-      <td><p>list of trait ids</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>extra arguments</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Queries covariates from database for a given vector of trait id's
+            </h1>
+
+            <div class="hidden name"><code>query.covariates.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Queries covariates from database for a given vector of trait id's
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.covariates</span>(<span class='no'>trait.ids</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.ids</th>
+              <td><p>list of trait ids</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>extra arguments</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          David LeBauer
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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index 298287a..c3aeb8d 100644
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+++ b/base/db/docs/reference/query.data.html
@@ -2,191 +2,268 @@
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+      Query data and transform stats to SE by calling <code><a
+      href='fetch.stats2se.html'>fetch.stats2se</a></code>; — query.data •
+      PEcAn.DB
+    </title>
+
+    <!-- jquery -->
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+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+                    data-toggle="dropdown"
+                    role="button"
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+                  </a>
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+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Query data and transform stats to SE by calling <code><a href='fetch.stats2se.html'>fetch.stats2se</a></code>;</h1>
-    
-    <div class="hidden name"><code>query.data.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to query data from database for specific species and convert stat to SE</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.data</span>(<span class='no'>trait</span>, <span class='no'>spstr</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Query data and transform stats to SE by calling
+              <code><a href="fetch.stats2se.html">fetch.stats2se</a></code
+              >;
+            </h1>
+
+            <div class="hidden name"><code>query.data.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to query data from database for specific species and
+              convert stat to SE
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.data</span>(<span class='no'>trait</span>, <span class='no'>spstr</span>,
   <span class='kw'>extra.columns</span> <span class='kw'>=</span> <span class='st'>"ST_X(ST_CENTROID(sites.geometry)) AS lon, ST_Y(ST_CENTROID(sites.geometry)) AS lat, "</span>,
   <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>store.unconverted</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>ids_are_cultivars</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait</th>
-      <td><p>trait to query from the database</p></td>
-    </tr>
-    <tr>
-      <th>spstr</th>
-      <td><p>IDs of species to query from, as a single comma-separated string</p></td>
-    </tr>
-    <tr>
-      <th>extra.columns</th>
-      <td><p>other query terms to pass in. If unspecified, retrieves latitude and longitude</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    <tr>
-      <th>ids_are_cultivars</th>
-      <td><p>if TRUE, ids is a vector of cultivar IDs, otherwise they are species IDs</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>extra arguments</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>used in <code><a href='query.trait.data.html'>query.trait.data</a></code>; <code><a href='fetch.stats2se.html'>fetch.stats2se</a></code>; <code>transformstats</code> performs transformation calculations</p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#see-also">See also</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait</th>
+              <td><p>trait to query from the database</p></td>
+            </tr>
+            <tr>
+              <th>spstr</th>
+              <td>
+                <p>
+                  IDs of species to query from, as a single comma-separated
+                  string
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>extra.columns</th>
+              <td>
+                <p>
+                  other query terms to pass in. If unspecified, retrieves
+                  latitude and longitude
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+            <tr>
+              <th>ids_are_cultivars</th>
+              <td>
+                <p>
+                  if TRUE, ids is a vector of cultivar IDs, otherwise they are
+                  species IDs
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>extra arguments</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              used in
+              <code><a href="query.trait.data.html">query.trait.data</a></code
+              >; <code><a href="fetch.stats2se.html">fetch.stats2se</a></code
+              >; <code>transformstats</code> performs transformation
+              calculations
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Carl Davidson
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/base/db/docs/reference/query.file.path.html b/base/db/docs/reference/query.file.path.html
index 8529fc0..da09f68 100644
--- a/base/db/docs/reference/query.file.path.html
+++ b/base/db/docs/reference/query.file.path.html
@@ -2,170 +2,213 @@
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get file path given id and machine</h1>
-    
-    <div class="hidden name"><code>query.file.path.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get file path given id and machine</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.file.path</span>(<span class='no'>input.id</span>, <span class='no'>host_name</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>host_name</th>
-      <td><p>character: machine where the file lives</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>: database connection</p></td>
-    </tr>
-    <tr>
-      <th>input_id</th>
-      <td><p>numeric: BETY id of the file ("container") to find</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get file path given id and machine</h1>
+
+            <div class="hidden name"><code>query.file.path.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get file path given id and machine</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.file.path</span>(<span class='no'>input.id</span>, <span class='no'>host_name</span>, <span class='no'>con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>host_name</th>
+              <td><p>character: machine where the file lives</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>: database connection</p></td>
+            </tr>
+            <tr>
+              <th>input_id</th>
+              <td><p>numeric: BETY id of the file ("container") to find</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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index 7dbdcde..addfe3b 100644
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Given input_id, return formats table and table of variables and units</h1>
-    
-    <div class="hidden name"><code>query.format.vars.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Given input_id, return formats table and table of variables and units</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.format.vars</span>(<span class='no'>bety</span>, <span class='kw'>input.id</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>format.id</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>var.ids</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>database connection</p></td>
-    </tr>
-    <tr>
-      <th>var.ids</th>
-      <td><p>optional vector of variable IDs. If provided, limits results to these variables</p></td>
-    </tr>
-    <tr>
-      <th>input_id, format.id</th>
-      <td><p>numeric. Defaults to format.id if both provided</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery, Ankur Desai, Istem Fer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Given input_id, return formats table and table of variables and
+              units
+            </h1>
+
+            <div class="hidden name"><code>query.format.vars.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Given input_id, return formats table and table of variables and
+              units
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.format.vars</span>(<span class='no'>bety</span>, <span class='kw'>input.id</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>format.id</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>var.ids</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>database connection</p></td>
+            </tr>
+            <tr>
+              <th>var.ids</th>
+              <td>
+                <p>
+                  optional vector of variable IDs. If provided, limits results
+                  to these variables
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>input_id, format.id</th>
+              <td><p>numeric. Defaults to format.id if both provided</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery, Ankur Desai, Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-   </div>
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diff --git a/base/db/docs/reference/query.pft_cultivars.html b/base/db/docs/reference/query.pft_cultivars.html
index 23db52d..33bb6d9 100644
--- a/base/db/docs/reference/query.pft_cultivars.html
+++ b/base/db/docs/reference/query.pft_cultivars.html
@@ -2,185 +2,244 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Select cultivars associated with a PFT — query.pft_cultivars • PEcAn.DB
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Select cultivars associated with a PFT — query.pft_cultivars"
+    />
+
+    <meta
+      property="og:description"
+      content="Given a PFT name and optionally a modeltype, finds its pft_id and
+returns the cultivars associated with it."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-    </div>
-
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-  <a href="../index.html">
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
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+                type="button"
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+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Select cultivars associated with a PFT</h1>
-    
-    <div class="hidden name"><code>query.pft_cultivars.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Given a PFT name and optionally a modeltype, finds its pft_id and
-returns the cultivars associated with it.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.pft_cultivars</span>(<span class='no'>pft</span>, <span class='kw'>modeltype</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pft</th>
-      <td><p>string pft name</p></td>
-    </tr>
-    <tr>
-      <th>modeltype</th>
-      <td><p>type of model that is used, this is used to distinguish between different pfts with the same name.</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>tibble containing names and ids for each cultivar
-  and the species it comes from</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>A PFT is allowed to have associated species or associated
-cultivars, but not both. If this function returns no results, try checking
-your PFT with <code><a href='query.pft_species.html'>query.pft_species</a></code> instead.
-Note that the cultivars associated with one PFT *are* allowed to come from
-multiple species, if desired.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Select cultivars associated with a PFT</h1>
+
+            <div class="hidden name"><code>query.pft_cultivars.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Given a PFT name and optionally a modeltype, finds its pft_id and
+              returns the cultivars associated with it.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.pft_cultivars</span>(<span class='no'>pft</span>, <span class='kw'>modeltype</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pft</th>
+              <td><p>string pft name</p></td>
+            </tr>
+            <tr>
+              <th>modeltype</th>
+              <td>
+                <p>
+                  type of model that is used, this is used to distinguish
+                  between different pfts with the same name.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            tibble containing names and ids for each cultivar and the species it
+            comes from
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            A PFT is allowed to have associated species or associated cultivars,
+            but not both. If this function returns no results, try checking your
+            PFT with
+            <code><a href="query.pft_species.html">query.pft_species</a></code>
+            instead. Note that the cultivars associated with one PFT *are*
+            allowed to come from multiple species, if desired.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/base/db/docs/reference/query.pft_species.html b/base/db/docs/reference/query.pft_species.html
index 3257cd0..74839e6 100644
--- a/base/db/docs/reference/query.pft_species.html
+++ b/base/db/docs/reference/query.pft_species.html
@@ -2,183 +2,237 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
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-
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Query species given pft name</h1>
-    
-    <div class="hidden name"><code>query.pft_species.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>select plant id's associated with pft</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.pft_species</span>(<span class='no'>pft</span>, <span class='kw'>modeltype</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pft</th>
-      <td><p>string pft name</p></td>
-    </tr>
-    <tr>
-      <th>modeltype</th>
-      <td><p>type of model that is used, this is used to distinguish between different pfts with the same name.</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data.frame containing id, genus, species, scientificname of each species associated with pft</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Query species given pft name</h1>
+
+            <div class="hidden name"><code>query.pft_species.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>select plant id's associated with pft</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.pft_species</span>(<span class='no'>pft</span>, <span class='kw'>modeltype</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pft</th>
+              <td><p>string pft name</p></td>
+            </tr>
+            <tr>
+              <th>modeltype</th>
+              <td>
+                <p>
+                  type of model that is used, this is used to distinguish
+                  between different pfts with the same name.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            data.frame containing id, genus, species, scientificname of each
+            species associated with pft
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>query.pft_species</span>(<span class='st'>'ebifarm.pavi'</span>)
 <span class='fu'>query.pft_species</span>(<span class='kw'>settings</span> <span class='kw'>=</span> <span class='fu'>read.settings</span>(<span class='st'>"pecan.xml"</span>))
 <span class='co'># }</span></pre>
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-      <li><a href="#value">Value</a></li>
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-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
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-    </div>
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-    
-    <p>Query priors associated with a string of traits and plant functional type</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.priors</span>(<span class='no'>pft</span>, <span class='kw'>trstr</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>out</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pft</th>
-      <td><p>ID number of the PFT in the database</p></td>
-    </tr>
-    <tr>
-      <th>trstr</th>
-      <td><p>string of traits to query priors for</p></td>
-    </tr>
-    <tr>
-      <th>out</th>
-      <td><p>output location</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection, can be list of arguments for connecting to database</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>optional arguments for connecting to database (e.g. password, user name, database)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>priors for a given pft</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Query Priors</h1>
+
+            <div class="hidden name"><code>query.priors.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Query priors associated with a string of traits and plant
+              functional type
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.priors</span>(<span class='no'>pft</span>, <span class='kw'>trstr</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>out</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pft</th>
+              <td><p>ID number of the PFT in the database</p></td>
+            </tr>
+            <tr>
+              <th>trstr</th>
+              <td><p>string of traits to query priors for</p></td>
+            </tr>
+            <tr>
+              <th>out</th>
+              <td><p>output location</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td>
+                <p>
+                  database connection, can be list of arguments for connecting
+                  to database
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  optional arguments for connecting to database (e.g. password,
+                  user name, database)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>priors for a given pft</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>query.priors</span>(<span class='st'>'ebifarm.pavi'</span>, <span class='fu'>vecpaste</span>(<span class='st'>'SLA'</span>, <span class='st'>'Vcmax'</span>, <span class='st'>'leaf_width'</span>))
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          David LeBauer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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diff --git a/base/db/docs/reference/query.site.html b/base/db/docs/reference/query.site.html
index e9c85df..a21a377 100644
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    <meta
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+    <meta name="twitter:card" content="summary" />
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-    Articles
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-      <a href="../articles/betydb_access.html">BETYdb Access</a>
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
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+                  >1.6.0</span
+                >
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+            </div>
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+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
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+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
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+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Given site_id, return site table</h1>
-    
-    <div class="hidden name"><code>query.site.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Given site_id, return site table</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.site</span>(<span class='no'>site.id</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>con</th>
-      <td><p>: database connection</p></td>
-    </tr>
-    <tr>
-      <th>site_id</th>
-      <td><p>numeric</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Given site_id, return site table</h1>
+
+            <div class="hidden name"><code>query.site.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Given site_id, return site table</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.site</span>(<span class='no'>site.id</span>, <span class='no'>con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>con</th>
+              <td><p>: database connection</p></td>
+            </tr>
+            <tr>
+              <th>site_id</th>
+              <td><p>numeric</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+          <p>Developed by .</p>
+        </div>
+
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diff --git a/base/db/docs/reference/query.trait.data.html b/base/db/docs/reference/query.trait.data.html
index 5627dc7..6e96f5d 100644
--- a/base/db/docs/reference/query.trait.data.html
+++ b/base/db/docs/reference/query.trait.data.html
@@ -2,192 +2,261 @@
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 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<meta property="og:title" content="Extract trait data from database — query.trait.data" />
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Extract trait data from database — query.trait.data • PEcAn.DB
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
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 converts all statistics to summary statistics, and prepares a dataframe for use in meta-analysis.
 For Vcmax and SLA data, only data collected between  April and July are queried, and only data collected from the top of the canopy (canopy height &amp;gt; 0.66).
 For Vcmax and root_respiration_rate, data are scaled
-converted from measurement temperature to \(25^oC\) via the arrhenius equation." />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Extract trait data from database</h1>
-    
-    <div class="hidden name"><code>query.trait.data.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Extracts data from database for a given trait and set of species,
-converts all statistics to summary statistics, and prepares a dataframe for use in meta-analysis.
-For Vcmax and SLA data, only data collected between  April and July are queried, and only data collected from the top of the canopy (canopy height &gt; 0.66).
-For Vcmax and root_respiration_rate, data are scaled
-converted from measurement temperature to \(25^oC\) via the arrhenius equation.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.trait.data</span>(<span class='no'>trait</span>, <span class='no'>spstr</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>update.check.only</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Extract trait data from database</h1>
+
+            <div class="hidden name"><code>query.trait.data.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Extracts data from database for a given trait and set of species,
+              converts all statistics to summary statistics, and prepares a
+              dataframe for use in meta-analysis. For Vcmax and SLA data, only
+              data collected between April and July are queried, and only data
+              collected from the top of the canopy (canopy height &gt; 0.66).
+              For Vcmax and root_respiration_rate, data are scaled converted
+              from measurement temperature to \(25^oC\) via the arrhenius
+              equation.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.trait.data</span>(<span class='no'>trait</span>, <span class='no'>spstr</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>update.check.only</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>ids_are_cultivars</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait</th>
-      <td><p>is the trait name used in the database, stored in variables.name</p></td>
-    </tr>
-    <tr>
-      <th>spstr</th>
-      <td><p>is the species.id integer or string of integers associated with the species</p></td>
-    </tr>
-    <tr>
-      <th>ids_are_cultivars</th>
-      <td><p>if TRUE, the IDs in spstr are cultivar IDs, otherwise they are species IDs. Passed on to <code><a href='query.data.html'>query.data</a></code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dataframe ready for use in meta-analysis</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait</th>
+              <td>
+                <p>
+                  is the trait name used in the database, stored in
+                  variables.name
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>spstr</th>
+              <td>
+                <p>
+                  is the species.id integer or string of integers associated
+                  with the species
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ids_are_cultivars</th>
+              <td>
+                <p>
+                  if TRUE, the IDs in spstr are cultivar IDs, otherwise they are
+                  species IDs. Passed on to
+                  <code><a href="query.data.html">query.data</a></code>
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>dataframe ready for use in meta-analysis</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>settings</span> <span class='kw'>&lt;-</span> <span class='fu'>read.settings</span>()
 <span class='fu'>query.trait.data</span>(<span class='st'>"Vcmax"</span>, <span class='st'>"938"</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='no'>con</span>)
 <span class='co'># }</span></pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
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-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson, Shawn Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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+            <li><a href="#value">Value</a></li>
 
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+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
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+          <h2>Author</h2>
 
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index 4472c34..afc2880 100644
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+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Query trait data</h1>
-    
-    <div class="hidden name"><code>query.traits.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Query trait data</h1>
 
-    <div class="ref-description">
-    
-    <p>Query available trait data associated with a given pft and a list of traits</p>
-    
-    </div>
+            <div class="hidden name"><code>query.traits.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>query.traits</span>(<span class='no'>ids</span>, <span class='no'>priors</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>update.check.only</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+          <div class="ref-description">
+            <p>
+              Query available trait data associated with a given pft and a list
+              of traits
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.traits</span>(<span class='no'>ids</span>, <span class='no'>priors</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>update.check.only</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>ids_are_cultivars</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ids</th>
-      <td><p>vector of species or cultivar id's from trait database</p></td>
-    </tr>
-    <tr>
-      <th>priors</th>
-      <td><p>vector of parameters for which priors have been specified</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection object</p></td>
-    </tr>
-    <tr>
-      <th>update.check.only</th>
-      <td><p>if TRUE, returns results but does not print summaries</p></td>
-    </tr>
-    <tr>
-      <th>ids_are_cultivars</th>
-      <td><p>if TRUE, ids is a vector of cultivar IDs, otherwise they are species IDs</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list of dataframes, each with data for one trait</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p><code><a href='query.trait.data.html'>query.trait.data</a></code></p></div>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ids</th>
+              <td>
+                <p>vector of species or cultivar id's from trait database</p>
+              </td>
+            </tr>
+            <tr>
+              <th>priors</th>
+              <td>
+                <p>vector of parameters for which priors have been specified</p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection object</p></td>
+            </tr>
+            <tr>
+              <th>update.check.only</th>
+              <td>
+                <p>if TRUE, returns results but does not print summaries</p>
+              </td>
+            </tr>
+            <tr>
+              <th>ids_are_cultivars</th>
+              <td>
+                <p>
+                  if TRUE, ids is a vector of cultivar IDs, otherwise they are
+                  species IDs
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list of dataframes, each with data for one trait</p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              <code><a href="query.trait.data.html">query.trait.data</a></code>
+            </p>
+          </div>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>species</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='query.pft_species.html'>query.pft_species</a></span>(<span class='st'>'ebifarm.c4crop'</span>)
 <span class='no'>spstr</span> <span class='kw'>&lt;-</span> <span class='fu'>vecpaste</span>(<span class='no'>species</span>$<span class='no'>id</span>)
 <span class='no'>trvec</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>'leafN'</span>, <span class='st'>'SLA'</span>)
 <span class='no'>trait.data</span> <span class='kw'>&lt;-</span> <span class='fu'>query.traits</span>(<span class='no'>spstr</span>, <span class='no'>trvec</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#see-also">See also</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson, Shawn Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#see-also">See also</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          David LeBauer, Carl Davidson, Shawn Serbin
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/db/docs/reference/query.yields.html b/base/db/docs/reference/query.yields.html
index 4657e2d..ac63e78 100644
--- a/base/db/docs/reference/query.yields.html
+++ b/base/db/docs/reference/query.yields.html
@@ -2,189 +2,256 @@
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+
+    <title>
+      Query yield data and transform stats to SE by calling <code><a
+      href='fetch.stats2se.html'>fetch.stats2se</a></code>; — query.yields •
+      PEcAn.DB
+    </title>
+
+    <!-- jquery -->
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
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+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      property="og:title"
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+      property="og:description"
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+                        >Create PostGIS polygon</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Query yield data and transform stats to SE by calling <code><a href='fetch.stats2se.html'>fetch.stats2se</a></code>;</h1>
-    
-    <div class="hidden name"><code>query.yields.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to query yields data from database for specific species and convert stat to SE</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.yields</span>(<span class='kw'>trait</span> <span class='kw'>=</span> <span class='st'>"yield"</span>, <span class='no'>spstr</span>, <span class='kw'>extra.columns</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Query yield data and transform stats to SE by calling
+              <code><a href="fetch.stats2se.html">fetch.stats2se</a></code
+              >;
+            </h1>
+
+            <div class="hidden name"><code>query.yields.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to query yields data from database for specific species
+              and convert stat to SE
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.yields</span>(<span class='kw'>trait</span> <span class='kw'>=</span> <span class='st'>"yield"</span>, <span class='no'>spstr</span>, <span class='kw'>extra.columns</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>ids_are_cultivars</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait</th>
-      <td><p>yield trait to query</p></td>
-    </tr>
-    <tr>
-      <th>spstr</th>
-      <td><p>species to query for yield data</p></td>
-    </tr>
-    <tr>
-      <th>extra.columns</th>
-      <td><p>other query terms to pass in. Optional</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    <tr>
-      <th>ids_are_cultivars</th>
-      <td><p>if TRUE, spstr contains cultivar IDs, otherwise they are species IDs</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>extra arguments</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>used in <code><a href='query.trait.data.html'>query.trait.data</a></code>; <code><a href='fetch.stats2se.html'>fetch.stats2se</a></code>; <code>transformstats</code> performs transformation calculations</p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#see-also">See also</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait</th>
+              <td><p>yield trait to query</p></td>
+            </tr>
+            <tr>
+              <th>spstr</th>
+              <td><p>species to query for yield data</p></td>
+            </tr>
+            <tr>
+              <th>extra.columns</th>
+              <td><p>other query terms to pass in. Optional</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+            <tr>
+              <th>ids_are_cultivars</th>
+              <td>
+                <p>
+                  if TRUE, spstr contains cultivar IDs, otherwise they are
+                  species IDs
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>extra arguments</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              used in
+              <code><a href="query.trait.data.html">query.trait.data</a></code
+              >; <code><a href="fetch.stats2se.html">fetch.stats2se</a></code
+              >; <code>transformstats</code> performs transformation
+              calculations
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-&lt;unknown&gt;
+          <h2>Author</h2>
 
-  </div>
-</div>
+          &lt;unknown&gt;
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/db/docs/reference/reexports.html b/base/db/docs/reference/reexports.html
index 4d0d456..d6499f6 100644
--- a/base/db/docs/reference/reexports.html
+++ b/base/db/docs/reference/reexports.html
@@ -2,155 +2,192 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+                        >Create PostGIS polygon</a
+                      >
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+                  </ul>
+                </li>
+              </ul>
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Objects exported from other packages</h1>
-    
-    <div class="hidden name"><code>reexports.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>These objects are imported from other packages. Follow the links
-below to see their documentation.</p>
-<dl class='dl-horizontal'>
-  <dt>magrittr</dt><dd><p><code>%&gt;%</code></p></dd>
-</dl>
-    
-    </div>
-
-        
-
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Objects exported from other packages</h1>
+
+            <div class="hidden name"><code>reexports.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              These objects are imported from other packages. Follow the links
+              below to see their documentation.
+            </p>
+            <dl class="dl-horizontal">
+              <dt>magrittr</dt>
+              <dd>
+                <p><code>%&gt;%</code></p>
+              </dd>
+            </dl>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
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-</div>
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diff --git a/base/db/docs/reference/rename_jags_columns.html b/base/db/docs/reference/rename_jags_columns.html
index 88923ea..b18295a 100644
--- a/base/db/docs/reference/rename_jags_columns.html
+++ b/base/db/docs/reference/rename_jags_columns.html
@@ -2,168 +2,224 @@
 <!DOCTYPE html>
 <html>
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+      rename_jags_columns • PEcAn.DB
+    </title>
+
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+    />
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+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>renames the variables within output data frame trait.data</h1>
-    
-    <div class="hidden name"><code>rename_jags_columns.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>renames the variables within output data frame trait.data</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>rename_jags_columns</span>(<span class='no'>data</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data</th>
-      <td><p>data frame to with variables to rename</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>used with <code><a href='http://www.rdocumentation.org/packages/PEcAn.MA/topics/jagify'>jagify</a></code>;</p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#see-also">See also</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>renames the variables within output data frame trait.data</h1>
+
+            <div class="hidden name"><code>rename_jags_columns.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>renames the variables within output data frame trait.data</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>rename_jags_columns</span>(<span class='no'>data</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data</th>
+              <td><p>data frame to with variables to rename</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              used with
+              <code
+                ><a
+                  href="http://www.rdocumentation.org/packages/PEcAn.MA/topics/jagify"
+                  >jagify</a
+                ></code
+              >;
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/db/docs/reference/runs.html b/base/db/docs/reference/runs.html
index 0ce697d..511955f 100644
--- a/base/db/docs/reference/runs.html
+++ b/base/db/docs/reference/runs.html
@@ -2,162 +2,205 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<title>Get table of runs corresponding to a workflow — runs • PEcAn.DB</title>
-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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-
-<!-- sticky kit -->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Get table of runs corresponding to a workflow — runs • PEcAn.DB
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Get table of runs corresponding to a workflow — runs"
+    />
+
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+      property="og:description"
+      content="Get table of runs corresponding to a workflow"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-        <a class="navbar-link" href="../index.html">PEcAn.DB</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-
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-  <a href="../index.html">
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/betydb_access.html">BETYdb Access</a>
-    </li>
-    <li>
-      <a href="../articles/create_sites.geometry.html">Create PostGIS polygon</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.DB</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get table of runs corresponding to a workflow</h1>
-    
-    <div class="hidden name"><code>runs.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get table of runs corresponding to a workflow</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>runs</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
-    </tr>
-    <tr>
-      <th>workflow_id</th>
-      <td><p>Workflow ID</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get table of runs corresponding to a workflow</h1>
+
+            <div class="hidden name"><code>runs.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get table of runs corresponding to a workflow</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>runs</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+            <tr>
+              <th>workflow_id</th>
+              <td><p>Workflow ID</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/db/docs/reference/search_reference_single.html b/base/db/docs/reference/search_reference_single.html
index 1d4d61a..23b1ee4 100644
--- a/base/db/docs/reference/search_reference_single.html
+++ b/base/db/docs/reference/search_reference_single.html
@@ -2,172 +2,225 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Perform crossref search for a single reference — search_reference_single • PEcAn.DB</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Perform crossref search for a single reference — search_reference_single" />
-
-<meta property="og:description" content="Requires the `rcrossref` package." />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Perform crossref search for a single reference — search_reference_single •
+      PEcAn.DB
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      content="Perform crossref search for a single reference — search_reference_single"
+    />
+
+    <meta
+      property="og:description"
+      content="Requires the `rcrossref` package."
+    />
+    <meta name="twitter:card" content="summary" />
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
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+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Perform crossref search for a single reference</h1>
-    
-    <div class="hidden name"><code>search_reference_single.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Requires the `rcrossref` package.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>search_reference_single</span>(<span class='no'>query</span>, <span class='kw'>limit</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>min_score</span> <span class='kw'>=</span> <span class='fl'>85</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>query</th>
-      <td><p>Citation string (length 1) to search for DOI</p></td>
-    </tr>
-    <tr>
-      <th>limit</th>
-      <td><p>Number of results to return</p></td>
-    </tr>
-    <tr>
-      <th>min_score</th>
-      <td><p>Minimum match score. Default (85) is fairly strict.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`data.frame` containing crossref information converted to match bety citations table.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Perform crossref search for a single reference</h1>
+
+            <div class="hidden name">
+              <code>search_reference_single.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Requires the `rcrossref` package.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>search_reference_single</span>(<span class='no'>query</span>, <span class='kw'>limit</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>min_score</span> <span class='kw'>=</span> <span class='fl'>85</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>query</th>
+              <td><p>Citation string (length 1) to search for DOI</p></td>
+            </tr>
+            <tr>
+              <th>limit</th>
+              <td><p>Number of results to return</p></td>
+            </tr>
+            <tr>
+              <th>min_score</th>
+              <td>
+                <p>Minimum match score. Default (85) is fairly strict.</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            `data.frame` containing crossref information converted to match bety
+            citations table.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/search_references.html b/base/db/docs/reference/search_references.html
index 7a0e630..0da574d 100644
--- a/base/db/docs/reference/search_references.html
+++ b/base/db/docs/reference/search_references.html
@@ -2,172 +2,231 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      PEcAn.DB
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+    <!-- clipboard.js -->
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+    ></script>
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+    />
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+    <![endif]-->
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
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-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
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-  </a>
-  <ul class="dropdown-menu" role="menu">
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-      <a href="../articles/betydb_access.html">BETYdb Access</a>
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-        
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+                type="button"
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Perform crossref search for a list of references</h1>
-    
-    <div class="hidden name"><code>search_references.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Requires the `rcrossref` package.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>search_references</span>(<span class='no'>queries</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>queries</th>
-      <td><p>Character vector of queries</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Arguments passed on to <code>search_reference_single</code></p><dl class='dl-horizontal'>
-  <dt>query</dt><dd><p>Citation string (length 1) to search for DOI</p></dd>
-  <dt>min_score</dt><dd><p>Minimum match score. Default (85) is fairly strict.</p></dd>
-  <dt>limit</dt><dd><p>Number of results to return</p></dd>
-</dl></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`data.frame` containing crossref information converted to match bety citations table.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Perform crossref search for a list of references</h1>
+
+            <div class="hidden name"><code>search_references.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Requires the `rcrossref` package.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>search_references</span>(<span class='no'>queries</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>queries</th>
+              <td><p>Character vector of queries</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  Arguments passed on to <code>search_reference_single</code>
+                </p>
+                <dl class="dl-horizontal">
+                  <dt>query</dt>
+                  <dd><p>Citation string (length 1) to search for DOI</p></dd>
+                  <dt>min_score</dt>
+                  <dd>
+                    <p>Minimum match score. Default (85) is fairly strict.</p>
+                  </dd>
+                  <dt>limit</dt>
+                  <dd><p>Number of results to return</p></dd>
+                </dl>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            `data.frame` containing crossref information converted to match bety
+            citations table.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
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+      </div>
 
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index a6d0c1e..47a34d6 100644
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@@ -2,182 +2,231 @@
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Sample from normal distribution, given summary stats</h1>
-    
-    <div class="hidden name"><code>take.samples.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>sample from normal distribution, given summary stats</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>take.samples</span>(<span class='no'>summary</span>, <span class='kw'>sample.size</span> <span class='kw'>=</span> <span class='fl'>10</span>^<span class='fl'>6</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>summary</th>
-      <td><p>data.frame with values of mean and sd</p></td>
-    </tr>
-    <tr>
-      <th>sample.size</th>
-      <td><p>number of samples to take</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>sample of length sample.size</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Sample from normal distribution, given summary stats</h1>
+
+            <div class="hidden name"><code>take.samples.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>sample from normal distribution, given summary stats</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>take.samples</span>(<span class='no'>summary</span>, <span class='kw'>sample.size</span> <span class='kw'>=</span> <span class='fl'>10</span>^<span class='fl'>6</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>summary</th>
+              <td><p>data.frame with values of mean and sd</p></td>
+            </tr>
+            <tr>
+              <th>sample.size</th>
+              <td><p>number of samples to take</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>sample of length sample.size</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='co'>## return the mean when stat = NA</span>
 <span class='fu'>take.samples</span>(<span class='kw'>summary</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>mean</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>stat</span> <span class='kw'>=</span> <span class='fl'>NA</span>))
 <span class='co'>## return vector of length \code{sample.size} from N(mean,stat)</span>
 <span class='fu'>take.samples</span>(<span class='kw'>summary</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>mean</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>stat</span> <span class='kw'>=</span> <span class='fl'>10</span>), <span class='kw'>sample.size</span> <span class='kw'>=</span> <span class='fl'>10</span>)
 
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
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+          <h2>Author</h2>
 
-  
+          David LeBauer, Carl Davidson
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diff --git a/base/db/docs/reference/try2sqlite.html b/base/db/docs/reference/try2sqlite.html
index 70ed4ce..1995697 100644
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@@ -2,177 +2,233 @@
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+
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+read much faster thanks to lazy evaluation."
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+          <div class="container">
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+                type="button"
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+                <li class="dropdown">
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/betydb_access.html">BETYdb Access</a>
+                    </li>
+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert TRY text file to SQLite database</h1>
-    
-    <div class="hidden name"><code>try2sqlite.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>The TRY file is huge and unnecessarily long, which makes it difficult to 
-work with. The resulting SQLite database is much smaller on disk, and can be 
-read much faster thanks to lazy evaluation.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>try2sqlite</span>(<span class='no'>try_files</span>, <span class='kw'>sqlite_file</span> <span class='kw'>=</span> <span class='st'>"try.sqlite"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>try_files</th>
-      <td><p>Character vector of file names containing TRY data.
-Multiple files are combined with `data.table::rbindlist`.</p></td>
-    </tr>
-    <tr>
-      <th>sqlite_file</th>
-      <td><p>Target SQLite database file name, as character.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>The resulting TRY SQLite database contains the following tables:
- - `values` -- The actual TRY data. Links to all other tables through ID columns.
- - `traits` -- Description of trait and data names. Links to `values` through `DataID`. Similar to BETY `variables` table.
- - `datasets` -- Description of datasets and references/citations. Links to `values` through `DatasetID` and `ReferenceID`.
- - `species` -- Species. Links to `values` through `AccSpeciesID`.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert TRY text file to SQLite database</h1>
+
+            <div class="hidden name"><code>try2sqlite.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              The TRY file is huge and unnecessarily long, which makes it
+              difficult to work with. The resulting SQLite database is much
+              smaller on disk, and can be read much faster thanks to lazy
+              evaluation.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>try2sqlite</span>(<span class='no'>try_files</span>, <span class='kw'>sqlite_file</span> <span class='kw'>=</span> <span class='st'>"try.sqlite"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>try_files</th>
+              <td>
+                <p>
+                  Character vector of file names containing TRY data. Multiple
+                  files are combined with `data.table::rbindlist`.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sqlite_file</th>
+              <td><p>Target SQLite database file name, as character.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            The resulting TRY SQLite database contains the following tables: -
+            `values` -- The actual TRY data. Links to all other tables through
+            ID columns. - `traits` -- Description of trait and data names. Links
+            to `values` through `DataID`. Similar to BETY `variables` table. -
+            `datasets` -- Description of datasets and references/citations.
+            Links to `values` through `DatasetID` and `ReferenceID`. - `species`
+            -- Species. Links to `values` through `AccSpeciesID`.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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index 37191bc..52fc8ce 100644
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+++ b/base/db/docs/reference/var_names_all.html
@@ -2,166 +2,214 @@
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+      var_names_all • PEcAn.DB
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+
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                        >Create PostGIS polygon</a
+                      >
+                    </li>
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+            </div>
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get vector of variable names for a particular workflow and run ID</h1>
-    
-    <div class="hidden name"><code>var_names_all.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get vector of variable names for a particular workflow and run ID</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>var_names_all</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>, <span class='no'>run_id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
-    </tr>
-    <tr>
-      <th>workflow_id</th>
-      <td><p>Workflow ID</p></td>
-    </tr>
-    <tr>
-      <th>run_id</th>
-      <td><p>Run ID</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Get vector of variable names for a particular workflow and run ID
+            </h1>
+
+            <div class="hidden name"><code>var_names_all.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Get vector of variable names for a particular workflow and run ID
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>var_names_all</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>, <span class='no'>run_id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+            <tr>
+              <th>workflow_id</th>
+              <td><p>Workflow ID</p></td>
+            </tr>
+            <tr>
+              <th>run_id</th>
+              <td><p>Run ID</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/workflow.html b/base/db/docs/reference/workflow.html
index a144d47..47351b1 100644
--- a/base/db/docs/reference/workflow.html
+++ b/base/db/docs/reference/workflow.html
@@ -2,162 +2,203 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                    </li>
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+                        >Create PostGIS polygon</a
+                      >
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get single workflow by workflow_id</h1>
-    
-    <div class="hidden name"><code>workflow.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get single workflow by workflow_id</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>workflow</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
-    </tr>
-    <tr>
-      <th>workflow_id</th>
-      <td><p>Workflow ID</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get single workflow by workflow_id</h1>
+
+            <div class="hidden name"><code>workflow.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get single workflow by workflow_id</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>workflow</span>(<span class='no'>bety</span>, <span class='no'>workflow_id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+            <tr>
+              <th>workflow_id</th>
+              <td><p>Workflow ID</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/base/db/docs/reference/workflows.html b/base/db/docs/reference/workflows.html
index cde1f5c..1661997 100644
--- a/base/db/docs/reference/workflows.html
+++ b/base/db/docs/reference/workflows.html
@@ -2,162 +2,200 @@
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+                    <li>
+                      <a href="../articles/create_sites.geometry.html"
+                        >Create PostGIS polygon</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>list of workflows that exist</h1>
-    
-    <div class="hidden name"><code>workflows.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>list of workflows that exist</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>workflows</span>(<span class='no'>bety</span>, <span class='kw'>ensemble</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
-    </tr>
-    <tr>
-      <th>ensemble</th>
-      <td><p>Logical. Use workflows from ensembles table.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>list of workflows that exist</h1>
+
+            <div class="hidden name"><code>workflows.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>list of workflows that exist</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>workflows</span>(<span class='no'>bety</span>, <span class='kw'>ensemble</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>BETYdb connection, as opened by `betyConnect()`</p></td>
+            </tr>
+            <tr>
+              <th>ensemble</th>
+              <td><p>Logical. Use workflows from ensembles table.</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/logger/docs/LICENSE-text.html b/base/logger/docs/LICENSE-text.html
index 76cf618..4d96c85 100644
--- a/base/logger/docs/LICENSE-text.html
+++ b/base/logger/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.logger</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="index.html">
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/authors.html b/base/logger/docs/authors.html
index 1ce6ca1..a7776a2 100644
--- a/base/logger/docs/authors.html
+++ b/base/logger/docs/authors.html
@@ -2,126 +2,146 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
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+
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+                <a class="navbar-link" href="index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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-<div class="row">
-  <div class="contents col-md-9">
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-      <h1>Authors</h1>
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-
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-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
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-        <p><strong>Alexey Shiklomanov</strong>. . 
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+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Alexey Shiklomanov</strong>. .</p>
+            </li>
+          </ul>
+        </div>
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       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/docsearch.css b/base/logger/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/base/logger/docs/docsearch.css
+++ b/base/logger/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/base/logger/docs/docsearch.js b/base/logger/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/base/logger/docs/docsearch.js
+++ b/base/logger/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/base/logger/docs/index.html b/base/logger/docs/index.html
index 89ca163..994c030 100644
--- a/base/logger/docs/index.html
+++ b/base/logger/docs/index.html
@@ -1,103 +1,156 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Logger functions for PEcAn • PEcAn.logger</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="Logger functions for PEcAn">
-<meta property="og:description" content="Special logger functions for tracking execution status and the environment.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Logger functions for PEcAn • PEcAn.logger</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta property="og:title" content="Logger functions for PEcAn" />
+    <meta
+      property="og:description"
+      content="Special logger functions for tracking execution status and the environment."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.logger</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    Special logger functions for tracking execution status and the environment.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          Special logger functions for tracking execution status and the
+          environment.
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/base/logger/docs/pkgdown.css b/base/logger/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/base/logger/docs/pkgdown.css
+++ b/base/logger/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/base/logger/docs/pkgdown.js b/base/logger/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/base/logger/docs/pkgdown.js
+++ b/base/logger/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/base/logger/docs/reference/check_conditions.html b/base/logger/docs/reference/check_conditions.html
index 10159d1..3185533 100644
--- a/base/logger/docs/reference/check_conditions.html
+++ b/base/logger/docs/reference/check_conditions.html
@@ -2,133 +2,157 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Check a list of conditions — check_conditions • PEcAn.logger</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Check a list of conditions — check_conditions" />
-
-<meta property="og:description" content="Check a list of conditions" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Check a list of conditions — check_conditions • PEcAn.logger</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Check a list of conditions — check_conditions"
+    />
+
+    <meta property="og:description" content="Check a list of conditions" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.logger</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check a list of conditions</h1>
-    
-    <div class="hidden name"><code>check_conditions.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check a list of conditions</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check a list of conditions</h1>
 
-    <pre class="usage"><span class='fu'>check_conditions</span>(<span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>check_conditions.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Check a list of conditions</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>check_conditions</span>(<span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/index.html b/base/logger/docs/reference/index.html
index d5caf7c..95e292f 100644
--- a/base/logger/docs/reference/index.html
+++ b/base/logger/docs/reference/index.html
@@ -2,234 +2,335 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-<title>Function reference • PEcAn.logger</title>
+    <title>Function reference • PEcAn.logger</title>
 
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
 
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
 
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
 
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
 
+    <meta property="og:title" content="Function reference" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.logger</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-      </header>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
 
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="check_conditions.html">check_conditions()</a></code> </p>
-        </td>
-        <td><p>Check a list of conditions</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="is_definitely_true.html">is_definitely_true()</a></code> </p>
-        </td>
-        <td><p>Robust logical check</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.debug.html">logger.debug()</a></code> </p>
-        </td>
-        <td><p>Prints a debug message.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.error.html">logger.error()</a></code> </p>
-        </td>
-        <td><p>Prints an error message.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.getLevel.html">logger.getLevel()</a></code> </p>
-        </td>
-        <td><p>Get configured logging level.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.getLevelNumber.html">logger.getLevelNumber()</a></code> </p>
-        </td>
-        <td><p>Returns numeric value for string</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.info.html">logger.info()</a></code> </p>
-        </td>
-        <td><p>Prints an informational message.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.message.html">logger.message()</a></code> </p>
-        </td>
-        <td><p>Prints a message at a certain log level.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.setLevel.html">logger.setLevel()</a></code> </p>
-        </td>
-        <td><p>Configure logging level.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.setOutputFile.html">logger.setOutputFile()</a></code> </p>
-        </td>
-        <td><p>Configure logging output filename.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.setQuitOnSevere.html">logger.setQuitOnSevere()</a></code> </p>
-        </td>
-        <td><p>Configure whether severe should quit.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.setUseConsole.html">logger.setUseConsole()</a></code> </p>
-        </td>
-        <td><p>Configure logging to console.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.setWidth.html">logger.setWidth()</a></code> </p>
-        </td>
-        <td><p>Configure the number of chars per line</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.severe.html">logger.severe()</a></code> </p>
-        </td>
-        <td><p>Prints an severe message and stops execution.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.warn.html">logger.warn()</a></code> </p>
-        </td>
-        <td><p>Prints a warning message.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="severeifnot.html">severeifnot()</a></code> <code><a href="severeifnot.html">errorifnot()</a></code> <code><a href="severeifnot.html">warnifnot()</a></code> <code><a href="severeifnot.html">infoifnot()</a></code> <code><a href="severeifnot.html">debugifnot()</a></code> </p>
-        </td>
-        <td><p>Logger message if conditions are not met</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check_conditions.html"
+                        >check_conditions()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check a list of conditions</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="is_definitely_true.html"
+                        >is_definitely_true()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Robust logical check</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="logger.debug.html">logger.debug()</a></code>
+                  </p>
+                </td>
+                <td><p>Prints a debug message.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="logger.error.html">logger.error()</a></code>
+                  </p>
+                </td>
+                <td><p>Prints an error message.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="logger.getLevel.html"
+                        >logger.getLevel()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get configured logging level.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="logger.getLevelNumber.html"
+                        >logger.getLevelNumber()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Returns numeric value for string</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="logger.info.html">logger.info()</a></code>
+                  </p>
+                </td>
+                <td><p>Prints an informational message.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="logger.message.html">logger.message()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Prints a message at a certain log level.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="logger.setLevel.html"
+                        >logger.setLevel()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Configure logging level.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="logger.setOutputFile.html"
+                        >logger.setOutputFile()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Configure logging output filename.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="logger.setQuitOnSevere.html"
+                        >logger.setQuitOnSevere()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Configure whether severe should quit.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="logger.setUseConsole.html"
+                        >logger.setUseConsole()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Configure logging to console.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="logger.setWidth.html"
+                        >logger.setWidth()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Configure the number of chars per line</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="logger.severe.html">logger.severe()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Prints an severe message and stops execution.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="logger.warn.html">logger.warn()</a></code>
+                  </p>
+                </td>
+                <td><p>Prints a warning message.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="severeifnot.html">severeifnot()</a></code>
+                    <code><a href="severeifnot.html">errorifnot()</a></code>
+                    <code><a href="severeifnot.html">warnifnot()</a></code>
+                    <code><a href="severeifnot.html">infoifnot()</a></code>
+                    <code><a href="severeifnot.html">debugifnot()</a></code>
+                  </p>
+                </td>
+                <td><p>Logger message if conditions are not met</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-      </footer>
-   </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
-  
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/is_definitely_true.html b/base/logger/docs/reference/is_definitely_true.html
index d7edc56..150ff70 100644
--- a/base/logger/docs/reference/is_definitely_true.html
+++ b/base/logger/docs/reference/is_definitely_true.html
@@ -2,133 +2,157 @@
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 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
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-<script src="../pkgdown.js"></script>
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-<![endif]-->
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+    <meta charset="utf-8" />
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Robust logical check — is_definitely_true"
+    />
+
+    <meta property="og:description" content="Robust logical check" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <span class="icon-bar"></span>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.logger</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Robust logical check</h1>
-    
-    <div class="hidden name"><code>is_definitely_true.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Robust logical check</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Robust logical check</h1>
 
-    <pre class="usage"><span class='fu'>is_definitely_true</span>(<span class='no'>x</span>)</pre>
-        
+            <div class="hidden name"><code>is_definitely_true.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Robust logical check</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>is_definitely_true</span>(<span class='no'>x</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/logger.debug.html b/base/logger/docs/reference/logger.debug.html
index f9bd566..2f7a867 100644
--- a/base/logger/docs/reference/logger.debug.html
+++ b/base/logger/docs/reference/logger.debug.html
@@ -2,157 +2,193 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Prints a debug message. — logger.debug • PEcAn.logger</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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+    />
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+    <!-- sticky kit -->
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+                <span
+                  class="label label-default"
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+                  >1.6.0</span
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+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Prints a debug message.</h1>
-    
-    <div class="hidden name"><code>logger.debug.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function will print a debug message.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.debug</span>(<span class='no'>msg</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>msg</th>
-      <td><p>the message that should be printed.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>any additional text that should be printed.</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Prints a debug message.</h1>
+
+            <div class="hidden name"><code>logger.debug.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>This function will print a debug message.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.debug</span>(<span class='no'>msg</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>msg</th>
+              <td><p>the message that should be printed.</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>any additional text that should be printed.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.debug</span>(<span class='st'>'variable'</span>, <span class='fl'>5</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
-
diff --git a/base/logger/docs/reference/logger.error.html b/base/logger/docs/reference/logger.error.html
index df84af5..6af8f29 100644
--- a/base/logger/docs/reference/logger.error.html
+++ b/base/logger/docs/reference/logger.error.html
@@ -2,157 +2,193 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<!-- clipboard.js -->
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-
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-<script src="../pkgdown.js"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Prints an error message. — logger.error • PEcAn.logger</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Prints an error message. — logger.error"
+    />
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+      content="This function will print an error message."
+    />
+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Prints an error message.</h1>
-    
-    <div class="hidden name"><code>logger.error.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function will print an error message.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.error</span>(<span class='no'>msg</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>msg</th>
-      <td><p>the message that should be printed.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>any additional text that should be printed.</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Prints an error message.</h1>
+
+            <div class="hidden name"><code>logger.error.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>This function will print an error message.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.error</span>(<span class='no'>msg</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>msg</th>
+              <td><p>the message that should be printed.</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>any additional text that should be printed.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.error</span>(<span class='st'>'system did not converge'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/logger.getLevel.html b/base/logger/docs/reference/logger.getLevel.html
index 06eca06..566b520 100644
--- a/base/logger/docs/reference/logger.getLevel.html
+++ b/base/logger/docs/reference/logger.getLevel.html
@@ -2,149 +2,186 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
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-<script src="../pkgdown.js"></script>
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>
+      Get configured logging level. — logger.getLevel • PEcAn.logger
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Get configured logging level. — logger.getLevel"
+    />
+
+    <meta
+      property="og:description"
+      content="This will return the current level configured of the logging messages"
+    />
+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get configured logging level.</h1>
-    
-    <div class="hidden name"><code>logger.getLevel.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get configured logging level.</h1>
 
-    <div class="ref-description">
-    
-    <p>This will return the current level configured of the logging messages</p>
-    
-    </div>
+            <div class="hidden name"><code>logger.getLevel.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This will return the current level configured of the logging
+              messages
+            </p>
+          </div>
+
+          <pre class="usage"><span class='fu'>logger.getLevel</span>()</pre>
 
-    <pre class="usage"><span class='fu'>logger.getLevel</span>()</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
 
-    <p>level the level of the message (ALL, DEBUG, INFO, WARN, ERROR, OFF)</p>
-    
+          <p>
+            level the level of the message (ALL, DEBUG, INFO, WARN, ERROR, OFF)
+          </p>
 
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.getLevel</span>()
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/logger.getLevelNumber.html b/base/logger/docs/reference/logger.getLevelNumber.html
index fe352df..ecb7159 100644
--- a/base/logger/docs/reference/logger.getLevelNumber.html
+++ b/base/logger/docs/reference/logger.getLevelNumber.html
@@ -2,155 +2,183 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
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-<meta property="og:title" content="Returns numeric value for string — logger.getLevelNumber" />
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Returns numeric value for string — logger.getLevelNumber • PEcAn.logger
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Returns numeric value for string — logger.getLevelNumber"
+    />
+
+    <meta
+      property="og:description"
+      content="Given the string representation this will return the numeric value
 ALL   =  0
 DEBUG = 10
 INFO  = 20
 WARN  = 30
 ERROR = 40
-ALL   = 99" />
-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+ALL   = 99"
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+                type="button"
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+                  class="label label-default"
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+                  >1.6.0</span
+                >
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+            </div>
+
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+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Returns numeric value for string</h1>
-    
-    <div class="hidden name"><code>logger.getLevelNumber.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Given the string representation this will return the numeric value
-ALL   =  0
-DEBUG = 10
-INFO  = 20
-WARN  = 30
-ERROR = 40
-ALL   = 99</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.getLevelNumber</span>(<span class='no'>level</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>level the level of the message</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Returns numeric value for string</h1>
+
+            <div class="hidden name"><code>logger.getLevelNumber.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Given the string representation this will return the numeric value
+              ALL = 0 DEBUG = 10 INFO = 20 WARN = 30 ERROR = 40 ALL = 99
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.getLevelNumber</span>(<span class='no'>level</span>)</pre>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>level the level of the message</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/logger.info.html b/base/logger/docs/reference/logger.info.html
index 4f25bfa..b4b1e7f 100644
--- a/base/logger/docs/reference/logger.info.html
+++ b/base/logger/docs/reference/logger.info.html
@@ -2,157 +2,193 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Prints an informational message. — logger.info • PEcAn.logger</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Prints an informational message. — logger.info" />
-
-<meta property="og:description" content="This function will print an informational message." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Prints an informational message. — logger.info • PEcAn.logger</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Prints an informational message. — logger.info"
+    />
+
+    <meta
+      property="og:description"
+      content="This function will print an informational message."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.logger</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    <div id="navbar" class="navbar-collapse collapse">
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-  <a href="../index.html">
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Prints an informational message.</h1>
-    
-    <div class="hidden name"><code>logger.info.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function will print an informational message.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.info</span>(<span class='no'>msg</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>msg</th>
-      <td><p>the message that should be printed.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>any additional text that should be printed.</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Prints an informational message.</h1>
+
+            <div class="hidden name"><code>logger.info.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>This function will print an informational message.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.info</span>(<span class='no'>msg</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>msg</th>
+              <td><p>the message that should be printed.</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>any additional text that should be printed.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.info</span>(<span class='st'>'PEcAn version 1.2'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/logger.message.html b/base/logger/docs/reference/logger.message.html
index b1aed8b..96a5785 100644
--- a/base/logger/docs/reference/logger.message.html
+++ b/base/logger/docs/reference/logger.message.html
@@ -2,175 +2,227 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Prints a message at a certain log level. — logger.message • PEcAn.logger</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Prints a message at a certain log level. — logger.message" />
-
-<meta property="og:description" content="This function will print a message. This is the function that is responsible for
-the actual printing of the message." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Prints a message at a certain log level. — logger.message • PEcAn.logger
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Prints a message at a certain log level. — logger.message"
+    />
+
+    <meta
+      property="og:description"
+      content="This function will print a message. This is the function that is responsible for
+the actual printing of the message."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Prints a message at a certain log level.</h1>
-    
-    <div class="hidden name"><code>logger.message.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function will print a message. This is the function that is responsible for
-the actual printing of the message.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.message</span>(<span class='no'>level</span>, <span class='no'>msg</span>, <span class='no'>...</span>, <span class='kw'>wrap</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>level</th>
-      <td><p>the level of the message (DEBUG, INFO, WARN, ERROR)</p></td>
-    </tr>
-    <tr>
-      <th>msg</th>
-      <td><p>the message that should be printed.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>any additional text that should be printed.</p></td>
-    </tr>
-    <tr>
-      <th>wrap</th>
-      <td><p>Whether or not to wrap long messages (default =
-<code>TRUE</code>). If <code>FALSE</code>, preserve format of original string. Useful
-for specifically formatted error messages.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This is a place holder and will be later filled in with a more complex logging set</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Prints a message at a certain log level.</h1>
+
+            <div class="hidden name"><code>logger.message.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function will print a message. This is the function that is
+              responsible for the actual printing of the message.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.message</span>(<span class='no'>level</span>, <span class='no'>msg</span>, <span class='no'>...</span>, <span class='kw'>wrap</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>level</th>
+              <td>
+                <p>the level of the message (DEBUG, INFO, WARN, ERROR)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>msg</th>
+              <td><p>the message that should be printed.</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>any additional text that should be printed.</p></td>
+            </tr>
+            <tr>
+              <th>wrap</th>
+              <td>
+                <p>
+                  Whether or not to wrap long messages (default =
+                  <code>TRUE</code>). If <code>FALSE</code>, preserve format of
+                  original string. Useful for specifically formatted error
+                  messages.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This is a place holder and will be later filled in with a more
+            complex logging set
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.message</span>(<span class='st'>'DEBUG'</span>, <span class='st'>'variable'</span>, <span class='fl'>5</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/logger.setLevel.html b/base/logger/docs/reference/logger.setLevel.html
index d74997c..9103c4d 100644
--- a/base/logger/docs/reference/logger.setLevel.html
+++ b/base/logger/docs/reference/logger.setLevel.html
@@ -2,155 +2,197 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
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-
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-
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Configure logging level. — logger.setLevel"
+    />
+
+    <meta
+      property="og:description"
+      content="This will configure the logger level. This allows to turn DEBUG, INFO,
+WARN and ERROR messages on and off."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.logger</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../index.html">
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
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-</div><!--/.navbar -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Configure logging level.</h1>
-    
-    <div class="hidden name"><code>logger.setLevel.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This will configure the logger level. This allows to turn DEBUG, INFO,
-WARN and ERROR messages on and off.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.setLevel</span>(<span class='no'>level</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>level</th>
-      <td><p>the level of the message (ALL, DEBUG, INFO, WARN, ERROR, OFF)</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Configure logging level.</h1>
+
+            <div class="hidden name"><code>logger.setLevel.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This will configure the logger level. This allows to turn DEBUG,
+              INFO, WARN and ERROR messages on and off.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.setLevel</span>(<span class='no'>level</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>level</th>
+              <td>
+                <p>
+                  the level of the message (ALL, DEBUG, INFO, WARN, ERROR, OFF)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.setLevel</span>(<span class='st'>'DEBUG'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/logger.setOutputFile.html b/base/logger/docs/reference/logger.setOutputFile.html
index 7e5fb60..d236558 100644
--- a/base/logger/docs/reference/logger.setOutputFile.html
+++ b/base/logger/docs/reference/logger.setOutputFile.html
@@ -2,153 +2,199 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Configure logging output filename. — logger.setOutputFile • PEcAn.logger</title>
-
-<!-- jquery -->
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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-
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-
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Configure logging output filename.</h1>
-    
-    <div class="hidden name"><code>logger.setOutputFile.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>The name of the file where the logging information should be written to.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.setOutputFile</span>(<span class='no'>filename</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>filename</th>
-      <td><p>the file to send the log messages to (or NA to not write to file)</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Configure logging output filename.</h1>
+
+            <div class="hidden name"><code>logger.setOutputFile.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              The name of the file where the logging information should be
+              written to.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.setOutputFile</span>(<span class='no'>filename</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>filename</th>
+              <td>
+                <p>
+                  the file to send the log messages to (or NA to not write to
+                  file)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.setOutputFile</span>(<span class='st'>'pecan.log'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
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+          </p>
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-
diff --git a/base/logger/docs/reference/logger.setQuitOnSevere.html b/base/logger/docs/reference/logger.setQuitOnSevere.html
index cce5138..2db5a15 100644
--- a/base/logger/docs/reference/logger.setQuitOnSevere.html
+++ b/base/logger/docs/reference/logger.setQuitOnSevere.html
@@ -2,157 +2,201 @@
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 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      PEcAn.logger
+    </title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Configure whether severe should quit. — logger.setQuitOnSevere"
+    />
+
+    <meta
+      property="og:description"
+      content="The default is for a non-interactive session to quit. Setting this to false is
 especially useful for running tests when placed in inst/tests/test.&amp;lt;fn&amp;gt;.R,
-but is not passed from tests/run.all.R." />
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-<![endif]-->
+but is not passed from tests/run.all.R."
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Configure whether severe should quit.</h1>
-    
-    <div class="hidden name"><code>logger.setQuitOnSevere.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>The default is for a non-interactive session to quit. Setting this to false is
-especially useful for running tests when placed in <code>inst/tests/test.&lt;fn&gt;.R</code>,
-but is not passed from <code>tests/run.all.R</code>.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.setQuitOnSevere</span>(<span class='no'>severeQuits</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>severeQuits</th>
-      <td><p>should R quit on a severe error.</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Configure whether severe should quit.</h1>
+
+            <div class="hidden name">
+              <code>logger.setQuitOnSevere.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              The default is for a non-interactive session to quit. Setting this
+              to false is especially useful for running tests when placed in
+              <code>inst/tests/test.&lt;fn&gt;.R</code>, but is not passed from
+              <code>tests/run.all.R</code>.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.setQuitOnSevere</span>(<span class='no'>severeQuits</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>severeQuits</th>
+              <td><p>should R quit on a severe error.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.setQuitOnSevere</span>(<span class='fl'>FALSE</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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 </html>
-
diff --git a/base/logger/docs/reference/logger.setUseConsole.html b/base/logger/docs/reference/logger.setUseConsole.html
index 8526617..254bf02 100644
--- a/base/logger/docs/reference/logger.setUseConsole.html
+++ b/base/logger/docs/reference/logger.setUseConsole.html
@@ -2,157 +2,200 @@
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 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Configure logging to console. — logger.setUseConsole • PEcAn.logger
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      content="Configure logging to console. — logger.setUseConsole"
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+    />
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+                  class="label label-default"
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Configure logging to console.</h1>
-    
-    <div class="hidden name"><code>logger.setUseConsole.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Should the logging to be printed to the console or not.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.setUseConsole</span>(<span class='no'>console</span>, <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>console</th>
-      <td><p>set to true to print logging to console.</p></td>
-    </tr>
-    <tr>
-      <th>stderr</th>
-      <td><p>set to true (default) to use stderr instead of stdout for logging</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Configure logging to console.</h1>
+
+            <div class="hidden name"><code>logger.setUseConsole.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Should the logging to be printed to the console or not.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.setUseConsole</span>(<span class='no'>console</span>, <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>console</th>
+              <td><p>set to true to print logging to console.</p></td>
+            </tr>
+            <tr>
+              <th>stderr</th>
+              <td>
+                <p>
+                  set to true (default) to use stderr instead of stdout for
+                  logging
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.setUseConsole</span>(<span class='fl'>TRUE</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
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-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
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-
diff --git a/base/logger/docs/reference/logger.setWidth.html b/base/logger/docs/reference/logger.setWidth.html
index 430e1df..9641d64 100644
--- a/base/logger/docs/reference/logger.setWidth.html
+++ b/base/logger/docs/reference/logger.setWidth.html
@@ -2,155 +2,197 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<script src="../pkgdown.js"></script>
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-<meta property="og:title" content="Configure the number of chars per line — logger.setWidth" />
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-wrap the line when printing a message at that many chars." />
-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Configure the number of chars per line — logger.setWidth • PEcAn.logger
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Configure the number of chars per line — logger.setWidth"
+    />
+
+    <meta
+      property="og:description"
+      content="The default is for 60 chars per line. Setting this to any value will
+wrap the line when printing a message at that many chars."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+    <![endif]-->
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Configure the number of chars per line</h1>
-    
-    <div class="hidden name"><code>logger.setWidth.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>The default is for 60 chars per line. Setting this to any value will
-wrap the line when printing a message at that many chars.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.setWidth</span>(<span class='no'>width</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>width</th>
-      <td><p>number of chars to print before wrapping to next line.</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Configure the number of chars per line</h1>
+
+            <div class="hidden name"><code>logger.setWidth.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              The default is for 60 chars per line. Setting this to any value
+              will wrap the line when printing a message at that many chars.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.setWidth</span>(<span class='no'>width</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>width</th>
+              <td>
+                <p>number of chars to print before wrapping to next line.</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.setWidth</span>(<span class='fl'>70</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          David LeBauer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/logger.severe.html b/base/logger/docs/reference/logger.severe.html
index a76377f..1a84641 100644
--- a/base/logger/docs/reference/logger.severe.html
+++ b/base/logger/docs/reference/logger.severe.html
@@ -2,173 +2,227 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Prints an severe message and stops execution. — logger.severe" />
-
-<meta property="og:description" content="This function will print a message and stop execution of the code. This
-should only be used if the application should terminate." />
-<meta name="twitter:card" content="summary" />
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Prints an severe message and stops execution. — logger.severe •
+      PEcAn.logger
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Prints an severe message and stops execution. — logger.severe"
+    />
+
+    <meta
+      property="og:description"
+      content="This function will print a message and stop execution of the code. This
+should only be used if the application should terminate."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-        <a class="navbar-link" href="../index.html">PEcAn.logger</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.logger</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Prints an severe message and stops execution.</h1>
-    
-    <div class="hidden name"><code>logger.severe.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function will print a message and stop execution of the code. This
-should only be used if the application should terminate.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.severe</span>(<span class='no'>msg</span>, <span class='no'>...</span>, <span class='kw'>wrap</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>msg</th>
-      <td><p>the message that should be printed.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>any additional text that should be printed.</p></td>
-    </tr>
-    <tr>
-      <th>wrap</th>
-      <td><p>Whether or not to wrap long messages (default =
-<code>TRUE</code>). If <code>FALSE</code>, preserve format of original string. Useful
-for specifically formatted error messages.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>set <code><a href='logger.setQuitOnSevere.html'>logger.setQuitOnSevere(FALSE)</a></code>. To avoid terminating
-the session. This is set by default to TRUE if interactive or running
-inside Rstudio.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Prints an severe message and stops execution.</h1>
+
+            <div class="hidden name"><code>logger.severe.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function will print a message and stop execution of the code.
+              This should only be used if the application should terminate.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.severe</span>(<span class='no'>msg</span>, <span class='no'>...</span>, <span class='kw'>wrap</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>msg</th>
+              <td><p>the message that should be printed.</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>any additional text that should be printed.</p></td>
+            </tr>
+            <tr>
+              <th>wrap</th>
+              <td>
+                <p>
+                  Whether or not to wrap long messages (default =
+                  <code>TRUE</code>). If <code>FALSE</code>, preserve format of
+                  original string. Useful for specifically formatted error
+                  messages.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            set
+            <code
+              ><a href="logger.setQuitOnSevere.html"
+                >logger.setQuitOnSevere(FALSE)</a
+              ></code
+            >. To avoid terminating the session. This is set by default to TRUE
+            if interactive or running inside Rstudio.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.severe</span>(<span class='st'>'missing parameters'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/logger/docs/reference/logger.warn.html b/base/logger/docs/reference/logger.warn.html
index 607f792..1a0079f 100644
--- a/base/logger/docs/reference/logger.warn.html
+++ b/base/logger/docs/reference/logger.warn.html
@@ -2,157 +2,193 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Prints a warning message. — logger.warn" />
-
-<meta property="og:description" content="This function will print a warning message." />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Prints a warning message. — logger.warn • PEcAn.logger</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
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+    <script
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+    <!-- pkgdown -->
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+    <meta
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+      content="Prints a warning message. — logger.warn"
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-<div class="row">
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-    <div class="page-header">
-    <h1>Prints a warning message.</h1>
-    
-    <div class="hidden name"><code>logger.warn.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function will print a warning message.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>logger.warn</span>(<span class='no'>msg</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>msg</th>
-      <td><p>the message that should be printed.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>any additional text that should be printed.</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Prints a warning message.</h1>
+
+            <div class="hidden name"><code>logger.warn.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>This function will print a warning message.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>logger.warn</span>(<span class='no'>msg</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>msg</th>
+              <td><p>the message that should be printed.</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>any additional text that should be printed.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>logger.warn</span>(<span class='st'>'detected NA values'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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-  <p>Developed by .</p>
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-</div>
+            <li><a href="#examples">Examples</a></li>
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+          <h2>Author</h2>
 
-  
+          Rob Kooper
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 </html>
-
diff --git a/base/logger/docs/reference/severeifnot.html b/base/logger/docs/reference/severeifnot.html
index b137572..b362c53 100644
--- a/base/logger/docs/reference/severeifnot.html
+++ b/base/logger/docs/reference/severeifnot.html
@@ -2,110 +2,152 @@
 <!DOCTYPE html>
 <html>
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+    <!-- Bootstrap -->
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+      crossorigin="anonymous"
+    ></script>
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+    />
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+      content="Similar to base::stopifnot, but allows you to use a custom message and
+logger level. If all conditions are TRUE, silently exit."
+    />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Logger message if conditions are not met</h1>
-    
-    <div class="hidden name"><code>severeifnot.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Similar to <a href='http://www.rdocumentation.org/packages/base/topics/stopifnot'>base::stopifnot</a>, but allows you to use a custom message and
-logger level. If all conditions are <code>TRUE</code>, silently exit.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>severeifnot</span>(<span class='no'>msg</span>, <span class='no'>...</span>)
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Logger message if conditions are not met</h1>
+
+            <div class="hidden name"><code>severeifnot.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Similar to
+              <a
+                href="http://www.rdocumentation.org/packages/base/topics/stopifnot"
+                >base::stopifnot</a
+              >, but allows you to use a custom message and logger level. If all
+              conditions are <code>TRUE</code>, silently exit.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>severeifnot</span>(<span class='no'>msg</span>, <span class='no'>...</span>)
 
 <span class='fu'>errorifnot</span>(<span class='no'>msg</span>, <span class='no'>...</span>)
 
@@ -114,33 +156,50 @@ <h1>Logger message if conditions are not met</h1>
 <span class='fu'>infoifnot</span>(<span class='no'>msg</span>, <span class='no'>...</span>)
 
 <span class='fu'>debugifnot</span>(<span class='no'>msg</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>msg</th>
-      <td><p>Logger message to write, as a single character string.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Conditions to evaluate</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Invisibly, <code>TRUE</code> if conditions are met, <code>FALSE</code> otherwise</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Conditions can be vectorized, or can return non-logical values.The
-underlying function automatically applies <code>isTRUE(all(.))</code> to the
-conditions.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>msg</th>
+              <td>
+                <p>Logger message to write, as a single character string.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>Conditions to evaluate</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Invisibly, <code>TRUE</code> if conditions are met,
+            <code>FALSE</code> otherwise
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Conditions can be vectorized, or can return non-logical values.The
+            underlying function automatically applies
+            <code>isTRUE(all(.))</code> to the conditions.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>a</span> <span class='kw'>&lt;-</span> <span class='fl'>1</span>:<span class='fl'>5</span>
 <span class='no'>b</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='fl'>6</span>, <span class='fl'>7</span>, <span class='fl'>8</span>)
 <span class='fu'>debugifnot</span>(<span class='st'>"By the way, something is not a list."</span>, <span class='fu'>is.list</span>(<span class='no'>a</span>), <span class='fu'>is.list</span>(<span class='no'>b</span>))
@@ -151,36 +210,32 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
   <span class='fu'>severeifnot</span>(<span class='st'>"I absolutely cannot deal with the fact that something is not a list."</span>, <span class='fu'>is.list</span>(<span class='no'>a</span>), <span class='fu'>is.list</span>(<span class='no'>b</span>))
 })
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#details">Details</a></li>
 
-  
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
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-
diff --git a/base/qaqc/docs/LICENSE-text.html b/base/qaqc/docs/LICENSE-text.html
index b0cb007..ec64926 100644
--- a/base/qaqc/docs/LICENSE-text.html
+++ b/base/qaqc/docs/LICENSE-text.html
@@ -2,121 +2,160 @@
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 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<title>License • PEcAn.qaqc</title>
-
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-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <title>License • PEcAn.qaqc</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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-      <a href="articles/Pre-release-database-cleanup.html">Pre Release database Cleanup</a>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.qaqc</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/Pre-release-database-cleanup.html"
+                        >Pre Release database Cleanup</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/compare_ED2.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="articles/function_relationships.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/lebauer2013ffb.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="articles/module_output.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -145,27 +184,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/qaqc/docs/articles/Pre-release-database-cleanup.html b/base/qaqc/docs/articles/Pre-release-database-cleanup.html
index e1dd6b7..c2dba00 100644
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+++ b/base/qaqc/docs/articles/Pre-release-database-cleanup.html
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+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
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+    <!-- jquery -->
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+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+      crossorigin="anonymous"
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+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+    <meta property="og:title" content="Pre Release database Cleanup" />
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+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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     <div class="container template-article">
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+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.qaqc</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
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-<li>
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-      
-      </header><div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header toc-ignore">
-      <h1>Pre Release database Cleanup</h1>
-            
-      
-      
-      <div class="hidden name"><code>Pre-release-database-cleanup.Rmd</code></div>
+                    <span class="caret"></span>
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+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/Pre-release-database-cleanup.html"
+                        >Pre Release database Cleanup</a
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+                      <a href="../articles/module_output.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
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+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header toc-ignore">
+            <h1>Pre Release database Cleanup</h1>
 
-    </div>
+            <div class="hidden name">
+              <code>Pre-release-database-cleanup.Rmd</code>
+            </div>
+          </div>
 
-    
-    
-<p>This is an quick script for cleaning up the database. For further documentation see the README.rmd file in the main <code>qaqc</code> folder.</p>
-<p><strong>Step 1: set up an outdir and a connection to bety</strong> The outdir is where temporary editing files will be written, and where a backup of bety will be stored.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">con &lt;-<span class="st"> </span>RPostgreSQL<span class="op">::</span><span class="kw">dbConnect</span>(RPostgreSQL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/RPostgreSQL/topics/PostgreSQL">PostgreSQL</a></span>(),
+          <p>
+            This is an quick script for cleaning up the database. For further
+            documentation see the README.rmd file in the main
+            <code>qaqc</code> folder.
+          </p>
+          <p>
+            <strong>Step 1: set up an outdir and a connection to bety</strong>
+            The outdir is where temporary editing files will be written, and
+            where a backup of bety will be stored.
+          </p>
+          <div class="sourceCode">
+            <pre
+              class="sourceCode r"
+            ><code class="sourceCode r">con &lt;-<span class="st"> </span>RPostgreSQL<span class="op">::</span><span class="kw">dbConnect</span>(RPostgreSQL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/RPostgreSQL/topics/PostgreSQL">PostgreSQL</a></span>(),
 <span class="dt">dbname =</span> <span class="st">"bety"</span>,
 <span class="dt">password =</span> <span class="st">'bety'</span>,
 <span class="dt">host =</span> <span class="st">'psql-pecan.bu.edu'</span>,
@@ -101,64 +171,115 @@ <h1>Pre Release database Cleanup</h1>
 outdir&lt;-<span class="kw">as.character</span>(<span class="kw">getwd</span>()) <span class="co">#set as prefered out directory</span>
 bety_backup_directory&lt;-<span class="kw">as.character</span>(<span class="kw">getwd</span>()) <span class="co">#set as prefered directory for bety backup.</span>
 
-<span class="kw">options</span>(<span class="dt">scipen=</span><span class="dv">999</span>) <span class="co">#To view full id values</span></code></pre></div>
-<p><strong>Step 2: Back up bety</strong> Before any major deletion processes, it makes sense to make a back-up version of the database. Don’t skip this step.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">system</span>(<span class="st">'TODAY=$( date +"%d" )'</span>)
+<span class="kw">options</span>(<span class="dt">scipen=</span><span class="dv">999</span>) <span class="co">#To view full id values</span></code></pre>
+          </div>
+          <p>
+            <strong>Step 2: Back up bety</strong> Before any major deletion
+            processes, it makes sense to make a back-up version of the database.
+            Don’t skip this step.
+          </p>
+          <div class="sourceCode">
+            <pre
+              class="sourceCode r"
+            ><code class="sourceCode r"><span class="kw">system</span>(<span class="st">'TODAY=$( date +"%d" )'</span>)
 backup_dir&lt;-<span class="kw">paste</span>(<span class="st">'pg_dump -U bety -d bety | gzip -9 &gt; '</span>, bety_backup_directory,<span class="st">'/bety-pre-culling${TODAY}.sql.gz'</span>, <span class="dt">sep=</span><span class="st">""</span>)
 
-<span class="kw">system</span>(backup_dir)</code></pre></div>
-<p><strong>Step 3: find all of the entries that should be deleted </strong>*</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">formats&lt;-<span class="kw">find_formats_without_inputs</span>(<span class="dt">con=</span>con, <span class="dt">created_before =</span> <span class="st">"2016-01-01"</span>, <span class="dt">user_id =</span> <span class="ot">NULL</span>, <span class="dt">updated_after =</span> <span class="st">"2016-01-01"</span>) <span class="co">#Ideally, date should be set to the date of the last release </span>
+<span class="kw">system</span>(backup_dir)</code></pre>
+          </div>
+          <p>
+            <strong
+              >Step 3: find all of the entries that should be deleted </strong
+            >*
+          </p>
+          <div class="sourceCode">
+            <pre
+              class="sourceCode r"
+            ><code class="sourceCode r">formats&lt;-<span class="kw">find_formats_without_inputs</span>(<span class="dt">con=</span>con, <span class="dt">created_before =</span> <span class="st">"2016-01-01"</span>, <span class="dt">user_id =</span> <span class="ot">NULL</span>, <span class="dt">updated_after =</span> <span class="st">"2016-01-01"</span>) <span class="co">#Ideally, date should be set to the date of the last release </span>
 
-inputs&lt;-<span class="kw">find_inputs_without_formats</span>(<span class="dt">con=</span>con, <span class="dt">created_before =</span> <span class="st">"2014-01-01"</span>,<span class="dt">updated_after =</span> <span class="ot">NULL</span>, <span class="dt">user_id =</span> <span class="ot">NULL</span>)</code></pre></div>
-<p>Since just a dump of every column can be hard to read, just choose the columns that are important.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">column_names&lt;-<span class="kw">get_table_column_names</span>(<span class="dt">table =</span> formats, <span class="dt">con =</span> con)
+inputs&lt;-<span class="kw">find_inputs_without_formats</span>(<span class="dt">con=</span>con, <span class="dt">created_before =</span> <span class="st">"2014-01-01"</span>,<span class="dt">updated_after =</span> <span class="ot">NULL</span>, <span class="dt">user_id =</span> <span class="ot">NULL</span>)</code></pre>
+          </div>
+          <p>
+            Since just a dump of every column can be hard to read, just choose
+            the columns that are important.
+          </p>
+          <div class="sourceCode">
+            <pre
+              class="sourceCode r"
+            ><code class="sourceCode r">column_names&lt;-<span class="kw">get_table_column_names</span>(<span class="dt">table =</span> formats, <span class="dt">con =</span> con)
 column_names<span class="op">$</span>formats
 
 column_names&lt;-column_names<span class="op">$</span>formats[column_names<span class="op">$</span>formats <span class="op">%in%</span><span class="st"> </span><span class="kw">c</span>(<span class="st">"id"</span>,<span class="st">"created_at"</span>, <span class="st">"name"</span>, <span class="st">"notes"</span>, <span class="st">"table_name"</span>)]
-column_names</code></pre></div>
-<p>** Option 1: Edit an R object ***</p>
-<p>This is the most important step! Navigate to the written out table and <em>delete entries that should remain in the database</em>.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">formats&lt;-formats[<span class="kw">colnames</span>(formats) <span class="op">%in%</span><span class="st"> </span>column_names] <span class="co">#subset for easy viewing</span>
+column_names</code></pre>
+          </div>
+          <p>** Option 1: Edit an R object ***</p>
+          <p>
+            This is the most important step! Navigate to the written out table
+            and <em>delete entries that should remain in the database</em>.
+          </p>
+          <div class="sourceCode">
+            <pre
+              class="sourceCode r"
+            ><code class="sourceCode r">formats&lt;-formats[<span class="kw">colnames</span>(formats) <span class="op">%in%</span><span class="st"> </span>column_names] <span class="co">#subset for easy viewing</span>
 <span class="kw">View</span>(formats)
 
 formats&lt;-formats[<span class="kw">grep</span>(<span class="st">"test"</span>,formats<span class="op">$</span>name),]
-<span class="kw">View</span>(formats)</code></pre></div>
-<p>** Option 2: Edit a file **</p>
-<p>This is also the most important step! Navigate to the written out table and <em>delete entries that should remain in the database</em>. If the tables are difficult to read, change what columns are retained by editing the “relevant_table_columns” parameter.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">write_out_table</span>(<span class="dt">table =</span> formats, <span class="dt">outdir =</span> outdir, <span class="dt">relevant_table_columns =</span> column_names, <span class="dt">table_name =</span> <span class="st">"formats"</span>)
-<span class="kw">write_out_table</span>(<span class="dt">table =</span> inputs,<span class="dt">outdir =</span> outdir, <span class="dt">relevant_table_columns =</span><span class="kw">c</span>(<span class="st">"id"</span>, <span class="st">"created_at"</span>, <span class="st">"name"</span>), <span class="dt">table_name =</span> <span class="st">"inputs"</span>)</code></pre></div>
-<p><strong>Step 5: Cull all remaining entries in the files</strong></p>
-<p>This will delete all entries remaining in the file, and place a delete log in the outdir directory.</p>
-<p><em>please do not run before editing either the table object or the “query_of” file</em></p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">### Note: Do not run before the editing step <span class="al">###</span>
+<span class="kw">View</span>(formats)</code></pre>
+          </div>
+          <p>** Option 2: Edit a file **</p>
+          <p>
+            This is also the most important step! Navigate to the written out
+            table and
+            <em>delete entries that should remain in the database</em>. If the
+            tables are difficult to read, change what columns are retained by
+            editing the “relevant_table_columns” parameter.
+          </p>
+          <div class="sourceCode">
+            <pre
+              class="sourceCode r"
+            ><code class="sourceCode r"><span class="kw">write_out_table</span>(<span class="dt">table =</span> formats, <span class="dt">outdir =</span> outdir, <span class="dt">relevant_table_columns =</span> column_names, <span class="dt">table_name =</span> <span class="st">"formats"</span>)
+<span class="kw">write_out_table</span>(<span class="dt">table =</span> inputs,<span class="dt">outdir =</span> outdir, <span class="dt">relevant_table_columns =</span><span class="kw">c</span>(<span class="st">"id"</span>, <span class="st">"created_at"</span>, <span class="st">"name"</span>), <span class="dt">table_name =</span> <span class="st">"inputs"</span>)</code></pre>
+          </div>
+          <p>
+            <strong>Step 5: Cull all remaining entries in the files</strong>
+          </p>
+          <p>
+            This will delete all entries remaining in the file, and place a
+            delete log in the outdir directory.
+          </p>
+          <p>
+            <em
+              >please do not run before editing either the table object or the
+              “query_of” file</em
+            >
+          </p>
+          <div class="sourceCode">
+            <pre
+              class="sourceCode r"
+            ><code class="sourceCode r">### Note: Do not run before the editing step <span class="al">###</span>
 
 ## From an R object ##
 <span class="co">#cull_database_entries(table=formats, outdir = outdir, con=con, table_name = "formats")</span>
 
 ## From a file ##
 <span class="co">#cull_database_entries(outdir = outdir,file_name ='query_of_formats', con=con, table_name = "formats")</span>
-<span class="co">#cull_database_entries(outdir = outdir,file_name ='query_of_inputs', con=con, table_name = "inputs")</span></code></pre></div>
-  </div>
+<span class="co">#cull_database_entries(outdir = outdir,file_name ='query_of_inputs', con=con, table_name = "inputs")</span></code></pre>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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diff --git a/base/qaqc/docs/articles/compare_ED2.html b/base/qaqc/docs/articles/compare_ED2.html
index c5830f5..c79f010 100644
--- a/base/qaqc/docs/articles/compare_ED2.html
+++ b/base/qaqc/docs/articles/compare_ED2.html
@@ -1,135 +1,196 @@
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-<a href="#title" class="anchor"></a>Title</h1>
-<div id="looking-at-how-read-output-works" class="section level2">
-<h2 class="hasAnchor">
-<a href="#looking-at-how-read-output-works" class="anchor"></a>looking at how read.output works</h2>
-</div>
-</div>
-  </div>
+          <div id="title" class="section level1">
+            <h1 class="hasAnchor"><a href="#title" class="anchor"></a>Title</h1>
+            <div id="looking-at-how-read-output-works" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#looking-at-how-read-output-works" class="anchor"></a
+                >looking at how read.output works
+              </h2>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li>
-<a href="#title">Title</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#looking-at-how-read-output-works">looking at how read.output works</a></li>
-      </ul>
-</li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#title">Title</a>
+                <ul class="nav nav-pills nav-stacked">
+                  <li>
+                    <a href="#looking-at-how-read-output-works"
+                      >looking at how read.output works</a
+                    >
+                  </li>
+                </ul>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
-</div>
-
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-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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+    </div>
   </body>
 </html>
diff --git a/base/qaqc/docs/articles/function_relationships.html b/base/qaqc/docs/articles/function_relationships.html
index 4d0caec..2c32a81 100644
--- a/base/qaqc/docs/articles/function_relationships.html
+++ b/base/qaqc/docs/articles/function_relationships.html
@@ -1,97 +1,156 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
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-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+<!-- Generated by pkgdown: do not edit by hand -->
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+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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+      crossorigin="anonymous"
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+    <meta property="og:title" content="" />
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+    <![endif]-->
+  </head>
+  <body>
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.qaqc</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
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+                  <a href="../reference/index.html">Reference</a>
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+                  <a
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+                    Articles
 
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-    <div class="page-header toc-ignore">
-      <h1></h1>
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+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/Pre-release-database-cleanup.html"
+                        >Pre Release database Cleanup</a
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+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
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+          <div class="page-header toc-ignore">
+            <h1></h1>
 
-    </div>
+            <div class="hidden name">
+              <code>function_relationships.Rmd</code>
+            </div>
+          </div>
 
-    
-    
-<!--
+          <!--
 #-------------------------------------------------------------------------------
 # Copyright (c) 2012 University of Illinois, NCSA.
 # All rights reserved. This program and the accompanying materials
@@ -101,50 +160,67 @@ <h1></h1>
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 -->
-<div id="package-interdependencies" class="section level1">
-<h1 class="hasAnchor">
-<a href="#package-interdependencies" class="anchor"></a>Package Interdependencies</h1>
-<p>This some code helps to visualize the interdependence of functions within PEcAn</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(mvbutils)
+          <div id="package-interdependencies" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#package-interdependencies" class="anchor"></a>Package
+              Interdependencies
+            </h1>
+            <p>
+              This some code helps to visualize the interdependence of functions
+              within PEcAn
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(mvbutils)
 <span class="kw">library</span>(PEcAn.utils)
 <span class="kw">library</span>(PEcAn.ED2)
 <span class="kw">library</span>(PEcAn.BIOCRO)
-<span class="kw">library</span>(PEcAn.SIPNET)</code></pre></div>
-<div id="reading-model-output" class="section level3">
-<h3 class="hasAnchor">
-<a href="#reading-model-output" class="anchor"></a>Reading model output</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">foodweb</span>(<span class="dt">where =</span> <span class="kw">list</span>(<span class="st">"package:PEcAn.utils"</span>, <span class="st">"package:PEcAn.BIOCRO"</span>), <span class="dt">prune =</span> <span class="kw">c</span>(<span class="st">"output"</span>, <span class="st">"read"</span>, <span class="st">"results"</span>, <span class="st">"model2netcdf"</span>), <span class="dt">desc =</span> <span class="ot">FALSE</span>)
+<span class="kw">library</span>(PEcAn.SIPNET)</code></pre>
+            </div>
+            <div id="reading-model-output" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#reading-model-output" class="anchor"></a>Reading model
+                output
+              </h3>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">foodweb</span>(<span class="dt">where =</span> <span class="kw">list</span>(<span class="st">"package:PEcAn.utils"</span>, <span class="st">"package:PEcAn.BIOCRO"</span>), <span class="dt">prune =</span> <span class="kw">c</span>(<span class="st">"output"</span>, <span class="st">"read"</span>, <span class="st">"results"</span>, <span class="st">"model2netcdf"</span>), <span class="dt">desc =</span> <span class="ot">FALSE</span>)
 <span class="kw">foodweb</span>(<span class="dt">where =</span> <span class="kw">list</span>(<span class="st">"package:PEcAn.utils"</span>, <span class="st">"package:PEcAn.ED2"</span>), <span class="dt">prune =</span> <span class="kw">c</span>(<span class="st">"output"</span>, <span class="st">"read"</span>, <span class="st">"results"</span>, <span class="st">"model2netcdf"</span>), <span class="dt">desc =</span> <span class="ot">FALSE</span>)
-<span class="kw">foodweb</span>(<span class="dt">where =</span> <span class="kw">list</span>(<span class="st">"package:PEcAn.utils"</span>, <span class="st">"package:PEcAn.SIPNET"</span>), <span class="dt">prune =</span> <span class="kw">c</span>(<span class="st">"output"</span>, <span class="st">"read"</span>, <span class="st">"results"</span>, <span class="st">"model2netcdf"</span>), <span class="dt">desc =</span> <span class="ot">FALSE</span>)</code></pre></div>
-</div>
-</div>
-  </div>
+<span class="kw">foodweb</span>(<span class="dt">where =</span> <span class="kw">list</span>(<span class="st">"package:PEcAn.utils"</span>, <span class="st">"package:PEcAn.SIPNET"</span>), <span class="dt">prune =</span> <span class="kw">c</span>(<span class="st">"output"</span>, <span class="st">"read"</span>, <span class="st">"results"</span>, <span class="st">"model2netcdf"</span>), <span class="dt">desc =</span> <span class="ot">FALSE</span>)</code></pre>
+              </div>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#package-interdependencies">Package Interdependencies</a></li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#package-interdependencies"
+                  >Package Interdependencies</a
+                >
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
-</div>
-
-
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
diff --git a/base/qaqc/docs/articles/index.html b/base/qaqc/docs/articles/index.html
index b1bc569..c2e5586 100644
--- a/base/qaqc/docs/articles/index.html
+++ b/base/qaqc/docs/articles/index.html
@@ -2,149 +2,190 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-
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-
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-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+          <div id="lebauer-2013-analysis" class="section level1">
+            <h1 class="hasAnchor">
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index fd7885f..e3242a0 100644
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+            <div class="hidden name"><code>module_output.Rmd</code></div>
+          </div>
 
-    
-    
-<!--
+          <!--
 #-------------------------------------------------------------------------------
 # Copyright (c) 2012 University of Illinois, NCSA.
 # All rights reserved. This program and the accompanying materials
@@ -101,50 +158,72 @@ <h1></h1>
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 -->
-<div id="modules-and-outputs" class="section level1">
-<h1 class="hasAnchor">
-<a href="#modules-and-outputs" class="anchor"></a>Modules and outputs</h1>
-<p>To get a better understanding on what files are created where, Rob created a workflow as an SVG diagram. You can find the diagram at</p>
-<p><a href="http://isda.ncsa.illinois.edu/~kooper/EBI/workflow.svg" class="uri">http://isda.ncsa.illinois.edu/~kooper/EBI/workflow.svg</a></p>
-<p>In this graph the square boxes represent processes running, the rhomboids are inputs and outputs.</p>
-<p>To create this I used the trace functionality in R to capture the files saved/loaded</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">trace</span>(nc_open, <span class="kw">quote</span>(<span class="kw">cat</span>(<span class="kw">c</span>(<span class="st">"LOAD : "</span>, filename, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>), <span class="dt">file=</span><span class="st">"files.txt"</span>, <span class="dt">append=</span><span class="ot">TRUE</span>)))
+          <div id="modules-and-outputs" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#modules-and-outputs" class="anchor"></a>Modules and
+              outputs
+            </h1>
+            <p>
+              To get a better understanding on what files are created where, Rob
+              created a workflow as an SVG diagram. You can find the diagram at
+            </p>
+            <p>
+              <a
+                href="http://isda.ncsa.illinois.edu/~kooper/EBI/workflow.svg"
+                class="uri"
+                >http://isda.ncsa.illinois.edu/~kooper/EBI/workflow.svg</a
+              >
+            </p>
+            <p>
+              In this graph the square boxes represent processes running, the
+              rhomboids are inputs and outputs.
+            </p>
+            <p>
+              To create this I used the trace functionality in R to capture the
+              files saved/loaded
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">trace</span>(nc_open, <span class="kw">quote</span>(<span class="kw">cat</span>(<span class="kw">c</span>(<span class="st">"LOAD : "</span>, filename, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>), <span class="dt">file=</span><span class="st">"files.txt"</span>, <span class="dt">append=</span><span class="ot">TRUE</span>)))
 <span class="kw">trace</span>(nc_create, <span class="kw">quote</span>(<span class="kw">cat</span>(<span class="kw">c</span>(<span class="st">"SAVE : "</span>, filename, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>), <span class="dt">file=</span><span class="st">"files.txt"</span>, <span class="dt">append=</span><span class="ot">TRUE</span>)))
 <span class="kw">trace</span>(save, <span class="kw">quote</span>(<span class="kw">cat</span>(<span class="kw">c</span>(<span class="st">"SAVE : "</span>, file, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>), <span class="dt">file=</span><span class="st">"files.txt"</span>, <span class="dt">append=</span><span class="ot">TRUE</span>)))
 <span class="kw">trace</span>(load, <span class="kw">quote</span>(<span class="kw">cat</span>(<span class="kw">c</span>(<span class="st">"LOAD : "</span>, file, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>), <span class="dt">file=</span><span class="st">"files.txt"</span>, <span class="dt">append=</span><span class="ot">TRUE</span>)))
 <span class="kw">trace</span>(cat, <span class="kw">quote</span>(<span class="cf">if</span> ((raster<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/raster/topics/trim">trim</a></span>(file) <span class="op">!=</span><span class="st"> ""</span>) <span class="op">&amp;&amp;</span><span class="st"> </span>(file <span class="op">!=</span><span class="st"> "files.txt"</span>) <span class="op">&amp;&amp;</span><span class="st"> </span>(file <span class="op">!=</span><span class="st"> </span><span class="kw">stdout</span>()) <span class="op">&amp;&amp;</span><span class="st"> </span>(file <span class="op">!=</span><span class="st"> </span><span class="kw">stderr</span>())) { 
   <span class="kw">cat</span>(<span class="kw">c</span>(<span class="st">"CAT  : "</span>, file, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>), <span class="dt">file=</span><span class="st">"files.txt"</span>, <span class="dt">append=</span><span class="ot">TRUE</span>)}))
 <span class="kw">trace</span>(writeLines, <span class="kw">quote</span>(<span class="cf">if</span> ((con <span class="op">!=</span><span class="st"> </span><span class="kw">stdout</span>()) <span class="op">&amp;&amp;</span><span class="st"> </span>(con <span class="op">!=</span><span class="st"> </span><span class="kw">stderr</span>()))
-  {<span class="kw">cat</span>(<span class="kw">c</span>(<span class="st">"WRIT : "</span>, con, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>), <span class="dt">file=</span><span class="st">"files.txt"</span>, <span class="dt">append=</span><span class="ot">TRUE</span>)}))</code></pre></div>
-<p>Once these traces are set, you can run a PEcAn workflow.R and get a list of the files output at each stage</p>
-</div>
-  </div>
+  {<span class="kw">cat</span>(<span class="kw">c</span>(<span class="st">"WRIT : "</span>, con, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>), <span class="dt">file=</span><span class="st">"files.txt"</span>, <span class="dt">append=</span><span class="ot">TRUE</span>)}))</code></pre>
+            </div>
+            <p>
+              Once these traces are set, you can run a PEcAn workflow.R and get
+              a list of the files output at each stage
+            </p>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#modules-and-outputs">Modules and outputs</a></li>
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-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
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+            <ul class="nav nav-pills nav-stacked">
+              <li><a href="#modules-and-outputs">Modules and outputs</a></li>
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+          </div>
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index 5446b81..7d634f9 100644
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+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.qaqc</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/Pre-release-database-cleanup.html">Pre Release database Cleanup</a>
-    </li>
-    <li>
-      <a href="articles/compare_ED2.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/function_relationships.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/lebauer2013ffb.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/module_output.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.qaqc</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/Pre-release-database-cleanup.html"
+                        >Pre Release database Cleanup</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/compare_ED2.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="articles/function_relationships.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/lebauer2013ffb.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="articles/module_output.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/qaqc/docs/docsearch.css b/base/qaqc/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/base/qaqc/docs/docsearch.css
+++ b/base/qaqc/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/base/qaqc/docs/docsearch.js b/base/qaqc/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/base/qaqc/docs/docsearch.js
+++ b/base/qaqc/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/base/qaqc/docs/index.html b/base/qaqc/docs/index.html
index 5e82b85..02c05b3 100644
--- a/base/qaqc/docs/index.html
+++ b/base/qaqc/docs/index.html
@@ -1,157 +1,281 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>QAQC • PEcAn.qaqc</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="QAQC">
-<meta property="og:description" content="PEcAn integration and model skill testing">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>QAQC • PEcAn.qaqc</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta property="og:title" content="QAQC" />
+    <meta
+      property="og:description"
+      content="PEcAn integration and model skill testing"
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-article">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.qaqc</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/Pre-release-database-cleanup.html">Pre Release database Cleanup</a>
-    </li>
-    <li>
-      <a href="articles/compare_ED2.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/function_relationships.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/lebauer2013ffb.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/module_output.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="col-md-9 contents">
-    
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.qaqc</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    
-    
-<div id="pecan-functions-for-cleaning-up-a-version-of-the-bety-database" class="section level2">
-<h2 class="hasAnchor">
-<a href="#pecan-functions-for-cleaning-up-a-version-of-the-bety-database" class="anchor"></a>PEcAn functions for cleaning up a version of the bety database</h2>
-<p>This package includes several wrapper functions for common database queries for entries that cause problems, or take up space. Please refer to the <code>Pre-release-clean-up</code> script located in the <code>vignettes</code> folder for best-practices in using these functions. See “Intended use” for more information.</p>
-<p>Many queries and checks are net yet implemented. If you’d like to contribute to this package, look at issue <a href="https://github.com/PecanProject/pecan/issues/1630">#1630</a> and [this list of bety issues] (<a href="https://github.com/PecanProject/bety/issues?utf8=%E2%9C%93&amp;q=is%3Aopen%20%22needed%20cleanup%22%20">https://github.com/PecanProject/bety/issues?utf8=%E2%9C%93&amp;q=is%3Aopen%20%22needed%20cleanup%22%20</a>) to see what functions still need to be made. Add these functions to the <code>Pre-release-clean-up</code> vignette. See “Structure of functions” for more information.</p>
-</div>
-<div id="intended-use" class="section level2">
-<h2 class="hasAnchor">
-<a href="#intended-use" class="anchor"></a>Intended use</h2>
-<p>These functions are intended to be used interactively. The <code>find*</code> functions return a table of all of the entries that fit the terms provided. The <code>write_table</code> function then exports that table to a specific file. That file can then be <em>manually edited</em> in any text-editor. <em>This is the most important step, as there will likely be entries with utility that only a person familiar with ongoing/recent projects would know.</em></p>
-<p>After the editing process, the file can be fed into the <code>cull_database_entries</code> function. This will parse the file, and <em>delete all the entried that are listed on the file</em>. It will also provide a log of what was deleted.</p>
-</div>
-<div id="structure-of-functions" class="section level2">
-<h2 class="hasAnchor">
-<a href="#structure-of-functions" class="anchor"></a>Structure of functions</h2>
-<p><strong>find functions</strong></p>
-<ul>
-<li><p>All find functions should have descriptive names of the form “find_TABLE_ relationship _TABLE2“. All functions will return entries from the first named table ie: <code>find_inputs_without_formats</code> will return input table entries.</p></li>
-<li><p>All find functions need to return and object with a column “table_name” with the name of the table it’s returning entries from.</p></li>
-<li><p>All find functions must return an object where there is an “id” column with “id” entries that are associated with the entries from the first table in the function</p></li>
-</ul>
-<p><strong>check functions</strong></p>
-<ul>
-<li>Not yet implemented.</li>
-</ul>
-</div>
-  </div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/Pre-release-database-cleanup.html"
+                        >Pre Release database Cleanup</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/compare_ED2.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="articles/function_relationships.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/lebauer2013ffb.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="articles/module_output.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div
+            id="pecan-functions-for-cleaning-up-a-version-of-the-bety-database"
+            class="section level2"
+          >
+            <h2 class="hasAnchor">
+              <a
+                href="#pecan-functions-for-cleaning-up-a-version-of-the-bety-database"
+                class="anchor"
+              ></a
+              >PEcAn functions for cleaning up a version of the bety database
+            </h2>
+            <p>
+              This package includes several wrapper functions for common
+              database queries for entries that cause problems, or take up
+              space. Please refer to the
+              <code>Pre-release-clean-up</code> script located in the
+              <code>vignettes</code> folder for best-practices in using these
+              functions. See “Intended use” for more information.
+            </p>
+            <p>
+              Many queries and checks are net yet implemented. If you’d like to
+              contribute to this package, look at issue
+              <a href="https://github.com/PecanProject/pecan/issues/1630"
+                >#1630</a
+              >
+              and [this list of bety issues] (<a
+                href="https://github.com/PecanProject/bety/issues?utf8=%E2%9C%93&amp;q=is%3Aopen%20%22needed%20cleanup%22%20"
+                >https://github.com/PecanProject/bety/issues?utf8=%E2%9C%93&amp;q=is%3Aopen%20%22needed%20cleanup%22%20</a
+              >) to see what functions still need to be made. Add these
+              functions to the <code>Pre-release-clean-up</code> vignette. See
+              “Structure of functions” for more information.
+            </p>
+          </div>
+          <div id="intended-use" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#intended-use" class="anchor"></a>Intended use
+            </h2>
+            <p>
+              These functions are intended to be used interactively. The
+              <code>find*</code> functions return a table of all of the entries
+              that fit the terms provided. The <code>write_table</code> function
+              then exports that table to a specific file. That file can then be
+              <em>manually edited</em> in any text-editor.
+              <em
+                >This is the most important step, as there will likely be
+                entries with utility that only a person familiar with
+                ongoing/recent projects would know.</em
+              >
+            </p>
+            <p>
+              After the editing process, the file can be fed into the
+              <code>cull_database_entries</code> function. This will parse the
+              file, and
+              <em>delete all the entried that are listed on the file</em>. It
+              will also provide a log of what was deleted.
+            </p>
+          </div>
+          <div id="structure-of-functions" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#structure-of-functions" class="anchor"></a>Structure of
+              functions
+            </h2>
+            <p><strong>find functions</strong></p>
+            <ul>
+              <li>
+                <p>
+                  All find functions should have descriptive names of the form
+                  “find_TABLE_ relationship _TABLE2“. All functions will return
+                  entries from the first named table ie:
+                  <code>find_inputs_without_formats</code> will return input
+                  table entries.
+                </p>
+              </li>
+              <li>
+                <p>
+                  All find functions need to return and object with a column
+                  “table_name” with the name of the table it’s returning entries
+                  from.
+                </p>
+              </li>
+              <li>
+                <p>
+                  All find functions must return an object where there is an
+                  “id” column with “id” entries that are associated with the
+                  entries from the first table in the function
+                </p>
+              </li>
+            </ul>
+            <p><strong>check functions</strong></p>
+            <ul>
+              <li>Not yet implemented.</li>
+            </ul>
+          </div>
+        </div>
 
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
       </div>
 
-</div>
-
-
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/base/qaqc/docs/pkgdown.css b/base/qaqc/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/base/qaqc/docs/pkgdown.css
+++ b/base/qaqc/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/base/qaqc/docs/pkgdown.js b/base/qaqc/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/base/qaqc/docs/pkgdown.js
+++ b/base/qaqc/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/base/qaqc/docs/reference/index.html b/base/qaqc/docs/reference/index.html
index 1e90f52..7da04d8 100644
--- a/base/qaqc/docs/reference/index.html
+++ b/base/qaqc/docs/reference/index.html
@@ -2,168 +2,207 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.qaqc</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
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-
-<!-- clipboard.js -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.qaqc</title>
+
+    <!-- jquery -->
+    <script
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+    ></script>
+    <!-- Bootstrap -->
+
+    <link
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+      crossorigin="anonymous"
+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
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+
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+              <col class="alias" />
+              <col class="title" />
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+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="new.taylor.html">new.taylor()</a></code>
+                  </p>
+                </td>
+                <td><p>Taylor Diagram</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
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diff --git a/base/qaqc/docs/reference/new.taylor.html b/base/qaqc/docs/reference/new.taylor.html
index eee9e92..9d8f5e2 100644
--- a/base/qaqc/docs/reference/new.taylor.html
+++ b/base/qaqc/docs/reference/new.taylor.html
@@ -2,167 +2,214 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Taylor Diagram</h1>
-    
-    <div class="hidden name"><code>new.taylor.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Plot taylor diagram for benchmark sites</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>new.taylor</span>(<span class='no'>dataset</span>, <span class='no'>runid</span>, <span class='no'>siteid</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>runid</th>
-      <td><p>a numeric vector with the id(s) of one or more runs (folder in runs) to plot</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Taylor Diagram</h1>
+
+            <div class="hidden name"><code>new.taylor.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Plot taylor diagram for benchmark sites</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>new.taylor</span>(<span class='no'>dataset</span>, <span class='no'>runid</span>, <span class='no'>siteid</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>runid</th>
+              <td>
+                <p>
+                  a numeric vector with the id(s) of one or more runs (folder in
+                  runs) to plot
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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index 7a7375e..d35c9fb 100644
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="License" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>License • PEcAn.remote</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/authors.html b/base/remote/docs/authors.html
index 7a4f5b2..4ecc9da 100644
--- a/base/remote/docs/authors.html
+++ b/base/remote/docs/authors.html
@@ -2,134 +2,152 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.remote</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.remote</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Alexey Shiklomanov</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Alexey Shiklomanov</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/docsearch.css b/base/remote/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/base/remote/docs/docsearch.css
+++ b/base/remote/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/base/remote/docs/docsearch.js b/base/remote/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/base/remote/docs/docsearch.js
+++ b/base/remote/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/base/remote/docs/index.html b/base/remote/docs/index.html
index 40c8e51..7c2be5b 100644
--- a/base/remote/docs/index.html
+++ b/base/remote/docs/index.html
@@ -1,105 +1,158 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn model execution utilities • PEcAn.remote</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn model execution utilities">
-<meta property="og:description" content="This package contains utilities for communicating with and executing code on local and remote hosts.
-    In particular, it has PEcAn-specific utilities for starting ecosystem model runs.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn model execution utilities • PEcAn.remote</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta property="og:title" content="PEcAn model execution utilities" />
+    <meta
+      property="og:description"
+      content="This package contains utilities for communicating with and executing code on local and remote hosts.
+    In particular, it has PEcAn-specific utilities for starting ecosystem model runs."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    This package contains utilities for communicating with and executing code on local and remote hosts.
-    In particular, it has PEcAn-specific utilities for starting ecosystem model runs.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          This package contains utilities for communicating with and executing
+          code on local and remote hosts. In particular, it has PEcAn-specific
+          utilities for starting ecosystem model runs.
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/base/remote/docs/pkgdown.css b/base/remote/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/base/remote/docs/pkgdown.css
+++ b/base/remote/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/base/remote/docs/pkgdown.js b/base/remote/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/base/remote/docs/pkgdown.js
+++ b/base/remote/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
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diff --git a/base/remote/docs/reference/check_model_run.html b/base/remote/docs/reference/check_model_run.html
index ebb9363..919e23b 100644
--- a/base/remote/docs/reference/check_model_run.html
+++ b/base/remote/docs/reference/check_model_run.html
@@ -2,153 +2,197 @@
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 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Check if model run was successful — check_model_run • PEcAn.remote
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
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+      crossorigin="anonymous"
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+
+    <!-- sticky kit -->
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+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    <meta name="twitter:card" content="summary" />
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+                type="button"
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+              <span class="navbar-brand">
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+                  >1.6.0</span
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+
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+                  <a href="../index.html">
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+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check if model run was successful</h1>
-    
-    <div class="hidden name"><code>check_model_run.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check if model run was successful</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check_model_run</span>(<span class='no'>out</span>, <span class='kw'>stop.on.error</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>out</th>
-      <td><p>Output from model execution, as a character.</p></td>
-    </tr>
-    <tr>
-      <th>stop.on.error</th>
-      <td><p>Throw error if <em>any</em> of the runs fails. Default TRUE.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>TRUE</code> if model run succeeded. If model run failed, throw an error if <code>stop.on.error</code>, or return FALSE.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check if model run was successful</h1>
+
+            <div class="hidden name"><code>check_model_run.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check if model run was successful</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_model_run</span>(<span class='no'>out</span>, <span class='kw'>stop.on.error</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>out</th>
+              <td><p>Output from model execution, as a character.</p></td>
+            </tr>
+            <tr>
+              <th>stop.on.error</th>
+              <td>
+                <p>
+                  Throw error if <em>any</em> of the runs fails. Default TRUE.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            <code>TRUE</code> if model run succeeded. If model run failed, throw
+            an error if <code>stop.on.error</code>, or return FALSE.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
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diff --git a/base/remote/docs/reference/fqdn.html b/base/remote/docs/reference/fqdn.html
index c9d3ef1..e44d978 100644
--- a/base/remote/docs/reference/fqdn.html
+++ b/base/remote/docs/reference/fqdn.html
@@ -2,153 +2,187 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
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+    ></script>
+    <!-- Bootstrap -->
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Returns the fully qualified hostname. — fqdn"
+    />
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+      property="og:description"
+      content="Returns the fully qualified hostname. This is potentially different from Sys.info()['nodename']
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+pecan.ncsa.illinois.edu will return just that as fqdn but only pecan for hostname."
+    />
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+                  class="label label-default"
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-    <h1>Returns the fully qualified hostname.</h1>
-    
-    <div class="hidden name"><code>fqdn.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Returns the fully qualified hostname.</h1>
 
-    <div class="ref-description">
-    
-    <p>Returns the fully qualified hostname. This is potentially different from <code>Sys.info()['nodename']</code>
-which can return just the hostname part and not the domain as well. For example the machine
-pecan.ncsa.illinois.edu will return just that as fqdn but only pecan for hostname.</p>
-    
-    </div>
+            <div class="hidden name"><code>fqdn.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Returns the fully qualified hostname. This is potentially
+              different from <code>Sys.info()['nodename']</code> which can
+              return just the hostname part and not the domain as well. For
+              example the machine pecan.ncsa.illinois.edu will return just that
+              as fqdn but only pecan for hostname.
+            </p>
+          </div>
+
+          <pre class="usage"><span class='fu'>fqdn</span>()</pre>
 
-    <pre class="usage"><span class='fu'>fqdn</span>()</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
 
-    <p>fully qualified hostname</p>
-    
+          <p>fully qualified hostname</p>
 
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>fqdn</span>()
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/index.html b/base/remote/docs/reference/index.html
index 90988cf..4cbf5c0 100644
--- a/base/remote/docs/reference/index.html
+++ b/base/remote/docs/reference/index.html
@@ -2,252 +2,364 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-<title>Function reference • PEcAn.remote</title>
+    <title>Function reference • PEcAn.remote</title>
 
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
 
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
 
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
 
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
 
+    <meta property="og:title" content="Function reference" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-      </header>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
 
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="check_model_run.html">check_model_run()</a></code> </p>
-        </td>
-        <td><p>Check if model run was successful</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="fqdn.html">fqdn()</a></code> </p>
-        </td>
-        <td><p>Returns the fully qualified hostname.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="is.localhost.html">is.localhost()</a></code> </p>
-        </td>
-        <td><p>Check if local host</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="kill.tunnel.html">kill.tunnel()</a></code> </p>
-        </td>
-        <td><p>kill.tunnel</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="open_tunnel.html">open_tunnel()</a></code> </p>
-        </td>
-        <td><p>Open an SSH tunnel, prompting for passwords as needed</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="qsub_get_jobid.html">qsub_get_jobid()</a></code> </p>
-        </td>
-        <td><p>Get Job ID from qsub output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="qsub_run_finished.html">qsub_run_finished()</a></code> </p>
-        </td>
-        <td><p>Check if qsub run finished</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="remote.copy.from.html">remote.copy.from()</a></code> </p>
-        </td>
-        <td><p>Copy file from remote to local</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="remote.copy.to.html">remote.copy.to()</a></code> </p>
-        </td>
-        <td><p>Copy file/dir to remote server from local server</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="remote.copy.update.html">remote.copy.update()</a></code> </p>
-        </td>
-        <td><p>Copy to remote and update DB</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="remote.execute.R.html">remote.execute.R()</a></code> </p>
-        </td>
-        <td><p>Execute command remotely</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="remote.execute.cmd.html">remote.execute.cmd()</a></code> </p>
-        </td>
-        <td><p>Execute command remotely</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="setup_modellauncher.html">setup_modellauncher()</a></code> </p>
-        </td>
-        <td><p>Setup model launcher script and job list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="stamp_started.html">stamp_started()</a></code> <code><a href="stamp_started.html">stamp_finished()</a></code> </p>
-        </td>
-        <td><p>Stamp start and stop times of runs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="start.model.runs.html">start(<i>&lt;model.runs&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Start selected ecosystem model runs within PEcAn workflow</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="start_qsub.html">start_qsub()</a></code> </p>
-        </td>
-        <td><p>Start qsub runs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="start_rabbitmq.html">start_rabbitmq()</a></code> </p>
-        </td>
-        <td><p>Start model execution using rabbitmq</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="start_serial.html">start_serial()</a></code> </p>
-        </td>
-        <td><p>Start model execution in serial mode</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="test_remote.html">test_remote()</a></code> </p>
-        </td>
-        <td><p>Test remote execution</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check_model_run.html"
+                        >check_model_run()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check if model run was successful</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="fqdn.html">fqdn()</a></code>
+                  </p>
+                </td>
+                <td><p>Returns the fully qualified hostname.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="is.localhost.html">is.localhost()</a></code>
+                  </p>
+                </td>
+                <td><p>Check if local host</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="kill.tunnel.html">kill.tunnel()</a></code>
+                  </p>
+                </td>
+                <td><p>kill.tunnel</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="open_tunnel.html">open_tunnel()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Open an SSH tunnel, prompting for passwords as needed</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="qsub_get_jobid.html">qsub_get_jobid()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get Job ID from qsub output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="qsub_run_finished.html"
+                        >qsub_run_finished()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check if qsub run finished</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="remote.copy.from.html"
+                        >remote.copy.from()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Copy file from remote to local</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="remote.copy.to.html">remote.copy.to()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Copy file/dir to remote server from local server</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="remote.copy.update.html"
+                        >remote.copy.update()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Copy to remote and update DB</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="remote.execute.R.html"
+                        >remote.execute.R()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Execute command remotely</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="remote.execute.cmd.html"
+                        >remote.execute.cmd()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Execute command remotely</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="setup_modellauncher.html"
+                        >setup_modellauncher()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Setup model launcher script and job list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="stamp_started.html">stamp_started()</a></code
+                    >
+                    <code
+                      ><a href="stamp_started.html">stamp_finished()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Stamp start and stop times of runs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="start.model.runs.html"
+                        >start(<i>&lt;model.runs&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Start selected ecosystem model runs within PEcAn workflow
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="start_qsub.html">start_qsub()</a></code>
+                  </p>
+                </td>
+                <td><p>Start qsub runs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="start_rabbitmq.html">start_rabbitmq()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Start model execution using rabbitmq</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="start_serial.html">start_serial()</a></code>
+                  </p>
+                </td>
+                <td><p>Start model execution in serial mode</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="test_remote.html">test_remote()</a></code>
+                  </p>
+                </td>
+                <td><p>Test remote execution</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-      </footer>
-   </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
-  
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/is.localhost.html b/base/remote/docs/reference/is.localhost.html
index 7cc319f..0fcc161 100644
--- a/base/remote/docs/reference/is.localhost.html
+++ b/base/remote/docs/reference/is.localhost.html
@@ -2,166 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Check if local host — is.localhost • PEcAn.remote</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Check if local host — is.localhost" />
-
-<meta property="og:description" content="Check if host is local" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Check if local host — is.localhost • PEcAn.remote</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Check if local host — is.localhost" />
+
+    <meta property="og:description" content="Check if host is local" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check if local host</h1>
-    
-    <div class="hidden name"><code>is.localhost.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check if host is local</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>is.localhost</span>(<span class='no'>host</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>host</th>
-      <td><p>the hostname to be checked</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>true if the host is the local host name</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Given the hostname is this the localhost. This returns true if either
-the value is localhost, or the value is the same as the fqdn.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check if local host</h1>
+
+            <div class="hidden name"><code>is.localhost.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check if host is local</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>is.localhost</span>(<span class='no'>host</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>host</th>
+              <td><p>the hostname to be checked</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>true if the host is the local host name</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Given the hostname is this the localhost. This returns true if
+            either the value is localhost, or the value is the same as the fqdn.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>is.localhost</span>(<span class='fu'><a href='fqdn.html'>fqdn</a></span>())
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/kill.tunnel.html b/base/remote/docs/reference/kill.tunnel.html
index 323a52d..7d684c3 100644
--- a/base/remote/docs/reference/kill.tunnel.html
+++ b/base/remote/docs/reference/kill.tunnel.html
@@ -2,137 +2,158 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>kill.tunnel — kill.tunnel • PEcAn.remote</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="kill.tunnel — kill.tunnel" />
-
-<meta property="og:description" content="kill tunnel to remote machine" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>kill.tunnel — kill.tunnel • PEcAn.remote</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="kill.tunnel — kill.tunnel" />
+
+    <meta property="og:description" content="kill tunnel to remote machine" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>kill.tunnel</h1>
-    
-    <div class="hidden name"><code>kill.tunnel.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>kill.tunnel</h1>
 
-    <div class="ref-description">
-    
-    <p>kill tunnel to remote machine</p>
-    
-    </div>
+            <div class="hidden name"><code>kill.tunnel.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>kill.tunnel</span>(<span class='no'>settings</span>, <span class='kw'>exe</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-        
+          <div class="ref-description">
+            <p>kill tunnel to remote machine</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>kill.tunnel</span>(<span class='no'>settings</span>, <span class='kw'>exe</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
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diff --git a/base/remote/docs/reference/open_tunnel.html b/base/remote/docs/reference/open_tunnel.html
index bd19572..82383dd 100644
--- a/base/remote/docs/reference/open_tunnel.html
+++ b/base/remote/docs/reference/open_tunnel.html
@@ -2,171 +2,226 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Open an SSH tunnel, prompting for passwords as needed — open_tunnel •
+      PEcAn.remote
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Open an SSH tunnel, prompting for passwords as needed — open_tunnel"
+    />
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+    <meta
+      property="og:description"
+      content="Open an SSH tunnel, prompting for passwords as needed"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Open an SSH tunnel, prompting for passwords as needed</h1>
-    
-    <div class="hidden name"><code>open_tunnel.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Open an SSH tunnel, prompting for passwords as needed</h1>
 
-    <div class="ref-description">
-    
-    <p>Open an SSH tunnel, prompting for passwords as needed</p>
-    
-    </div>
+            <div class="hidden name"><code>open_tunnel.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>open_tunnel</span>(<span class='no'>remote_host</span>, <span class='kw'>user</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>password</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>Open an SSH tunnel, prompting for passwords as needed</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>open_tunnel</span>(<span class='no'>remote_host</span>, <span class='kw'>user</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>password</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>tunnel_dir</span> <span class='kw'>=</span> <span class='st'>"~/.pecan/tunnel/"</span>, <span class='kw'>wait.time</span> <span class='kw'>=</span> <span class='fl'>15</span>,
   <span class='kw'>tunnel_script</span> <span class='kw'>=</span> <span class='st'>"~/pecan/web/sshtunnel.sh"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>remote_host</th>
-      <td><p>name of remote server to connect to (e.g. geo.bu.edu)</p></td>
-    </tr>
-    <tr>
-      <th>user</th>
-      <td><p>username on remote_host</p></td>
-    </tr>
-    <tr>
-      <th>password</th>
-      <td><p>password on remote_host</p></td>
-    </tr>
-    <tr>
-      <th>tunnel_dir</th>
-      <td><p>directory to store tunnel file in, typically from settings$host</p></td>
-    </tr>
-    <tr>
-      <th>wait.time</th>
-      <td><p>how long to give system to connect before deleting password (seconds)</p></td>
-    </tr>
-    <tr>
-      <th>tunnel_script</th>
-      <td><p>Path to sshtunnel.sh script file for opening tunnel</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>numeric giving ssh PID if configured, otherwise logical with TRUE = success</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>remote_host</th>
+              <td>
+                <p>name of remote server to connect to (e.g. geo.bu.edu)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>user</th>
+              <td><p>username on remote_host</p></td>
+            </tr>
+            <tr>
+              <th>password</th>
+              <td><p>password on remote_host</p></td>
+            </tr>
+            <tr>
+              <th>tunnel_dir</th>
+              <td>
+                <p>
+                  directory to store tunnel file in, typically from
+                  settings$host
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>wait.time</th>
+              <td>
+                <p>
+                  how long to give system to connect before deleting password
+                  (seconds)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>tunnel_script</th>
+              <td>
+                <p>Path to sshtunnel.sh script file for opening tunnel</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            numeric giving ssh PID if configured, otherwise logical with TRUE =
+            success
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
-
diff --git a/base/remote/docs/reference/qsub_get_jobid.html b/base/remote/docs/reference/qsub_get_jobid.html
index eb08fc6..9a349ef 100644
--- a/base/remote/docs/reference/qsub_get_jobid.html
+++ b/base/remote/docs/reference/qsub_get_jobid.html
@@ -2,158 +2,199 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    />
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   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get Job ID from qsub output</h1>
-    
-    <div class="hidden name"><code>qsub_get_jobid.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get Job ID from qsub output</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>qsub_get_jobid</span>(<span class='no'>out</span>, <span class='no'>qsub.jobid</span>, <span class='no'>stop.on.error</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>out</th>
-      <td><p>Output from model execution, as a character.</p></td>
-    </tr>
-    <tr>
-      <th>qsub.jobid</th>
-      <td><p>(character) Regular expression string for extracting job ID from qsub output.
-Usually from <code>settings$host$qsub.jobid</code></p></td>
-    </tr>
-    <tr>
-      <th>stop.on.error</th>
-      <td><p>Throw error if <em>any</em> of the runs fails. Default TRUE.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Job ID, as a string</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get Job ID from qsub output</h1>
+
+            <div class="hidden name"><code>qsub_get_jobid.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get Job ID from qsub output</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>qsub_get_jobid</span>(<span class='no'>out</span>, <span class='no'>qsub.jobid</span>, <span class='no'>stop.on.error</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>out</th>
+              <td><p>Output from model execution, as a character.</p></td>
+            </tr>
+            <tr>
+              <th>qsub.jobid</th>
+              <td>
+                <p>
+                  (character) Regular expression string for extracting job ID
+                  from qsub output. Usually from
+                  <code>settings$host$qsub.jobid</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>stop.on.error</th>
+              <td>
+                <p>
+                  Throw error if <em>any</em> of the runs fails. Default TRUE.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Job ID, as a string</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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   </body>
 </html>
-
diff --git a/base/remote/docs/reference/qsub_run_finished.html b/base/remote/docs/reference/qsub_run_finished.html
index aa82bc3..139c571 100644
--- a/base/remote/docs/reference/qsub_run_finished.html
+++ b/base/remote/docs/reference/qsub_run_finished.html
@@ -2,157 +2,189 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
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+    />
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+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check if qsub run finished</h1>
-    
-    <div class="hidden name"><code>qsub_run_finished.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check if qsub run finished</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>qsub_run_finished</span>(<span class='no'>run</span>, <span class='no'>host</span>, <span class='no'>qstat</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>run</th>
-      <td><p>run ID, as an integer</p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>host structure to execute command on</p></td>
-    </tr>
-    <tr>
-      <th>qstat</th>
-      <td><p>(string) qstat command for checking job status</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>TRUE</code> if run is marked as DONE, otherwise FALSE.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check if qsub run finished</h1>
+
+            <div class="hidden name"><code>qsub_run_finished.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check if qsub run finished</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>qsub_run_finished</span>(<span class='no'>run</span>, <span class='no'>host</span>, <span class='no'>qstat</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>run</th>
+              <td><p>run ID, as an integer</p></td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td><p>host structure to execute command on</p></td>
+            </tr>
+            <tr>
+              <th>qstat</th>
+              <td><p>(string) qstat command for checking job status</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>TRUE</code> if run is marked as DONE, otherwise FALSE.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/remote.copy.from.html b/base/remote/docs/reference/remote.copy.from.html
index 3bb04a6..88417bd 100644
--- a/base/remote/docs/reference/remote.copy.from.html
+++ b/base/remote/docs/reference/remote.copy.from.html
@@ -2,183 +2,233 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Copy file from remote to local — remote.copy.from • PEcAn.remote</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Copy file from remote to local</h1>
-    
-    <div class="hidden name"><code>remote.copy.from.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Copy file/dir from remote server to local server</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>remote.copy.from</span>(<span class='no'>host</span>, <span class='no'>src</span>, <span class='no'>dst</span>, <span class='kw'>delete</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>host</th>
-      <td><p>list with server, user and optionally tunnel to use.</p></td>
-    </tr>
-    <tr>
-      <th>src</th>
-      <td><p>remote file/dir to copy</p></td>
-    </tr>
-    <tr>
-      <th>dst</th>
-      <td><p>local file/dir to copy to</p></td>
-    </tr>
-    <tr>
-      <th>delete</th>
-      <td><p>in case of local dir should all non-existent files be removed</p></td>
-    </tr>
-    <tr>
-      <th>stderr</th>
-      <td><p>should stderr be returned</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>output of command executed</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Copies the file/dir from the remote server to the local server. If the dst
-is a folder it will copy the file into that folder.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Copy file from remote to local</h1>
+
+            <div class="hidden name"><code>remote.copy.from.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Copy file/dir from remote server to local server</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>remote.copy.from</span>(<span class='no'>host</span>, <span class='no'>src</span>, <span class='no'>dst</span>, <span class='kw'>delete</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>host</th>
+              <td>
+                <p>list with server, user and optionally tunnel to use.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>src</th>
+              <td><p>remote file/dir to copy</p></td>
+            </tr>
+            <tr>
+              <th>dst</th>
+              <td><p>local file/dir to copy to</p></td>
+            </tr>
+            <tr>
+              <th>delete</th>
+              <td>
+                <p>
+                  in case of local dir should all non-existent files be removed
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>stderr</th>
+              <td><p>should stderr be returned</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>output of command executed</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Copies the file/dir from the remote server to the local server. If
+            the dst is a folder it will copy the file into that folder.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='no'>host</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>name</span><span class='kw'>=</span><span class='st'>'geo.bu.edu'</span>, <span class='kw'>user</span><span class='kw'>=</span><span class='st'>'kooper'</span>, <span class='kw'>tunnel</span><span class='kw'>=</span><span class='st'>'/tmp/geo.tunnel'</span>)
   <span class='fu'>remote.copy.from</span>(<span class='no'>host</span>, <span class='st'>'/tmp/kooper'</span>, <span class='st'>'/tmp/geo.tmp'</span>, <span class='kw'>delete</span><span class='kw'>=</span><span class='fl'>TRUE</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
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+
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-
diff --git a/base/remote/docs/reference/remote.copy.to.html b/base/remote/docs/reference/remote.copy.to.html
index 4d9d562..f2944cd 100644
--- a/base/remote/docs/reference/remote.copy.to.html
+++ b/base/remote/docs/reference/remote.copy.to.html
@@ -2,178 +2,225 @@
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+      Copy file/dir to remote server from local server — remote.copy.to •
+      PEcAn.remote
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Copy file/dir to remote server from local server — remote.copy.to"
+    />
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+      property="og:description"
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+is a folder it will copy the file into that folder."
+    />
+    <meta name="twitter:card" content="summary" />
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+                type="button"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Copy file/dir to remote server from local server</h1>
-    
-    <div class="hidden name"><code>remote.copy.to.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Copies the file/dir to the remote server from the local server. If the dst
-is a folder it will copy the file into that folder.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>remote.copy.to</span>(<span class='no'>host</span>, <span class='no'>src</span>, <span class='no'>dst</span>, <span class='kw'>delete</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>host</th>
-      <td><p>host structure to execute command on</p></td>
-    </tr>
-    <tr>
-      <th>src</th>
-      <td><p>local file/dir to copy</p></td>
-    </tr>
-    <tr>
-      <th>dst</th>
-      <td><p>remote file/dir to copy to</p></td>
-    </tr>
-    <tr>
-      <th>delete</th>
-      <td><p>in case of local dir should all non-existent files be removed</p></td>
-    </tr>
-    <tr>
-      <th>stderr</th>
-      <td><p>should stderr be returned as well.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>output of command executed</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Copy file/dir to remote server from local server</h1>
+
+            <div class="hidden name"><code>remote.copy.to.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Copies the file/dir to the remote server from the local server. If
+              the dst is a folder it will copy the file into that folder.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>remote.copy.to</span>(<span class='no'>host</span>, <span class='no'>src</span>, <span class='no'>dst</span>, <span class='kw'>delete</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>host</th>
+              <td><p>host structure to execute command on</p></td>
+            </tr>
+            <tr>
+              <th>src</th>
+              <td><p>local file/dir to copy</p></td>
+            </tr>
+            <tr>
+              <th>dst</th>
+              <td><p>remote file/dir to copy to</p></td>
+            </tr>
+            <tr>
+              <th>delete</th>
+              <td>
+                <p>
+                  in case of local dir should all non-existent files be removed
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>stderr</th>
+              <td><p>should stderr be returned as well.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>output of command executed</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='no'>host</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>name</span><span class='kw'>=</span><span class='st'>'geo.bu.edu'</span>, <span class='kw'>user</span><span class='kw'>=</span><span class='st'>'kooper'</span>, <span class='kw'>tunnel</span><span class='kw'>=</span><span class='st'>'/tmp/geo.tunnel'</span>)
   <span class='fu'>remote.copy.to</span>(<span class='no'>host</span>, <span class='st'>'/tmp/kooper'</span>, <span class='st'>'/tmp/kooper'</span>, <span class='kw'>delete</span><span class='kw'>=</span><span class='fl'>TRUE</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/remote.copy.update.html b/base/remote/docs/reference/remote.copy.update.html
index e8f49d2..8f833af 100644
--- a/base/remote/docs/reference/remote.copy.update.html
+++ b/base/remote/docs/reference/remote.copy.update.html
@@ -2,178 +2,221 @@
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 <html>
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-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Copy to remote and update DB — remote.copy.update • PEcAn.remote
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Copy to remote and update DB — remote.copy.update"
+    />
+
+    <meta property="og:description" content="Copy to remote and update DB" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-        <a class="navbar-link" href="../index.html">PEcAn.remote</a>
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-  <a href="../index.html">
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Copy to remote and update DB</h1>
-    
-    <div class="hidden name"><code>remote.copy.update.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Copy to remote and update DB</h1>
 
-    <div class="ref-description">
-    
-    <p>Copy to remote and update DB</p>
-    
-    </div>
+            <div class="hidden name"><code>remote.copy.update.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Copy to remote and update DB</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>remote.copy.update</span>(<span class='no'>input_id</span>, <span class='no'>remote_dir</span>, <span class='no'>local_file_path</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>remote.copy.update</span>(<span class='no'>input_id</span>, <span class='no'>remote_dir</span>, <span class='no'>local_file_path</span>,
   <span class='kw'>remote_file_name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>host</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>input_id</th>
-      <td><p>Input ID, as a numeric or character</p></td>
-    </tr>
-    <tr>
-      <th>remote_dir</th>
-      <td><p>remote folder path</p></td>
-    </tr>
-    <tr>
-      <th>local_file_path</th>
-      <td><p>full path name to local file that needs to be copied, e.g. "/fs/data1/dbfiles/.../.../*.css"</p></td>
-    </tr>
-    <tr>
-      <th>remote_file_name</th>
-      <td><p>remote file name, no need to provide if it's the same as local</p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>as in settings$host</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>BETY database connection</p></td>
-    </tr>
-    <tr>
-      <th>stderr</th>
-      <td><p>should stderr be returned</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>remote_id remote dbfile record</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>input_id</th>
+              <td><p>Input ID, as a numeric or character</p></td>
+            </tr>
+            <tr>
+              <th>remote_dir</th>
+              <td><p>remote folder path</p></td>
+            </tr>
+            <tr>
+              <th>local_file_path</th>
+              <td>
+                <p>
+                  full path name to local file that needs to be copied, e.g.
+                  "/fs/data1/dbfiles/.../.../*.css"
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>remote_file_name</th>
+              <td>
+                <p>
+                  remote file name, no need to provide if it's the same as local
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td><p>as in settings$host</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>BETY database connection</p></td>
+            </tr>
+            <tr>
+              <th>stderr</th>
+              <td><p>should stderr be returned</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>remote_id remote dbfile record</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/remote.execute.R.html b/base/remote/docs/reference/remote.execute.R.html
index 485fbf9..a4290f2 100644
--- a/base/remote/docs/reference/remote.execute.R.html
+++ b/base/remote/docs/reference/remote.execute.R.html
@@ -2,184 +2,223 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
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-
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Execute command remotely</h1>
-    
-    <div class="hidden name"><code>remote.execute.R.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Execute command remotely</h1>
 
-    <div class="ref-description">
-    
-    <p>Execute command remotely</p>
-    
-    </div>
+            <div class="hidden name"><code>remote.execute.R.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>remote.execute.R</span>(<span class='no'>script</span>, <span class='kw'>host</span> <span class='kw'>=</span> <span class='st'>"localhost"</span>, <span class='kw'>user</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+          <div class="ref-description">
+            <p>Execute command remotely</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>remote.execute.R</span>(<span class='no'>script</span>, <span class='kw'>host</span> <span class='kw'>=</span> <span class='st'>"localhost"</span>, <span class='kw'>user</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
   <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>R</span> <span class='kw'>=</span> <span class='st'>"R"</span>, <span class='kw'>scratchdir</span> <span class='kw'>=</span> <span class='fu'>tempdir</span>())</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>script</th>
-      <td><p>the script to be invoked, as a list of commands.</p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>settings host list</p></td>
-    </tr>
-    <tr>
-      <th>user</th>
-      <td><p>the username to use for remote login</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the output be printed to the console</p></td>
-    </tr>
-    <tr>
-      <th>args</th>
-      <td><p>a character vector of arguments to command.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>the captured output of the command (both stdout and stderr)</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Executes the given command on the remote host using ssh. If the user is set
-the system will login as the given user. If the host given is the local
-machine it will execute the command locally without ssh.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>script</th>
+              <td><p>the script to be invoked, as a list of commands.</p></td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td><p>settings host list</p></td>
+            </tr>
+            <tr>
+              <th>user</th>
+              <td><p>the username to use for remote login</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the output be printed to the console</p></td>
+            </tr>
+            <tr>
+              <th>args</th>
+              <td><p>a character vector of arguments to command.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>the captured output of the command (both stdout and stderr)</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Executes the given command on the remote host using ssh. If the user
+            is set the system will login as the given user. If the host given is
+            the local machine it will execute the command locally without ssh.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>remote.execute.R</span>(<span class='st'>'list.files()'</span>, <span class='kw'>host</span><span class='kw'>=</span><span class='st'>'localhost'</span>, <span class='kw'>verbose</span><span class='kw'>=</span><span class='fl'>FALSE</span>)
 <span class='co'># }</span></pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
+        </div>
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+
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diff --git a/base/remote/docs/reference/remote.execute.cmd.html b/base/remote/docs/reference/remote.execute.cmd.html
index 6809bf7..dfce2f5 100644
--- a/base/remote/docs/reference/remote.execute.cmd.html
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+    />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Execute command remotely</h1>
-    
-    <div class="hidden name"><code>remote.execute.cmd.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Execute command remotely</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>remote.execute.cmd</span>(<span class='no'>host</span>, <span class='no'>cmd</span>, <span class='kw'>args</span> <span class='kw'>=</span> <span class='fu'>character</span>(), <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>host</th>
-      <td><p>host structure to execute command on</p></td>
-    </tr>
-    <tr>
-      <th>args</th>
-      <td><p>a character vector of arguments to command.</p></td>
-    </tr>
-    <tr>
-      <th>stderr</th>
-      <td><p>should stderr be returned as well.</p></td>
-    </tr>
-    <tr>
-      <th>command</th>
-      <td><p>the system command to be invoked, as a character string.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>the captured output of the command (both stdout and stderr)</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Executes the given command on the remote host using ssh. If the user is set
-the system will login as the given user. If the host given is the local
-machine it will execute the command locally without ssh.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Execute command remotely</h1>
+
+            <div class="hidden name"><code>remote.execute.cmd.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Execute command remotely</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>remote.execute.cmd</span>(<span class='no'>host</span>, <span class='no'>cmd</span>, <span class='kw'>args</span> <span class='kw'>=</span> <span class='fu'>character</span>(), <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>host</th>
+              <td><p>host structure to execute command on</p></td>
+            </tr>
+            <tr>
+              <th>args</th>
+              <td><p>a character vector of arguments to command.</p></td>
+            </tr>
+            <tr>
+              <th>stderr</th>
+              <td><p>should stderr be returned as well.</p></td>
+            </tr>
+            <tr>
+              <th>command</th>
+              <td>
+                <p>the system command to be invoked, as a character string.</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>the captured output of the command (both stdout and stderr)</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Executes the given command on the remote host using ssh. If the user
+            is set the system will login as the given user. If the host given is
+            the local machine it will execute the command locally without ssh.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='no'>host</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>name</span><span class='kw'>=</span><span class='st'>'geo.bu.edu'</span>, <span class='kw'>user</span><span class='kw'>=</span><span class='st'>'kooper'</span>, <span class='kw'>tunnel</span><span class='kw'>=</span><span class='st'>'/tmp/geo.tunnel'</span>)
   <span class='fu'>print</span>(<span class='fu'>remote.execute.cmd</span>(<span class='no'>host</span>, <span class='st'>'ls'</span>, <span class='fu'>c</span>(<span class='st'>'-l'</span>, <span class='st'>'/'</span>), <span class='kw'>stderr</span><span class='kw'>=</span><span class='fl'>TRUE</span>))
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Rob Kooper
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/setup_modellauncher.html b/base/remote/docs/reference/setup_modellauncher.html
index b9a5007..79e9a5c 100644
--- a/base/remote/docs/reference/setup_modellauncher.html
+++ b/base/remote/docs/reference/setup_modellauncher.html
@@ -2,159 +2,214 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- jquery -->
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Setup model launcher script and job list — setup_modellauncher •
+      PEcAn.remote
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Setup model launcher script and job list — setup_modellauncher"
+    />
+
+    <meta
+      property="og:description"
+      content="Setup model launcher script and job list"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.remote</a>
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-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Setup model launcher script and job list</h1>
-    
-    <div class="hidden name"><code>setup_modellauncher.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Setup model launcher script and job list</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>setup_modellauncher</span>(<span class='no'>run</span>, <span class='no'>rundir</span>, <span class='no'>host_rundir</span>, <span class='no'>mpirun</span>, <span class='no'>binary</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>run</th>
-      <td><p>(numeric) run ID, as an integer</p></td>
-    </tr>
-    <tr>
-      <th>rundir</th>
-      <td><p>Local run directory. Usually from <code>settings$rundir</code></p></td>
-    </tr>
-    <tr>
-      <th>host_rundir</th>
-      <td><p>Remote host run directory. Usually from <code>settings$host$rundir</code></p></td>
-    </tr>
-    <tr>
-      <th>mpirun</th>
-      <td><p>MPI info, usually from <code>settings$host$modellauncher$mpirun</code></p></td>
-    </tr>
-    <tr>
-      <th>binary</th>
-      <td><p>Binary info, usually from <code>settings$host$modellauncher$binary</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Setup model launcher script and job list</h1>
+
+            <div class="hidden name"><code>setup_modellauncher.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Setup model launcher script and job list</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>setup_modellauncher</span>(<span class='no'>run</span>, <span class='no'>rundir</span>, <span class='no'>host_rundir</span>, <span class='no'>mpirun</span>, <span class='no'>binary</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>run</th>
+              <td><p>(numeric) run ID, as an integer</p></td>
+            </tr>
+            <tr>
+              <th>rundir</th>
+              <td>
+                <p>
+                  Local run directory. Usually from <code>settings$rundir</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>host_rundir</th>
+              <td>
+                <p>
+                  Remote host run directory. Usually from
+                  <code>settings$host$rundir</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>mpirun</th>
+              <td>
+                <p>
+                  MPI info, usually from
+                  <code>settings$host$modellauncher$mpirun</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>binary</th>
+              <td>
+                <p>
+                  Binary info, usually from
+                  <code>settings$host$modellauncher$binary</code>
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/stamp_started.html b/base/remote/docs/reference/stamp_started.html
index 44caeb7..5e78c79 100644
--- a/base/remote/docs/reference/stamp_started.html
+++ b/base/remote/docs/reference/stamp_started.html
@@ -2,155 +2,192 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
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-
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Stamp start and stop times of runs — stamp_started • PEcAn.remote
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
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+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Stamp start and stop times of runs — stamp_started"
+    />
+
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+      property="og:description"
+      content="Stamp start and stop times of runs"
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Stamp start and stop times of runs</h1>
-    
-    <div class="hidden name"><code>stamp_started.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Stamp start and stop times of runs</h1>
 
-    <div class="ref-description">
-    
-    <p>Stamp start and stop times of runs</p>
-    
-    </div>
+            <div class="hidden name"><code>stamp_started.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>stamp_started</span>(<span class='no'>con</span>, <span class='no'>run</span>)
+          <div class="ref-description">
+            <p>Stamp start and stop times of runs</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>stamp_started</span>(<span class='no'>con</span>, <span class='no'>run</span>)
 
 <span class='fu'>stamp_finished</span>(<span class='no'>con</span>, <span class='no'>run</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>con</th>
-      <td><p>BETY database connection</p></td>
-    </tr>
-    <tr>
-      <th>run</th>
-      <td><p>(numeric) run ID</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>NULL</code></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>con</th>
+              <td><p>BETY database connection</p></td>
+            </tr>
+            <tr>
+              <th>run</th>
+              <td><p>(numeric) run ID</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>NULL</code></p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/remote/docs/reference/start.model.runs.html b/base/remote/docs/reference/start.model.runs.html
index e295888..cd22163 100644
--- a/base/remote/docs/reference/start.model.runs.html
+++ b/base/remote/docs/reference/start.model.runs.html
@@ -2,163 +2,209 @@
 <!DOCTYPE html>
 <html>
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+      start.model.runs • PEcAn.remote
+    </title>
+
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+            <div id="navbar" class="navbar-collapse collapse">
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Start selected ecosystem model runs within PEcAn workflow</h1>
-    
-    <div class="hidden name"><code>start.model.runs.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Start selected ecosystem model runs within PEcAn workflow</h1>
 
-    <div class="ref-description">
-    
-    <p>Start selected ecosystem model runs within PEcAn workflow</p>
-    
-    </div>
+            <div class="hidden name"><code>start.model.runs.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for model.runs</span>
+          <div class="ref-description">
+            <p>Start selected ecosystem model runs within PEcAn workflow</p>
+          </div>
+
+          <pre class="usage"><span class='co'># S3 method for model.runs</span>
 <span class='fu'>start</span>(<span class='no'>settings</span>, <span class='kw'>write</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>stop.on.error</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>pecan settings object</p></td>
-    </tr>
-    <tr>
-      <th>write</th>
-      <td><p>(logical) Whether or not to write to the database. Default TRUE.</p></td>
-    </tr>
-    <tr>
-      <th>stop.on.error</th>
-      <td><p>Throw error if <em>any</em> of the runs fails. Default TRUE.</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>pecan settings object</p></td>
+            </tr>
+            <tr>
+              <th>write</th>
+              <td>
+                <p>
+                  (logical) Whether or not to write to the database. Default
+                  TRUE.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>stop.on.error</th>
+              <td>
+                <p>
+                  Throw error if <em>any</em> of the runs fails. Default TRUE.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>start.model.runs</span>(<span class='no'>settings</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Shawn Serbin, Rob Kooper, David LeBauer, Alexey Shiklomanov
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Shawn Serbin, Rob Kooper, David LeBauer, Alexey Shiklomanov
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/start_qsub.html b/base/remote/docs/reference/start_qsub.html
index 276cb32..c874ee4 100644
--- a/base/remote/docs/reference/start_qsub.html
+++ b/base/remote/docs/reference/start_qsub.html
@@ -2,186 +2,256 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Start qsub runs</h1>
-    
-    <div class="hidden name"><code>start_qsub.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Start qsub runs</h1>
 
-    <div class="ref-description">
-    
-    <p>Start qsub runs</p>
-    
-    </div>
+            <div class="hidden name"><code>start_qsub.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>start_qsub</span>(<span class='no'>run</span>, <span class='no'>qsub_string</span>, <span class='no'>rundir</span>, <span class='no'>host</span>, <span class='no'>host_rundir</span>, <span class='no'>host_outdir</span>,
+          <div class="ref-description">
+            <p>Start qsub runs</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>start_qsub</span>(<span class='no'>run</span>, <span class='no'>qsub_string</span>, <span class='no'>rundir</span>, <span class='no'>host</span>, <span class='no'>host_rundir</span>, <span class='no'>host_outdir</span>,
   <span class='no'>stdout_log</span>, <span class='no'>stderr_log</span>, <span class='no'>job_script</span>, <span class='kw'>qsub_extra</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>run</th>
-      <td><p>(numeric) run ID, as an integer</p></td>
-    </tr>
-    <tr>
-      <th>qsub_string</th>
-      <td><p>qsub command string, with arguments. Usually from <code>settings$host$qsub</code></p></td>
-    </tr>
-    <tr>
-      <th>rundir</th>
-      <td><p>Local run directory. Usually from <code>settings$rundir</code></p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>Remote host, as a list or character. Usually from <code>settings$host</code>.</p></td>
-    </tr>
-    <tr>
-      <th>host_rundir</th>
-      <td><p>Remote host run directory. Usually from <code>settings$host$rundir</code></p></td>
-    </tr>
-    <tr>
-      <th>host_outdir</th>
-      <td><p>Remote host output directory. Usually from <code>settings$host$outdir</code></p></td>
-    </tr>
-    <tr>
-      <th>stdout_log</th>
-      <td><p>Logfile for redirecting <code>stdout</code>.</p></td>
-    </tr>
-    <tr>
-      <th>stderr_log</th>
-      <td><p>Logfile for redirecting <code>stderr</code></p></td>
-    </tr>
-    <tr>
-      <th>job_script</th>
-      <td><p>Base name (no path) of script to run. Usually either <code>job.sh</code> or <code>launcher.sh</code>.</p></td>
-    </tr>
-    <tr>
-      <th>qsub_extra</th>
-      <td><p>Extra <code>qsub</code> arguments. Usually from <code>settings$host$modellauncher$qsub.extra</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Output of qsub command, as a character. This output can be parsed for ascertaining submission success.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>run</th>
+              <td><p>(numeric) run ID, as an integer</p></td>
+            </tr>
+            <tr>
+              <th>qsub_string</th>
+              <td>
+                <p>
+                  qsub command string, with arguments. Usually from
+                  <code>settings$host$qsub</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>rundir</th>
+              <td>
+                <p>
+                  Local run directory. Usually from <code>settings$rundir</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td>
+                <p>
+                  Remote host, as a list or character. Usually from
+                  <code>settings$host</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>host_rundir</th>
+              <td>
+                <p>
+                  Remote host run directory. Usually from
+                  <code>settings$host$rundir</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>host_outdir</th>
+              <td>
+                <p>
+                  Remote host output directory. Usually from
+                  <code>settings$host$outdir</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>stdout_log</th>
+              <td>
+                <p>Logfile for redirecting <code>stdout</code>.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>stderr_log</th>
+              <td>
+                <p>Logfile for redirecting <code>stderr</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>job_script</th>
+              <td>
+                <p>
+                  Base name (no path) of script to run. Usually either
+                  <code>job.sh</code> or <code>launcher.sh</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>qsub_extra</th>
+              <td>
+                <p>
+                  Extra <code>qsub</code> arguments. Usually from
+                  <code>settings$host$modellauncher$qsub.extra</code>
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Output of qsub command, as a character. This output can be parsed
+            for ascertaining submission success.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/base/remote/docs/reference/start_rabbitmq.html b/base/remote/docs/reference/start_rabbitmq.html
index 8307151..acfd180 100644
--- a/base/remote/docs/reference/start_rabbitmq.html
+++ b/base/remote/docs/reference/start_rabbitmq.html
@@ -2,139 +2,175 @@
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Start model execution using rabbitmq</h1>
-    
-    <div class="hidden name"><code>start_rabbitmq.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Start model execution using rabbitmq</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>start_rabbitmq</span>(<span class='no'>folder</span>, <span class='no'>rabbitmq_uri</span>, <span class='no'>rabbitmq_queue</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Output of execution command, as a character (see <code><a href='remote.execute.cmd.html'>remote.execute.cmd()</a></code>).</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Start model execution using rabbitmq</h1>
+
+            <div class="hidden name"><code>start_rabbitmq.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Start model execution using rabbitmq</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>start_rabbitmq</span>(<span class='no'>folder</span>, <span class='no'>rabbitmq_uri</span>, <span class='no'>rabbitmq_queue</span>)</pre>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Output of execution command, as a character (see
+            <code
+              ><a href="remote.execute.cmd.html">remote.execute.cmd()</a></code
+            >).
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/remote/docs/reference/start_serial.html b/base/remote/docs/reference/start_serial.html
index 7cce2ab..417dfd9 100644
--- a/base/remote/docs/reference/start_serial.html
+++ b/base/remote/docs/reference/start_serial.html
@@ -2,165 +2,226 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Start model execution in serial mode — start_serial • PEcAn.remote</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Start model execution in serial mode — start_serial • PEcAn.remote
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Start model execution in serial mode — start_serial"
+    />
+
+    <meta
+      property="og:description"
+      content="Start model execution in serial mode"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
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-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+                data-target="#navbar"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Start model execution in serial mode</h1>
-    
-    <div class="hidden name"><code>start_serial.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Start model execution in serial mode</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>start_serial</span>(<span class='no'>run</span>, <span class='no'>host</span>, <span class='no'>rundir</span>, <span class='no'>host_rundir</span>, <span class='no'>job_script</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>run</th>
-      <td><p>(numeric) run ID, as an integer</p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>Remote host, as a list or character. Usually from <code>settings$host</code>.</p></td>
-    </tr>
-    <tr>
-      <th>rundir</th>
-      <td><p>Local run directory. Usually from <code>settings$rundir</code></p></td>
-    </tr>
-    <tr>
-      <th>host_rundir</th>
-      <td><p>Remote host run directory. Usually from <code>settings$host$rundir</code></p></td>
-    </tr>
-    <tr>
-      <th>job_script</th>
-      <td><p>Base name (no path) of script to run. Usually either <code>job.sh</code> or <code>launcher.sh</code>.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Output of execution command, as a character (see <code><a href='remote.execute.cmd.html'>remote.execute.cmd()</a></code>).</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Start model execution in serial mode</h1>
+
+            <div class="hidden name"><code>start_serial.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Start model execution in serial mode</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>start_serial</span>(<span class='no'>run</span>, <span class='no'>host</span>, <span class='no'>rundir</span>, <span class='no'>host_rundir</span>, <span class='no'>job_script</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>run</th>
+              <td><p>(numeric) run ID, as an integer</p></td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td>
+                <p>
+                  Remote host, as a list or character. Usually from
+                  <code>settings$host</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>rundir</th>
+              <td>
+                <p>
+                  Local run directory. Usually from <code>settings$rundir</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>host_rundir</th>
+              <td>
+                <p>
+                  Remote host run directory. Usually from
+                  <code>settings$host$rundir</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>job_script</th>
+              <td>
+                <p>
+                  Base name (no path) of script to run. Usually either
+                  <code>job.sh</code> or <code>launcher.sh</code>.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Output of execution command, as a character (see
+            <code
+              ><a href="remote.execute.cmd.html">remote.execute.cmd()</a></code
+            >).
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
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diff --git a/base/remote/docs/reference/test_remote.html b/base/remote/docs/reference/test_remote.html
index fcec072..50de05e 100644
--- a/base/remote/docs/reference/test_remote.html
+++ b/base/remote/docs/reference/test_remote.html
@@ -2,132 +2,171 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<![endif]-->
-
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Test remote execution — test_remote" />
+
+    <meta property="og:description" content="Test remote execution" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+                <a class="navbar-link" href="../index.html">PEcAn.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  >1.6.0</span
+                >
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Test remote execution</h1>
-    
-    <div class="hidden name"><code>test_remote.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Test remote execution</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>test_remote</span>(<span class='no'>host</span>, <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>host</th>
-      <td><p>host structure to execute command on</p></td>
-    </tr>
-    <tr>
-      <th>stderr</th>
-      <td><p>should stderr be returned as well.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>TRUE</code> is remote execution is successful.
-If unsuccessful, depends on the value of <code>stderr</code>.
-If <code>stderr</code> = TRUE (default), this function will throw an error.
-If <code>stderr</code> = FALSE, this function will print a logger error and return FALSE.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Test remote execution</h1>
+
+            <div class="hidden name"><code>test_remote.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Test remote execution</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>test_remote</span>(<span class='no'>host</span>, <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>host</th>
+              <td><p>host structure to execute command on</p></td>
+            </tr>
+            <tr>
+              <th>stderr</th>
+              <td><p>should stderr be returned as well.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            <code>TRUE</code> is remote execution is successful. If
+            unsuccessful, depends on the value of <code>stderr</code>. If
+            <code>stderr</code> = TRUE (default), this function will throw an
+            error. If <code>stderr</code> = FALSE, this function will print a
+            logger error and return FALSE.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='co'># Localhost execution should always work</span>
 <span class='no'>good_host</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>name</span> <span class='kw'>=</span> <span class='st'>"localhost"</span>)
 <span class='fu'>test_remote</span>(<span class='no'>good_host</span>)
@@ -137,34 +176,30 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
   <span class='fu'>print</span>(<span class='st'>"Big Bad Wolf is a bad host."</span>)
 }
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/settings/docs/LICENSE-text.html b/base/settings/docs/LICENSE-text.html
index c37170f..f175839 100644
--- a/base/settings/docs/LICENSE-text.html
+++ b/base/settings/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
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+                <a class="navbar-link" href="index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+
+            <div id="navbar" class="navbar-collapse collapse">
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-      <h1>License</h1>
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+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
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-
+</pre
+          >
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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 </html>
-
diff --git a/base/settings/docs/authors.html b/base/settings/docs/authors.html
index 2051155..19725f5 100644
--- a/base/settings/docs/authors.html
+++ b/base/settings/docs/authors.html
@@ -2,126 +2,146 @@
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 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/docsearch.css b/base/settings/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/base/settings/docs/docsearch.css
+++ b/base/settings/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/base/settings/docs/docsearch.js b/base/settings/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/base/settings/docs/docsearch.js
+++ b/base/settings/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/base/settings/docs/index.html b/base/settings/docs/index.html
index beb0600..89e230c 100644
--- a/base/settings/docs/index.html
+++ b/base/settings/docs/index.html
@@ -1,103 +1,155 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn Settings package • PEcAn.settings</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn Settings package">
-<meta property="og:description" content="Contains functions to read PEcAn settings files">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn Settings package • PEcAn.settings</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta property="og:title" content="PEcAn Settings package" />
+    <meta
+      property="og:description"
+      content="Contains functions to read PEcAn settings files"
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    Contains functions to read PEcAn settings files
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          Contains functions to read PEcAn settings files
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/base/settings/docs/pkgdown.css b/base/settings/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/base/settings/docs/pkgdown.css
+++ b/base/settings/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/base/settings/docs/pkgdown.js b/base/settings/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/base/settings/docs/pkgdown.js
+++ b/base/settings/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/base/settings/docs/reference/MultiSettings.html b/base/settings/docs/reference/MultiSettings.html
index 342bb5e..6e77db5 100644
--- a/base/settings/docs/reference/MultiSettings.html
+++ b/base/settings/docs/reference/MultiSettings.html
@@ -2,137 +2,166 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Create a PEcAn MultiSettings object — MultiSettings • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Create a PEcAn MultiSettings object — MultiSettings" />
-
-<meta property="og:description" content="Create a PEcAn MultiSettings object" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Create a PEcAn MultiSettings object — MultiSettings • PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Create a PEcAn MultiSettings object — MultiSettings"
+    />
+
+    <meta
+      property="og:description"
+      content="Create a PEcAn MultiSettings object"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create a PEcAn MultiSettings object</h1>
-    
-    <div class="hidden name"><code>MultiSettings.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create a PEcAn MultiSettings object</h1>
 
-    <div class="ref-description">
-    
-    <p>Create a PEcAn MultiSettings object</p>
-    
-    </div>
+            <div class="hidden name"><code>MultiSettings.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>MultiSettings</span>(<span class='no'>...</span>)</pre>
-        
+          <div class="ref-description">
+            <p>Create a PEcAn MultiSettings object</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>MultiSettings</span>(<span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/SafeList.html b/base/settings/docs/reference/SafeList.html
index 0e99d57..559de16 100644
--- a/base/settings/docs/reference/SafeList.html
+++ b/base/settings/docs/reference/SafeList.html
@@ -2,187 +2,237 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Constrct SafeList Object — SafeList • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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+                <span
+                  class="label label-default"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Constrct SafeList Object</h1>
-    
-    <div class="hidden name"><code>SafeList.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Constrct SafeList Object</h1>
 
-    <div class="ref-description">
-    
-    <p>Create a SafeList object</p>
-    
-    </div>
+            <div class="hidden name"><code>SafeList.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Create a SafeList object</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>SafeList</span>(<span class='no'>...</span>)
+          <pre
+            class="usage"
+          ><span class='fu'>SafeList</span>(<span class='no'>...</span>)
 
 <span class='fu'>as.SafeList</span>(<span class='no'>x</span>)
 
 <span class='fu'>is.SafeList</span>(<span class='no'>x</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>...</th>
-      <td><p>A list to upgrade to SafeList, or elements to be added to a new SafeList</p></td>
-    </tr>
-    <tr>
-      <th>x</th>
-      <td><p>list to coerce</p></td>
-    </tr>
-    <tr>
-      <th>x</th>
-      <td><p>list object to be tested</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>The resulting SafeList</p>
-<p>a SafeList version of x</p>
-<p>logical</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>SafeList is a wrapper class for the normal R list. It should behave identically, except for
-the $ operator being overridden to require exact matches.</p>
-<p>The constructor works identical to list(...) unless:</p>
-<p>1) The only argument is a list, in which case the result is the same list, with its class
-attribute updated to include 'SafeList', or
-2) The only argument is a SafeList, in which case that argument is returned unchanged</p>
-    
-    <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2>
-
-    <ul>
-<li><p><code>as.SafeList</code>: Coerce an object to SafeList.</p></li>
-<li><p><code>is.SafeList</code>: Test if object is already a SafeList.</p></li>
-</ul>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#functions">Functions</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  A list to upgrade to SafeList, or elements to be added to a
+                  new SafeList
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>x</th>
+              <td><p>list to coerce</p></td>
+            </tr>
+            <tr>
+              <th>x</th>
+              <td><p>list object to be tested</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>The resulting SafeList</p>
+          <p>a SafeList version of x</p>
+          <p>logical</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            SafeList is a wrapper class for the normal R list. It should behave
+            identically, except for the $ operator being overridden to require
+            exact matches.
+          </p>
+          <p>The constructor works identical to list(...) unless:</p>
+          <p>
+            1) The only argument is a list, in which case the result is the same
+            list, with its class attribute updated to include 'SafeList', or 2)
+            The only argument is a SafeList, in which case that argument is
+            returned unchanged
+          </p>
+
+          <h2 class="hasAnchor" id="functions">
+            <a class="anchor" href="#functions"></a>Functions
+          </h2>
+
+          <ul>
+            <li>
+              <p><code>as.SafeList</code>: Coerce an object to SafeList.</p>
+            </li>
+            <li>
+              <p>
+                <code>is.SafeList</code>: Test if object is already a SafeList.
+              </p>
+            </li>
           </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+            <li><a href="#value">Value</a></li>
 
-  </div>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#functions">Functions</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Ryan Kelly
+        </div>
+      </div>
 
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-
diff --git a/base/settings/docs/reference/Settings.html b/base/settings/docs/reference/Settings.html
index 1e04b15..bab1996 100644
--- a/base/settings/docs/reference/Settings.html
+++ b/base/settings/docs/reference/Settings.html
@@ -2,147 +2,177 @@
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+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-<div class="row">
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-    <h1>Create a PEcAn Settings object</h1>
-    
-    <div class="hidden name"><code>Settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Create a PEcAn Settings object</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>Settings</span>(<span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>...</th>
-      <td><p>TODO</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Ryan Kelly
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create a PEcAn Settings object</h1>
+
+            <div class="hidden name"><code>Settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Create a PEcAn Settings object</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>Settings</span>(<span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>...</th>
+              <td><p>TODO</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/addSecrets.html b/base/settings/docs/reference/addSecrets.html
index dfefc30..5d8ab28 100644
--- a/base/settings/docs/reference/addSecrets.html
+++ b/base/settings/docs/reference/addSecrets.html
@@ -2,162 +2,198 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Add Users secrets — addSecrets • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Add Users secrets — addSecrets" />
-
-<meta property="og:description" content="Add secret information from ~/.pecan.xml" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Add Users secrets — addSecrets • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Add Users secrets — addSecrets" />
+
+    <meta
+      property="og:description"
+      content="Add secret information from ~/.pecan.xml"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Add Users secrets</h1>
-    
-    <div class="hidden name"><code>addSecrets.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Add secret information from ~/.pecan.xml</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>addSecrets</span>(<span class='no'>settings</span>, <span class='kw'>force</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>will return the updated settings values</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Copies certains sections from ~/.pecan.xml to the settings. This allows
-a user to have their own unique parameters also when sharing the
-pecan.xml file we don't expose these secrets.
-Currently this will copy the database and browndog sections</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Add Users secrets</h1>
+
+            <div class="hidden name"><code>addSecrets.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Add secret information from ~/.pecan.xml</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>addSecrets</span>(<span class='no'>settings</span>, <span class='kw'>force</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>will return the updated settings values</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Copies certains sections from ~/.pecan.xml to the settings. This
+            allows a user to have their own unique parameters also when sharing
+            the pecan.xml file we don't expose these secrets. Currently this
+            will copy the database and browndog sections
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/cash-.SafeList.html b/base/settings/docs/reference/cash-.SafeList.html
index b124c87..7204ad3 100644
--- a/base/settings/docs/reference/cash-.SafeList.html
+++ b/base/settings/docs/reference/cash-.SafeList.html
@@ -2,165 +2,206 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Extract SafeList component by name — $.SafeList • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Extract SafeList component by name — $.SafeList" />
-
-<meta property="og:description" content="Extract SafeList component by name" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Extract SafeList component by name — $.SafeList • PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Extract SafeList component by name — $.SafeList"
+    />
+
+    <meta
+      property="og:description"
+      content="Extract SafeList component by name"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Extract SafeList component by name</h1>
-    
-    <div class="hidden name"><code>cash-.SafeList.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Extract SafeList component by name</p>
-    
-    </div>
-
-    <pre class="usage"># S3 method for SafeList
-$(x, name)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>the SafeList object</p></td>
-    </tr>
-    <tr>
-      <th>name</th>
-      <td><p>the name of the component</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>The specified component</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Overrides `$`.list, and works just like it except forces exact match 
-(i.e., makes x$name behave exactly like x[[name, exact=T]])</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Extract SafeList component by name</h1>
+
+            <div class="hidden name"><code>cash-.SafeList.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Extract SafeList component by name</p>
+          </div>
+
+          <pre class="usage">
+# S3 method for SafeList
+$(x, name)</pre
+          >
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>the SafeList object</p></td>
+            </tr>
+            <tr>
+              <th>name</th>
+              <td><p>the name of the component</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>The specified component</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Overrides `$`.list, and works just like it except forces exact match
+            (i.e., makes x$name behave exactly like x[[name, exact=T]])
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/check.bety.version.html b/base/settings/docs/reference/check.bety.version.html
index 4ffbfca..b85eae1 100644
--- a/base/settings/docs/reference/check.bety.version.html
+++ b/base/settings/docs/reference/check.bety.version.html
@@ -2,143 +2,173 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Check BETY Version — check.bety.version • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Check BETY Version — check.bety.version" />
-
-<meta property="og:description" content="Check BETY Version" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Check BETY Version — check.bety.version • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Check BETY Version — check.bety.version"
+    />
+
+    <meta property="og:description" content="Check BETY Version" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check BETY Version</h1>
-    
-    <div class="hidden name"><code>check.bety.version.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check BETY Version</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.bety.version</span>(<span class='no'>dbcon</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check BETY Version</h1>
+
+            <div class="hidden name"><code>check.bety.version.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check BETY Version</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.bety.version</span>(<span class='no'>dbcon</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/check.database.html b/base/settings/docs/reference/check.database.html
index d8b3a7d..c8a4e14 100644
--- a/base/settings/docs/reference/check.database.html
+++ b/base/settings/docs/reference/check.database.html
@@ -2,143 +2,170 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Check Database — check.database • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Check Database — check.database" />
-
-<meta property="og:description" content="Check Database" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Check Database — check.database • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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   </head>
 
   <body>
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+            <div class="navbar-header">
+              <button
+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+              </ul>
+
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check Database</h1>
-    
-    <div class="hidden name"><code>check.database.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check Database</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.database</span>(<span class='no'>database</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check Database</h1>
+
+            <div class="hidden name"><code>check.database.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check Database</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.database</span>(<span class='no'>database</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/base/settings/docs/reference/check.database.settings.html b/base/settings/docs/reference/check.database.settings.html
index ef60280..61ee4c1 100644
--- a/base/settings/docs/reference/check.database.settings.html
+++ b/base/settings/docs/reference/check.database.settings.html
@@ -2,143 +2,177 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- clipboard.js -->
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-<script src="../pkgdown.js"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Check Database Settings — check.database.settings • PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Check Database Settings — check.database.settings"
+    />
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+    <meta property="og:description" content="Check Database Settings" />
+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
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-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../reference/index.html">Reference</a>
-</li>
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-  </div><!--/.container -->
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check Database Settings</h1>
-    
-    <div class="hidden name"><code>check.database.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check Database Settings</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.database.settings</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check Database Settings</h1>
+
+            <div class="hidden name">
+              <code>check.database.settings.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check Database Settings</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.database.settings</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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   </body>
 </html>
-
diff --git a/base/settings/docs/reference/check.ensemble.settings.html b/base/settings/docs/reference/check.ensemble.settings.html
index 46d2309..29c5ee5 100644
--- a/base/settings/docs/reference/check.ensemble.settings.html
+++ b/base/settings/docs/reference/check.ensemble.settings.html
@@ -2,143 +2,177 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Check ensemble Settings — check.ensemble.settings • PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
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+    ></script>
+
+    <!-- sticky kit -->
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+                <span
+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+
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+        <!--/.navbar -->
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check ensemble Settings</h1>
-    
-    <div class="hidden name"><code>check.ensemble.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check ensemble Settings</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.ensemble.settings</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check ensemble Settings</h1>
+
+            <div class="hidden name">
+              <code>check.ensemble.settings.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check ensemble Settings</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.ensemble.settings</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/base/settings/docs/reference/check.inputs.html b/base/settings/docs/reference/check.inputs.html
index 5bffa0b..83399fe 100644
--- a/base/settings/docs/reference/check.inputs.html
+++ b/base/settings/docs/reference/check.inputs.html
@@ -2,143 +2,176 @@
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 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- clipboard.js -->
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-
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-<link href="../pkgdown.css" rel="stylesheet">
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Check Inputs — check.inputs • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Check Inputs — check.inputs" />
+
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+      property="og:description"
+      content="check to see if inputs are specified - this should be part of the model code"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check Inputs</h1>
-    
-    <div class="hidden name"><code>check.inputs.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>check to see if inputs are specified - this should be part of the model code</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.inputs</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check Inputs</h1>
+
+            <div class="hidden name"><code>check.inputs.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              check to see if inputs are specified - this should be part of the
+              model code
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.inputs</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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   </body>
 </html>
-
diff --git a/base/settings/docs/reference/check.model.settings.html b/base/settings/docs/reference/check.model.settings.html
index 715d565..c1e86e3 100644
--- a/base/settings/docs/reference/check.model.settings.html
+++ b/base/settings/docs/reference/check.model.settings.html
@@ -2,143 +2,173 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
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-
-<!-- sticky kit -->
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-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>Check Model Settings — check.model.settings • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Check Model Settings — check.model.settings"
+    />
+
+    <meta property="og:description" content="Check Model Settings" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check Model Settings</h1>
-    
-    <div class="hidden name"><code>check.model.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check Model Settings</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.model.settings</span>(<span class='no'>settings</span>, <span class='kw'>dbcon</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check Model Settings</h1>
+
+            <div class="hidden name"><code>check.model.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check Model Settings</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.model.settings</span>(<span class='no'>settings</span>, <span class='kw'>dbcon</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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   </body>
 </html>
-
diff --git a/base/settings/docs/reference/check.run.settings.html b/base/settings/docs/reference/check.run.settings.html
index da630eb..bf66f95 100644
--- a/base/settings/docs/reference/check.run.settings.html
+++ b/base/settings/docs/reference/check.run.settings.html
@@ -2,143 +2,173 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Check Run Settings — check.run.settings" />
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-<meta name="twitter:card" content="summary" />
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Check Run Settings — check.run.settings • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Check Run Settings — check.run.settings"
+    />
+
+    <meta property="og:description" content="Check Run Settings" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
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-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
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-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check Run Settings</h1>
-    
-    <div class="hidden name"><code>check.run.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check Run Settings</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.run.settings</span>(<span class='no'>settings</span>, <span class='kw'>dbcon</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check Run Settings</h1>
+
+            <div class="hidden name"><code>check.run.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check Run Settings</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.run.settings</span>(<span class='no'>settings</span>, <span class='kw'>dbcon</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/check.settings.html b/base/settings/docs/reference/check.settings.html
index d88080f..0ebc711 100644
--- a/base/settings/docs/reference/check.settings.html
+++ b/base/settings/docs/reference/check.settings.html
@@ -2,162 +2,201 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Check Settings — check.settings • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Check Settings — check.settings" />
-
-<meta property="og:description" content="Sanity checks. Checks the settings file to make sure expected fields exist. It will try to use
-default values for any missing values, or stop the exection if no defaults are possible." />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Check Settings — check.settings • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Check Settings — check.settings" />
+
+    <meta
+      property="og:description"
+      content="Sanity checks. Checks the settings file to make sure expected fields exist. It will try to use
+default values for any missing values, or stop the exection if no defaults are possible."
+    />
+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check Settings</h1>
-    
-    <div class="hidden name"><code>check.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Sanity checks. Checks the settings file to make sure expected fields exist. It will try to use
-default values for any missing values, or stop the exection if no defaults are possible.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.settings</span>(<span class='no'>settings</span>, <span class='kw'>force</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>will return the updated settings values with defaults set.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Expected fields in settings file are:
-- pfts with at least one pft defined</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check Settings</h1>
+
+            <div class="hidden name"><code>check.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Sanity checks. Checks the settings file to make sure expected
+              fields exist. It will try to use default values for any missing
+              values, or stop the exection if no defaults are possible.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.settings</span>(<span class='no'>settings</span>, <span class='kw'>force</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>will return the updated settings values with defaults set.</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Expected fields in settings file are: - pfts with at least one pft
+            defined
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper, David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper, David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/check.workflow.settings.html b/base/settings/docs/reference/check.workflow.settings.html
index ee90662..e9f02ba 100644
--- a/base/settings/docs/reference/check.workflow.settings.html
+++ b/base/settings/docs/reference/check.workflow.settings.html
@@ -2,143 +2,177 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Check Workflow Settings — check.workflow.settings" />
-
-<meta property="og:description" content="Check Workflow Settings" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Check Workflow Settings — check.workflow.settings • PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Check Workflow Settings — check.workflow.settings"
+    />
+
+    <meta property="og:description" content="Check Workflow Settings" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-      <ul class="nav navbar-nav">
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-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check Workflow Settings</h1>
-    
-    <div class="hidden name"><code>check.workflow.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check Workflow Settings</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.workflow.settings</span>(<span class='no'>settings</span>, <span class='kw'>dbcon</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check Workflow Settings</h1>
+
+            <div class="hidden name">
+              <code>check.workflow.settings.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check Workflow Settings</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.workflow.settings</span>(<span class='no'>settings</span>, <span class='kw'>dbcon</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/clean.settings.html b/base/settings/docs/reference/clean.settings.html
index 20f4dea..fe19d50 100644
--- a/base/settings/docs/reference/clean.settings.html
+++ b/base/settings/docs/reference/clean.settings.html
@@ -2,169 +2,213 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Cleans PEcAn settings file — clean.settings • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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+    ></script>
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+      crossorigin="anonymous"
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+
+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      property="og:title"
+      content="Cleans PEcAn settings file — clean.settings"
+    />
+
+    <meta
+      property="og:description"
+      content="This will try and clean the settings file so it is ready for
 a new run. This will remove all run specific information and
-set the outdir to be 'pecan' for the next run." />
-<meta name="twitter:card" content="summary" />
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+set the outdir to be 'pecan' for the next run."
+    />
+    <meta name="twitter:card" content="summary" />
 
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   </head>
 
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
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+
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Cleans PEcAn settings file</h1>
-    
-    <div class="hidden name"><code>clean.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This will try and clean the settings file so it is ready for
-a new run. This will remove all run specific information and
-set the outdir to be 'pecan' for the next run.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>clean.settings</span>(<span class='kw'>inputfile</span> <span class='kw'>=</span> <span class='st'>"pecan.xml"</span>, <span class='kw'>outputfile</span> <span class='kw'>=</span> <span class='st'>"pecan.xml"</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Cleans PEcAn settings file</h1>
+
+            <div class="hidden name"><code>clean.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This will try and clean the settings file so it is ready for a new
+              run. This will remove all run specific information and set the
+              outdir to be 'pecan' for the next run.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>clean.settings</span>(<span class='kw'>inputfile</span> <span class='kw'>=</span> <span class='st'>"pecan.xml"</span>, <span class='kw'>outputfile</span> <span class='kw'>=</span> <span class='st'>"pecan.xml"</span>,
   <span class='kw'>write</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>inputfile</th>
-      <td><p>the PEcAn settings file to be used.</p></td>
-    </tr>
-    <tr>
-      <th>outputfile</th>
-      <td><p>the name of file to which the settings will be
-written inside the outputdir.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list of all settings as saved to the XML file(s)</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>inputfile</th>
+              <td><p>the PEcAn settings file to be used.</p></td>
+            </tr>
+            <tr>
+              <th>outputfile</th>
+              <td>
+                <p>
+                  the name of file to which the settings will be written inside
+                  the outputdir.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list of all settings as saved to the XML file(s)</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>clean.settings</span>(<span class='st'>'output/PEcAn_1/pecan.xml'</span>, <span class='st'>'pecan.xml'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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 </html>
-
diff --git a/base/settings/docs/reference/createMultiSiteSettings.html b/base/settings/docs/reference/createMultiSiteSettings.html
index def9d99..1a7ec0c 100644
--- a/base/settings/docs/reference/createMultiSiteSettings.html
+++ b/base/settings/docs/reference/createMultiSiteSettings.html
@@ -2,139 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<meta property="og:title" content="Transform Settings into multi-site MultiSettings — createMultiSiteSettings" />
-
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-sites" />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Transform Settings into multi-site MultiSettings — createMultiSiteSettings
+      • PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Transform Settings into multi-site MultiSettings — createMultiSiteSettings"
+    />
+
+    <meta
+      property="og:description"
+      content="Create a MultiSettings object containing (identical) run blocks for multiple different
+sites"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Transform Settings into multi-site MultiSettings</h1>
-    
-    <div class="hidden name"><code>createMultiSiteSettings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Create a MultiSettings object containing (identical) run blocks for multiple different
-sites</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>createMultiSiteSettings</span>(<span class='no'>templateSettings</span>, <span class='no'>siteIds</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>templateSettings</th>
-      <td><p>A <code><a href='Settings.html'>Settings</a></code> object that will be the template for the resulting
-MultiSettings.</p></td>
-    </tr>
-    <tr>
-      <th>siteIds</th>
-      <td><p>The site IDs to be used in the resulting MultiSettings</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A <code>MultiSettings</code> object with the same settings as <code>templateSettings</code> but replicated
-<code>run$site</code> blocks, one for each specified site ID.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Starts with a template settings object, and duplicates the <code>run$site</code> block once for each
-specified site ID. The resulting MultiSettings is thus identical to the input, except ready to run
-for each site in the vector of site IDs.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Transform Settings into multi-site MultiSettings</h1>
+
+            <div class="hidden name">
+              <code>createMultiSiteSettings.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Create a MultiSettings object containing (identical) run blocks
+              for multiple different sites
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>createMultiSiteSettings</span>(<span class='no'>templateSettings</span>, <span class='no'>siteIds</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>templateSettings</th>
+              <td>
+                <p>
+                  A <code><a href="Settings.html">Settings</a></code> object
+                  that will be the template for the resulting MultiSettings.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>siteIds</th>
+              <td>
+                <p>The site IDs to be used in the resulting MultiSettings</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A <code>MultiSettings</code> object with the same settings as
+            <code>templateSettings</code> but replicated
+            <code>run$site</code> blocks, one for each specified site ID.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Starts with a template settings object, and duplicates the
+            <code>run$site</code> block once for each specified site ID. The
+            resulting MultiSettings is thus identical to the input, except ready
+            to run for each site in the vector of site IDs.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>dontrun</span> <span class='kw'>&lt;-</span> <span class='kw'>function</span>() { <span class='co'>## Added by Alexey Shiklomanov so this doesn't run and break the build</span>
 
 <span class='co'># This isn't necessarily a fully working settings object. Enough to get the idea though. </span>
@@ -206,40 +269,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 
 } <span class='co'># dontrun</span>
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Ryan Kelly
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Ryan Kelly
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/createSitegroupMultiSettings.html b/base/settings/docs/reference/createSitegroupMultiSettings.html
index 61d6794..24f43a1 100644
--- a/base/settings/docs/reference/createSitegroupMultiSettings.html
+++ b/base/settings/docs/reference/createSitegroupMultiSettings.html
@@ -2,149 +2,227 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Create Sitegroup MultiSettings — createSitegroupMultiSettings • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Create Sitegroup MultiSettings — createSitegroupMultiSettings" />
-
-<meta property="og:description" content="Helps to create a MultiSettings object to run some or all sites in a Sitegroup." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Create Sitegroup MultiSettings — createSitegroupMultiSettings •
+      PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Create Sitegroup MultiSettings — createSitegroupMultiSettings"
+    />
+
+    <meta
+      property="og:description"
+      content="Helps to create a MultiSettings object to run some or all sites in a Sitegroup."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create Sitegroup MultiSettings</h1>
-    
-    <div class="hidden name"><code>createSitegroupMultiSettings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Helps to create a MultiSettings object to run some or all sites in a Sitegroup.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>createSitegroupMultiSettings</span>(<span class='no'>templateSettings</span>, <span class='no'>sitegroupId</span>, <span class='no'>nSite</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create Sitegroup MultiSettings</h1>
+
+            <div class="hidden name">
+              <code>createSitegroupMultiSettings.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Helps to create a MultiSettings object to run some or all sites in
+              a Sitegroup.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>createSitegroupMultiSettings</span>(<span class='no'>templateSettings</span>, <span class='no'>sitegroupId</span>, <span class='no'>nSite</span>,
   <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='no'>templateSettings</span>$<span class='no'>database</span>$<span class='no'>bety</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>templateSettings</th>
-      <td><p>A <code><a href='Settings.html'>Settings</a></code> object that will be the template for the resulting
-MultiSettings.</p></td>
-    </tr>
-    <tr>
-      <th>sitegroupId</th>
-      <td><p>The Bety ID of the sitegroup to draw from</p></td>
-    </tr>
-    <tr>
-      <th>nSite</th>
-      <td><p>The number of sites to randomly select (without replacement) from the siteGroup. Omit
-to use all sites in the group.</p></td>
-    </tr>
-    <tr>
-      <th>con, params</th>
-      <td><p>Bety DB connection or parameters. passed directly to <code><a href='http://www.rdocumentation.org/packages/PEcAn.DB/topics/db.query'>db.query</a></code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A <code>MultiSettings</code> object with the same settings as <code>templateSettings</code> but site
-information for the selected sites</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Starts with a template settings object, and fills in the <code>run</code> block with site info sampled from
-the sitegroup. The template could be fully set up except for the site info, or more or less empty if you 
-plan to fill in the other settings later. A <code><a href='MultiSettings.html'>MultiSettings</a></code> is created from <code>templateSettings</code>,
-<code>nSite</code> sites (or all of them, if <code>nSite</code> is unset) are selected from Bety, and their info
-is dropped into the <code>MultiSettings</code>.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>templateSettings</th>
+              <td>
+                <p>
+                  A <code><a href="Settings.html">Settings</a></code> object
+                  that will be the template for the resulting MultiSettings.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sitegroupId</th>
+              <td><p>The Bety ID of the sitegroup to draw from</p></td>
+            </tr>
+            <tr>
+              <th>nSite</th>
+              <td>
+                <p>
+                  The number of sites to randomly select (without replacement)
+                  from the siteGroup. Omit to use all sites in the group.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>con, params</th>
+              <td>
+                <p>
+                  Bety DB connection or parameters. passed directly to
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/PEcAn.DB/topics/db.query"
+                      >db.query</a
+                    ></code
+                  >
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A <code>MultiSettings</code> object with the same settings as
+            <code>templateSettings</code> but site information for the selected
+            sites
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Starts with a template settings object, and fills in the
+            <code>run</code> block with site info sampled from the sitegroup.
+            The template could be fully set up except for the site info, or more
+            or less empty if you plan to fill in the other settings later. A
+            <code><a href="MultiSettings.html">MultiSettings</a></code> is
+            created from <code>templateSettings</code>, <code>nSite</code> sites
+            (or all of them, if <code>nSite</code> is unset) are selected from
+            Bety, and their info is dropped into the <code>MultiSettings</code>.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>dontrun</span> <span class='kw'>&lt;-</span> <span class='kw'>function</span>() { <span class='co'>## Added by Alexey Shiklomanov so this doesn't run and break the build</span>
 
 <span class='co'># This isn't necessarily a fully working settings object. Enough to get the idea though. </span>
@@ -216,40 +294,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 
 } <span class='co'># dontrun</span>
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Ryan Kelly
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Ryan Kelly
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/fix.deprecated.settings.html b/base/settings/docs/reference/fix.deprecated.settings.html
index 4185fc0..bdb89dc 100644
--- a/base/settings/docs/reference/fix.deprecated.settings.html
+++ b/base/settings/docs/reference/fix.deprecated.settings.html
@@ -2,153 +2,192 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Fix Deprecated Settings — fix.deprecated.settings • PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Fix Deprecated Settings — fix.deprecated.settings"
+    />
+
+    <meta
+      property="og:description"
+      content="Checks for and attempts to fix deprecated settings structure"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Fix Deprecated Settings</h1>
-    
-    <div class="hidden name"><code>fix.deprecated.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Checks for and attempts to fix deprecated settings structure</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>fix.deprecated.settings</span>(<span class='no'>settings</span>, <span class='kw'>force</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings list</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>updated settings list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Fix Deprecated Settings</h1>
+
+            <div class="hidden name">
+              <code>fix.deprecated.settings.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Checks for and attempts to fix deprecated settings structure</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>fix.deprecated.settings</span>(<span class='no'>settings</span>, <span class='kw'>force</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings list</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>updated settings list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/getRunSettings.html b/base/settings/docs/reference/getRunSettings.html
index b21d8cf..0431835 100644
--- a/base/settings/docs/reference/getRunSettings.html
+++ b/base/settings/docs/reference/getRunSettings.html
@@ -2,147 +2,183 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Build run MultiSettings for a list of site id's — getRunSettings" />
-
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-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Build run MultiSettings for a list of site id's — getRunSettings •
+      PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Build run MultiSettings for a list of site id's — getRunSettings"
+    />
+
+    <meta
+      property="og:description"
+      content="Build run MultiSettings for a list of site id's"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="../reference/index.html">Reference</a>
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-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Build run MultiSettings for a list of site id's</h1>
-    
-    <div class="hidden name"><code>getRunSettings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Build run MultiSettings for a list of site id's</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>getRunSettings</span>(<span class='no'>templateSettings</span>, <span class='no'>siteId</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>templateSettings</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>siteId</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Build run MultiSettings for a list of site id's</h1>
+
+            <div class="hidden name"><code>getRunSettings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Build run MultiSettings for a list of site id's</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>getRunSettings</span>(<span class='no'>templateSettings</span>, <span class='no'>siteId</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>templateSettings</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>siteId</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/index.html b/base/settings/docs/reference/index.html
index f9a0815..8e6647c 100644
--- a/base/settings/docs/reference/index.html
+++ b/base/settings/docs/reference/index.html
@@ -2,300 +2,447 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-<title>Function reference • PEcAn.settings</title>
+    <title>Function reference • PEcAn.settings</title>
 
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
 
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
 
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
 
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
 
+    <meta property="og:title" content="Function reference" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
 
-      
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="MultiSettings.html">MultiSettings()</a></code> </p>
-        </td>
-        <td><p>Create a PEcAn MultiSettings object</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="SafeList.html">SafeList()</a></code> <code><a href="SafeList.html">as.SafeList()</a></code> <code><a href="SafeList.html">is.SafeList()</a></code> </p>
-        </td>
-        <td><p>Constrct SafeList Object</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="Settings.html">Settings()</a></code> </p>
-        </td>
-        <td><p>Create a PEcAn Settings object</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="addSecrets.html">addSecrets()</a></code> </p>
-        </td>
-        <td><p>Add Users secrets</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="cash-.SafeList.html">`$`(<i>&lt;SafeList&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Extract SafeList component by name</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.bety.version.html">check.bety.version()</a></code> </p>
-        </td>
-        <td><p>Check BETY Version</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.database.html">check.database()</a></code> </p>
-        </td>
-        <td><p>Check Database</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.database.settings.html">check.database.settings()</a></code> </p>
-        </td>
-        <td><p>Check Database Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.ensemble.settings.html">check.ensemble.settings()</a></code> </p>
-        </td>
-        <td><p>Check ensemble Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.inputs.html">check.inputs()</a></code> </p>
-        </td>
-        <td><p>Check Inputs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.model.settings.html">check.model.settings()</a></code> </p>
-        </td>
-        <td><p>Check Model Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.run.settings.html">check.run.settings()</a></code> </p>
-        </td>
-        <td><p>Check Run Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.settings.html">check.settings()</a></code> </p>
-        </td>
-        <td><p>Check Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.workflow.settings.html">check.workflow.settings()</a></code> </p>
-        </td>
-        <td><p>Check Workflow Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="clean.settings.html">clean.settings()</a></code> </p>
-        </td>
-        <td><p>Cleans PEcAn settings file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="createMultiSiteSettings.html">createMultiSiteSettings()</a></code> </p>
-        </td>
-        <td><p>Transform Settings into multi-site MultiSettings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="createSitegroupMultiSettings.html">createSitegroupMultiSettings()</a></code> </p>
-        </td>
-        <td><p>Create Sitegroup MultiSettings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="fix.deprecated.settings.html">fix.deprecated.settings()</a></code> </p>
-        </td>
-        <td><p>Fix Deprecated Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="getRunSettings.html">getRunSettings()</a></code> </p>
-        </td>
-        <td><p>Build run MultiSettings for a list of site id's</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="listToXml.default.html">listToXml(<i>&lt;default&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>List to XML</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="papply.html">papply()</a></code> </p>
-        </td>
-        <td><p>Apply functions to PEcAn MultiSettings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="prepare.settings.html">prepare.settings()</a></code> </p>
-        </td>
-        <td><p>Prepare Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.settings.html">read.settings()</a></code> </p>
-        </td>
-        <td><p>Loads PEcAn settings file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="setDates.html">setDates()</a></code> </p>
-        </td>
-        <td><p>Set the Dates of PEcAn Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="setOutDir.html">setOutDir()</a></code> </p>
-        </td>
-        <td><p>Set the Ouptu Directories of PEcAn Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="update.settings.html">update(<i>&lt;settings&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Update Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.settings.html">write.settings()</a></code> </p>
-        </td>
-        <td><p>Write settings</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="MultiSettings.html">MultiSettings()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create a PEcAn MultiSettings object</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="SafeList.html">SafeList()</a></code>
+                    <code><a href="SafeList.html">as.SafeList()</a></code>
+                    <code><a href="SafeList.html">is.SafeList()</a></code>
+                  </p>
+                </td>
+                <td><p>Constrct SafeList Object</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="Settings.html">Settings()</a></code>
+                  </p>
+                </td>
+                <td><p>Create a PEcAn Settings object</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="addSecrets.html">addSecrets()</a></code>
+                  </p>
+                </td>
+                <td><p>Add Users secrets</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="cash-.SafeList.html"
+                        >`$`(<i>&lt;SafeList&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Extract SafeList component by name</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check.bety.version.html"
+                        >check.bety.version()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check BETY Version</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check.database.html">check.database()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check Database</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check.database.settings.html"
+                        >check.database.settings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check Database Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check.ensemble.settings.html"
+                        >check.ensemble.settings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check ensemble Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="check.inputs.html">check.inputs()</a></code>
+                  </p>
+                </td>
+                <td><p>Check Inputs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check.model.settings.html"
+                        >check.model.settings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check Model Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check.run.settings.html"
+                        >check.run.settings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check Run Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check.settings.html">check.settings()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check.workflow.settings.html"
+                        >check.workflow.settings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check Workflow Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="clean.settings.html">clean.settings()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Cleans PEcAn settings file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="createMultiSiteSettings.html"
+                        >createMultiSiteSettings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Transform Settings into multi-site MultiSettings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="createSitegroupMultiSettings.html"
+                        >createSitegroupMultiSettings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create Sitegroup MultiSettings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="fix.deprecated.settings.html"
+                        >fix.deprecated.settings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Fix Deprecated Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="getRunSettings.html">getRunSettings()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Build run MultiSettings for a list of site id's</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="listToXml.default.html"
+                        >listToXml(<i>&lt;default&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>List to XML</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="papply.html">papply()</a></code>
+                  </p>
+                </td>
+                <td><p>Apply functions to PEcAn MultiSettings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="prepare.settings.html"
+                        >prepare.settings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Prepare Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.settings.html">read.settings()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Loads PEcAn settings file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="setDates.html">setDates()</a></code>
+                  </p>
+                </td>
+                <td><p>Set the Dates of PEcAn Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="setOutDir.html">setOutDir()</a></code>
+                  </p>
+                </td>
+                <td><p>Set the Ouptu Directories of PEcAn Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="update.settings.html"
+                        >update(<i>&lt;settings&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Update Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.settings.html">write.settings()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write settings</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/listToXml.default.html b/base/settings/docs/reference/listToXml.default.html
index 0a79ab3..89f9634 100644
--- a/base/settings/docs/reference/listToXml.default.html
+++ b/base/settings/docs/reference/listToXml.default.html
@@ -2,164 +2,198 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>List to XML — listToXml.default • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="List to XML — listToXml.default" />
-
-<meta property="og:description" content="Convert List to XML" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>List to XML — listToXml.default • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="List to XML — listToXml.default" />
+
+    <meta property="og:description" content="Convert List to XML" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>List to XML</h1>
-    
-    <div class="hidden name"><code>listToXml.default.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>List to XML</h1>
 
-    <div class="ref-description">
-    
-    <p>Convert List to XML</p>
-    
-    </div>
+            <div class="hidden name"><code>listToXml.default.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert List to XML</p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for default</span>
+          <pre class="usage"><span class='co'># S3 method for default</span>
 <span class='fu'>listToXml</span>(<span class='no'>item</span>, <span class='no'>tag</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>item</th>
-      <td><p>object to be converted. Despite the function name, need not actually be a list</p></td>
-    </tr>
-    <tr>
-      <th>tag</th>
-      <td><p>xml tag</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>xmlNode</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Can convert list or other object to an xml object using xmlNode</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>item</th>
+              <td>
+                <p>
+                  object to be converted. Despite the function name, need not
+                  actually be a list
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>tag</th>
+              <td><p>xml tag</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>xmlNode</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Can convert list or other object to an xml object using xmlNode</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson, Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Carl Davidson, Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/papply.html b/base/settings/docs/reference/papply.html
index 4f77d44..e31c46b 100644
--- a/base/settings/docs/reference/papply.html
+++ b/base/settings/docs/reference/papply.html
@@ -2,158 +2,256 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Apply functions to PEcAn MultiSettings — papply • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Apply functions to PEcAn MultiSettings — papply" />
-
-<meta property="og:description" content="Works like lapply(), but for PEcAn Settings and MultiSettings objects" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Apply functions to PEcAn MultiSettings — papply • PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Apply functions to PEcAn MultiSettings — papply"
+    />
+
+    <meta
+      property="og:description"
+      content="Works like lapply(), but for PEcAn Settings and MultiSettings objects"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
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+                type="button"
+                class="navbar-toggle collapsed"
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+                data-target="#navbar"
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Apply functions to PEcAn MultiSettings</h1>
-    
-    <div class="hidden name"><code>papply.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Works like lapply(), but for PEcAn Settings and MultiSettings objects</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>papply</span>(<span class='no'>settings</span>, <span class='no'>fn</span>, <span class='no'>...</span>, <span class='kw'>stop.on.error</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>A <code><a href='MultiSettings.html'>MultiSettings</a></code>, <code><a href='Settings.html'>Settings</a></code>, or <code><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></code>
-to operate on</p></td>
-    </tr>
-    <tr>
-      <th>fn</th>
-      <td><p>The function to apply to <code>settings</code></p></td>
-    </tr>
-    <tr>
-      <th>stop.on.error</th>
-      <td><p>Whether to halt execution if a single element in <code>settings</code> results 
-in error. See Details.</p></td>
-    </tr>
-    <tr>
-      <th><code>...</code></th>
-      <td><p>additional arguments to <code>fn</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A single <code>fn</code> return value, or a list of such values (coerced to <code>MultiSettings</code> 
-if appropriate; <em>see Details</em>)</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><code>papply</code> is mainly used to call a function on each <code><a href='Settings.html'>Settings</a></code> object in a 
-<code><a href='MultiSettings.html'>MultiSettings</a></code> object, and returning the results in a list. It has some additional 
-features, however:</p>
-<ul>
-<li><p>If the result of <code>fn</code> is a <code>Settings</code> object, then <code>papply</code> will coerce the 
-returned list into a new <code>MultiSettings</code>.</p></li>
-<li><p>If <code>settings</code> is a <code>Settings</code> object, then <code>papply</code> knows to call <code>fn</code> on 
-it directly.</p></li>
-<li><p>If <code>settings</code> is a generic <code>list</code>, then <code>papply</code> coerces it to a
-  <code>Settings</code> object and then calls <code>fn</code> on it directly. This is meant for backwards
-  compatibility with old-fashioned PEcAn settings lists, but could have unintended consequences</p></li>
-<li><p>By default, <code>papply</code> will proceed even if <code>fn</code> throws an error for one or more
-  of the elements in <code>settings</code>. Note that if this option is used, the returned results 
-  list will have entries for <em>only</em> those elements that did not result in an error.</p></li>
-</ul>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Apply functions to PEcAn MultiSettings</h1>
+
+            <div class="hidden name"><code>papply.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Works like lapply(), but for PEcAn Settings and MultiSettings
+              objects
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>papply</span>(<span class='no'>settings</span>, <span class='no'>fn</span>, <span class='no'>...</span>, <span class='kw'>stop.on.error</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  A <code><a href="MultiSettings.html">MultiSettings</a></code
+                  >, <code><a href="Settings.html">Settings</a></code
+                  >, or
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/base/topics/list"
+                      >list</a
+                    ></code
+                  >
+                  to operate on
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>fn</th>
+              <td>
+                <p>The function to apply to <code>settings</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>stop.on.error</th>
+              <td>
+                <p>
+                  Whether to halt execution if a single element in
+                  <code>settings</code> results in error. See Details.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th><code>...</code></th>
+              <td>
+                <p>additional arguments to <code>fn</code></p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A single <code>fn</code> return value, or a list of such values
+            (coerced to <code>MultiSettings</code> if appropriate;
+            <em>see Details</em>)
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            <code>papply</code> is mainly used to call a function on each
+            <code><a href="Settings.html">Settings</a></code> object in a
+            <code><a href="MultiSettings.html">MultiSettings</a></code> object,
+            and returning the results in a list. It has some additional
+            features, however:
+          </p>
+          <ul>
+            <li>
+              <p>
+                If the result of <code>fn</code> is a
+                <code>Settings</code> object, then <code>papply</code> will
+                coerce the returned list into a new <code>MultiSettings</code>.
+              </p>
+            </li>
+            <li>
+              <p>
+                If <code>settings</code> is a <code>Settings</code> object, then
+                <code>papply</code> knows to call <code>fn</code> on it
+                directly.
+              </p>
+            </li>
+            <li>
+              <p>
+                If <code>settings</code> is a generic <code>list</code>, then
+                <code>papply</code> coerces it to a <code>Settings</code> object
+                and then calls <code>fn</code> on it directly. This is meant for
+                backwards compatibility with old-fashioned PEcAn settings lists,
+                but could have unintended consequences
+              </p>
+            </li>
+            <li>
+              <p>
+                By default, <code>papply</code> will proceed even if
+                <code>fn</code> throws an error for one or more of the elements
+                in <code>settings</code>. Note that if this option is used, the
+                returned results list will have entries for <em>only</em> those
+                elements that did not result in an error.
+              </p>
+            </li>
+          </ul>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>f</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>settings</span>, <span class='no'>...</span>) {
   <span class='co'># Here's how I envisioned a typical use case within a standard PEcAn function</span>
   <span class='kw'>if</span>(<span class='fu'>is.MultiSettings</span>(<span class='no'>settings</span>)) {
@@ -182,40 +280,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='fu'>print</span>(<span class='fu'>f</span>(<span class='no'>multiSettings</span>, <span class='kw'>d</span><span class='kw'>=</span><span class='st'>"D"</span>), <span class='fl'>TRUE</span>)
 
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Ryan Kelly
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Ryan Kelly
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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   </body>
 </html>
-
diff --git a/base/settings/docs/reference/prepare.settings.html b/base/settings/docs/reference/prepare.settings.html
index 1d60c20..4bd9317 100644
--- a/base/settings/docs/reference/prepare.settings.html
+++ b/base/settings/docs/reference/prepare.settings.html
@@ -2,160 +2,200 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Prepare Settings — prepare.settings" />
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+      property="og:description"
+      content="Update, set defaults for, and otherwise prepare a PEcAn Settings object"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
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-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Prepare Settings</h1>
-    
-    <div class="hidden name"><code>prepare.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Update, set defaults for, and otherwise prepare a PEcAn Settings object</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>prepare.settings</span>(<span class='no'>settings</span>, <span class='kw'>force</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings list</p></td>
-    </tr>
-    <tr>
-      <th>force</th>
-      <td><p>Whether to force the function to run even if it determines it has been run on 
-these settings already.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Performs various checks, fixes deprecated contructs, and assigns missing values where possible.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Prepare Settings</h1>
+
+            <div class="hidden name"><code>prepare.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Update, set defaults for, and otherwise prepare a PEcAn Settings
+              object
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>prepare.settings</span>(<span class='no'>settings</span>, <span class='kw'>force</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings list</p></td>
+            </tr>
+            <tr>
+              <th>force</th>
+              <td>
+                <p>
+                  Whether to force the function to run even if it determines it
+                  has been run on these settings already.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Performs various checks, fixes deprecated contructs, and assigns
+            missing values where possible.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-Betsy Cowdery
-
-  </div>
-</div>
+          Ryan Kelly Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/read.settings.html b/base/settings/docs/reference/read.settings.html
index e9698c8..6b5ca4b 100644
--- a/base/settings/docs/reference/read.settings.html
+++ b/base/settings/docs/reference/read.settings.html
@@ -2,37 +2,66 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Loads PEcAn settings file — read.settings • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Loads PEcAn settings file — read.settings" />
-
-<meta property="og:description" content="This will try and find the PEcAn settings file in the following order:
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Loads PEcAn settings file — read.settings • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Loads PEcAn settings file — read.settings"
+    />
+
+    <meta
+      property="og:description"
+      content="This will try and find the PEcAn settings file in the following order:
 --settings &amp;lt;file&amp;gt;passed as command line argument using --settings
 inputfilepassed as argument to function
 PECAN_SETTINGSenvironment variable PECAN_SETTINGS pointing to a specific file
@@ -40,108 +69,144 @@
 Once the function finds a valid file, it will not look further. 
 Thus, if inputfile is supplied, PECAN_SETTINGS will be ignored. 
 Even if a file argument is passed, it will be ignored if a file is passed through
-a higher priority method." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+a higher priority method."
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Loads PEcAn settings file</h1>
-    
-    <div class="hidden name"><code>read.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This will try and find the PEcAn settings file in the following order:</p><ol>
-<li><p>--settings &lt;file&gt;passed as command line argument using --settings</p></li>
-<li><p>inputfilepassed as argument to function</p></li>
-<li><p>PECAN_SETTINGSenvironment variable PECAN_SETTINGS pointing to a specific file</p></li>
-<li><p>./pecan.xmlpecan.xml in the current folder</p></li>
-</ol><p>Once the function finds a valid file, it will not look further. 
-Thus, if <code>inputfile</code> is supplied, <code>PECAN_SETTINGS</code> will be ignored. 
-Even if a <code>file</code> argument is passed, it will be ignored if a file is passed through
-a higher priority method.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read.settings</span>(<span class='kw'>inputfile</span> <span class='kw'>=</span> <span class='st'>"pecan.xml"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>inputfile</th>
-      <td><p>the PEcAn settings file to be used.</p></td>
-    </tr>
-    <tr>
-      <th>outputfile</th>
-      <td><p>the name of file to which the settings will be
-written inside the outputdir. If set to null nothing is saved.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list of all settings as loaded from the XML file(s)</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"># NOT RUN {
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Loads PEcAn settings file</h1>
+
+            <div class="hidden name"><code>read.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This will try and find the PEcAn settings file in the following
+              order:
+            </p>
+            <ol>
+              <li>
+                <p>
+                  --settings &lt;file&gt;passed as command line argument using
+                  --settings
+                </p>
+              </li>
+              <li><p>inputfilepassed as argument to function</p></li>
+              <li>
+                <p>
+                  PECAN_SETTINGSenvironment variable PECAN_SETTINGS pointing to
+                  a specific file
+                </p>
+              </li>
+              <li><p>./pecan.xmlpecan.xml in the current folder</p></li>
+            </ol>
+            <p>
+              Once the function finds a valid file, it will not look further.
+              Thus, if <code>inputfile</code> is supplied,
+              <code>PECAN_SETTINGS</code> will be ignored. Even if a
+              <code>file</code> argument is passed, it will be ignored if a file
+              is passed through a higher priority method.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read.settings</span>(<span class='kw'>inputfile</span> <span class='kw'>=</span> <span class='st'>"pecan.xml"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>inputfile</th>
+              <td><p>the PEcAn settings file to be used.</p></td>
+            </tr>
+            <tr>
+              <th>outputfile</th>
+              <td>
+                <p>
+                  the name of file to which the settings will be written inside
+                  the outputdir. If set to null nothing is saved.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list of all settings as loaded from the XML file(s)</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples">
+# NOT RUN {
 ## bash shell:
 ## example workflow.R and pecan.xml files in pecan/tests
 R --vanilla -- --settings path/to/mypecan.xml < workflow.R 
@@ -153,47 +218,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 test.settings.file <- system.file("tests/test.xml", package = "PEcAn.all")
 settings <- read.settings(test.settings.file)
 # }
-</pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Shawn Serbin
+</pre
+          >
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-Rob Kooper
+            <li><a href="#value">Value</a></li>
 
-David LeBauer
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-Ryan Kelly
+          <h2>Author</h2>
 
-Betsy Cowdery
-
-  </div>
-</div>
+          Shawn Serbin Rob Kooper David LeBauer Ryan Kelly Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/setDates.html b/base/settings/docs/reference/setDates.html
index 95cbd06..42f5f45 100644
--- a/base/settings/docs/reference/setDates.html
+++ b/base/settings/docs/reference/setDates.html
@@ -2,165 +2,213 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Set the Dates of PEcAn Settings — setDates • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Set the Dates of PEcAn Settings — setDates" />
-
-<meta property="og:description" content="Sets the run, ensemble, and sensitivity analysis dates of PEcAn Settings" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Set the Dates of PEcAn Settings — setDates • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Set the Dates of PEcAn Settings — setDates"
+    />
+
+    <meta
+      property="og:description"
+      content="Sets the run, ensemble, and sensitivity analysis dates of PEcAn Settings"
+    />
+    <meta name="twitter:card" content="summary" />
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
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+                  title="Released package"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Set the Dates of PEcAn Settings</h1>
-    
-    <div class="hidden name"><code>setDates.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Sets the run, ensemble, and sensitivity analysis dates of PEcAn Settings</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>setDates</span>(<span class='no'>settings</span>, <span class='no'>startDate</span>, <span class='no'>endDate</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>A <code><a href='Settings.html'>Settings</a></code> object</p></td>
-    </tr>
-    <tr>
-      <th>startDate, endDate</th>
-      <td><p>The desired start and end dates</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>The original <code>Settings</code> object with updated dates</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Sets the start/end dates in <code>settings$run</code> to the specified dates, and sets the corresponding 
-years for <code>settings$ensemble</code> and <code>settings$sensitivity.analysis</code>. Either date can be 
-omitted to leave it unchanged.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Set the Dates of PEcAn Settings</h1>
+
+            <div class="hidden name"><code>setDates.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Sets the run, ensemble, and sensitivity analysis dates of PEcAn
+              Settings
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>setDates</span>(<span class='no'>settings</span>, <span class='no'>startDate</span>, <span class='no'>endDate</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  A <code><a href="Settings.html">Settings</a></code> object
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>startDate, endDate</th>
+              <td><p>The desired start and end dates</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>The original <code>Settings</code> object with updated dates</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Sets the start/end dates in <code>settings$run</code> to the
+            specified dates, and sets the corresponding years for
+            <code>settings$ensemble</code> and
+            <code>settings$sensitivity.analysis</code>. Either date can be
+            omitted to leave it unchanged.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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   </body>
 </html>
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diff --git a/base/settings/docs/reference/setOutDir.html b/base/settings/docs/reference/setOutDir.html
index 7d5b4cb..e2b33bd 100644
--- a/base/settings/docs/reference/setOutDir.html
+++ b/base/settings/docs/reference/setOutDir.html
@@ -2,166 +2,219 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Set the Ouptu Directories of PEcAn Settings — setOutDir • PEcAn.settings
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
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+      crossorigin="anonymous"
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+    />
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+      property="og:description"
+      content="Sets the main output directory and nulls out the others"
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Set the Ouptu Directories of PEcAn Settings</h1>
-    
-    <div class="hidden name"><code>setOutDir.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Sets the main output directory and nulls out the others</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>setOutDir</span>(<span class='no'>settings</span>, <span class='no'>outDir</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>A <code><a href='Settings.html'>Settings</a></code> object</p></td>
-    </tr>
-    <tr>
-      <th>outDir</th>
-      <td><p>The desired output directory</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>The original <code>Settings</code> object with updated output directories</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Sets the main output directory (<code>settings$outdir</code>) to <code>outDir</code>, and sets numerous others
-(<code>settings$modeloutdir</code>, <code>settings$host$rundir</code>, <code>settings$host$outdir</code>, 
-<code>settings$host$modeloutdir</code>) to NULL so they will revert to defaults when 
-<code><a href='check.settings.html'>check.settings</a></code> is run.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Set the Ouptu Directories of PEcAn Settings</h1>
+
+            <div class="hidden name"><code>setOutDir.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Sets the main output directory and nulls out the others</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>setOutDir</span>(<span class='no'>settings</span>, <span class='no'>outDir</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  A <code><a href="Settings.html">Settings</a></code> object
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outDir</th>
+              <td><p>The desired output directory</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            The original <code>Settings</code> object with updated output
+            directories
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Sets the main output directory (<code>settings$outdir</code>) to
+            <code>outDir</code>, and sets numerous others
+            (<code>settings$modeloutdir</code>,
+            <code>settings$host$rundir</code>,
+            <code>settings$host$outdir</code>,
+            <code>settings$host$modeloutdir</code>) to NULL so they will revert
+            to defaults when
+            <code><a href="check.settings.html">check.settings</a></code> is
+            run.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/update.settings.html b/base/settings/docs/reference/update.settings.html
index 7365d45..a153449 100644
--- a/base/settings/docs/reference/update.settings.html
+++ b/base/settings/docs/reference/update.settings.html
@@ -2,156 +2,188 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Update Settings — update.settings • PEcAn.settings</title>
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-<!-- Bootstrap -->
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Update Settings — update.settings" />
+
+    <meta
+      property="og:description"
+      content="Updates a pecan.xml file to match new layout. This will take care of the
+conversion to the latest pecan.xml file."
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Update Settings</h1>
-    
-    <div class="hidden name"><code>update.settings.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Update Settings</h1>
 
-    <div class="ref-description">
-    
-    <p>Updates a pecan.xml file to match new layout. This will take care of the
-conversion to the latest pecan.xml file.</p>
-    
-    </div>
+            <div class="hidden name"><code>update.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Updates a pecan.xml file to match new layout. This will take care
+              of the conversion to the latest pecan.xml file.
+            </p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for settings</span>
+          <pre class="usage"><span class='co'># S3 method for settings</span>
 <span class='fu'>update</span>(<span class='no'>settings</span>, <span class='kw'>force</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>will return the updated settings values</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>will return the updated settings values</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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-  
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+    </div>
   </body>
 </html>
-
diff --git a/base/settings/docs/reference/write.settings.html b/base/settings/docs/reference/write.settings.html
index d4476a3..1aedb4a 100644
--- a/base/settings/docs/reference/write.settings.html
+++ b/base/settings/docs/reference/write.settings.html
@@ -2,157 +2,188 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Write settings — write.settings • PEcAn.settings</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-
-<meta property="og:title" content="Write settings — write.settings" />
-
-<meta property="og:description" content="Takes in a settings object, performs a series of checks, fixes &amp;amp; updates settings and produces pecan.CHECKED.xml" />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Write settings — write.settings • PEcAn.settings</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Write settings — write.settings" />
+
+    <meta
+      property="og:description"
+      content="Takes in a settings object, performs a series of checks, fixes &amp;amp; updates settings and produces pecan.CHECKED.xml"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.settings</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-</li>
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-  <a href="../reference/index.html">Reference</a>
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-        
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-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.settings</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write settings</h1>
-    
-    <div class="hidden name"><code>write.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Takes in a settings object, performs a series of checks, fixes &amp; updates settings and produces pecan.CHECKED.xml</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.settings</span>(<span class='no'>settings</span>, <span class='no'>outputfile</span>, <span class='kw'>outputdir</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>outdir</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings list</p></td>
-    </tr>
-    <tr>
-      <th>outputfile</th>
-      <td><p>the file name to write to</p></td>
-    </tr>
-    <tr>
-      <th>outputdir</th>
-      <td><p>the directory to write to</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Ryan Kelly
-
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write settings</h1>
+
+            <div class="hidden name"><code>write.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Takes in a settings object, performs a series of checks, fixes
+              &amp; updates settings and produces pecan.CHECKED.xml
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.settings</span>(<span class='no'>settings</span>, <span class='no'>outputfile</span>, <span class='kw'>outputdir</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>outdir</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings list</p></td>
+            </tr>
+            <tr>
+              <th>outputfile</th>
+              <td><p>the file name to write to</p></td>
+            </tr>
+            <tr>
+              <th>outputdir</th>
+              <td><p>the directory to write to</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Ryan Kelly Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/LICENSE-text.html b/base/utils/docs/LICENSE-text.html
index 3eab9b5..4e1ae65 100644
--- a/base/utils/docs/LICENSE-text.html
+++ b/base/utils/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
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-
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-
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-
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+
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
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+    <!-- clipboard.js -->
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+    ></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <a class="navbar-link" href="index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="reference/index.html">Reference</a>
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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+    </div>
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 </html>
-
diff --git a/base/utils/docs/authors.html b/base/utils/docs/authors.html
index 977c320..c269a90 100644
--- a/base/utils/docs/authors.html
+++ b/base/utils/docs/authors.html
@@ -2,146 +2,161 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- jquery -->
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-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
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+    <![endif]-->
   </head>
 
   <body>
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       <header>
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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       </footer>
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   </body>
 </html>
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diff --git a/base/utils/docs/docsearch.css b/base/utils/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/base/utils/docs/docsearch.css
+++ b/base/utils/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/base/utils/docs/docsearch.js b/base/utils/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/base/utils/docs/docsearch.js
+++ b/base/utils/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/base/utils/docs/index.html b/base/utils/docs/index.html
index 721da8e..dc78802 100644
--- a/base/utils/docs/index.html
+++ b/base/utils/docs/index.html
@@ -1,117 +1,171 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for ecological forecasts and
-    reanalysis • PEcAn.utils</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and
-    reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis • PEcAn.utils
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and
+    reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer
     (PEcAn) is a scientific workflow management tool that
     is designed to simplify the management of model
     parameterization, execution, and analysis. The goal of
     PEcAn is to streamline the interaction between data and
     models, and to improve the efficacy of scientific
-    investigation.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer
-    (PEcAn) is a scientific workflow management tool that
-    is designed to simplify the management of model
-    parameterization, execution, and analysis. The goal of
-    PEcAn is to streamline the interaction between data and
-    models, and to improve the efficacy of scientific
-    investigation.
-  </div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PEcAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-  </div>
-</div>
-
-
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/base/utils/docs/pkgdown.css b/base/utils/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/base/utils/docs/pkgdown.css
+++ b/base/utils/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/base/utils/docs/pkgdown.js b/base/utils/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/base/utils/docs/pkgdown.js
+++ b/base/utils/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
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@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/base/utils/docs/reference/PEcAn.html b/base/utils/docs/reference/PEcAn.html
index ba30635..1ec47ef 100644
--- a/base/utils/docs/reference/PEcAn.html
+++ b/base/utils/docs/reference/PEcAn.html
@@ -2,151 +2,214 @@
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 <html>
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-
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>
+      R package to support PEcAn, the Predictive Ecosystem Analyzer — PEcAn •
+      PEcAn.utils
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
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+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="R package to support PEcAn, the Predictive Ecosystem Analyzer — PEcAn"
+    />
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+    <meta
+      property="og:description"
+      content="Instructions for the use of this package are provided in the project documentation https://pecan.gitbooks.io/pecan-documentation/content/."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>R package to support PEcAn, the Predictive Ecosystem Analyzer</h1>
-    
-    <div class="hidden name"><code>PEcAn.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Instructions for the use of this package are provided in the project documentation <a href='https://pecan.gitbooks.io/pecan-documentation/content/'>https://pecan.gitbooks.io/pecan-documentation/content/</a>.</p>
-    
-    </div>
-
-        
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Project homepage: <a href='pecanproject.org'>pecanproject.org</a></p>
-<p>Description of PEcAn</p>
-<p>The Predictive Ecosystem Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. PEcAn is an open source utility that encapsulates:</p>
-<p>1. acquisition of meteorological inputs
-2. synthesis of physiological trait data as the posterior distribution of a Bayesian meta-analysis
-3. sampling trait meta-analysis posterior distributions to parameterize ensembles of ED2 and other ecophysiological models
-4. probabilistic forecasts
-5. postprocessing to constrain forecasts and model parameters with field, meterological, eddy flux, and spectral data, and
-6. provenance tracking</p>
-<p>PECAn integrates available data into ecological forecasts by running ensembles of a terrestrial ecosystem model that is parameterized by the posterior distribution from a meta-analysis of available plant trait data.
-These trait data are assembled from field research and primary literature, and are stored in a PostgreSQL database. Current development focused on biofuel crops uses BETYdb.
-In addition to generating forecasts that reflect available data, PEcAn quantifies the contribution of each parameter to model uncertainty.
-This information informs targeted data collection and synthesis efforts that most efficiently reduce forecast uncertainty.</p>
-<p>Current development is focused on developing PEcAn into a real-time data assimilation and forecasting system. This system will provide a detailed analysis of the past and present ecosystem functioning that seamlessly transitions into forecasts.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              R package to support PEcAn, the Predictive Ecosystem Analyzer
+            </h1>
+
+            <div class="hidden name"><code>PEcAn.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Instructions for the use of this package are provided in the
+              project documentation
+              <a href="https://pecan.gitbooks.io/pecan-documentation/content/"
+                >https://pecan.gitbooks.io/pecan-documentation/content/</a
+              >.
+            </p>
+          </div>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Project homepage: <a href="pecanproject.org">pecanproject.org</a>
+          </p>
+          <p>Description of PEcAn</p>
+          <p>
+            The Predictive Ecosystem Analyzer (PEcAn) is a scientific workflow
+            management tool that is designed to simplify the management of model
+            parameterization, execution, and analysis. The goal of PEcAn is to
+            streamline the interaction between data and models, and to improve
+            the efficacy of scientific investigation. PEcAn is an open source
+            utility that encapsulates:
+          </p>
+          <p>
+            1. acquisition of meteorological inputs 2. synthesis of
+            physiological trait data as the posterior distribution of a Bayesian
+            meta-analysis 3. sampling trait meta-analysis posterior
+            distributions to parameterize ensembles of ED2 and other
+            ecophysiological models 4. probabilistic forecasts 5. postprocessing
+            to constrain forecasts and model parameters with field,
+            meterological, eddy flux, and spectral data, and 6. provenance
+            tracking
+          </p>
+          <p>
+            PECAn integrates available data into ecological forecasts by running
+            ensembles of a terrestrial ecosystem model that is parameterized by
+            the posterior distribution from a meta-analysis of available plant
+            trait data. These trait data are assembled from field research and
+            primary literature, and are stored in a PostgreSQL database. Current
+            development focused on biofuel crops uses BETYdb. In addition to
+            generating forecasts that reflect available data, PEcAn quantifies
+            the contribution of each parameter to model uncertainty. This
+            information informs targeted data collection and synthesis efforts
+            that most efficiently reduce forecast uncertainty.
+          </p>
+          <p>
+            Current development is focused on developing PEcAn into a real-time
+            data assimilation and forecasting system. This system will provide a
+            detailed analysis of the past and present ecosystem functioning that
+            seamlessly transitions into forecasts.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-</div>
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+          <p>Developed by .</p>
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 </html>
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diff --git a/base/utils/docs/reference/arrhenius.scaling.html b/base/utils/docs/reference/arrhenius.scaling.html
index 396a895..982f27d 100644
--- a/base/utils/docs/reference/arrhenius.scaling.html
+++ b/base/utils/docs/reference/arrhenius.scaling.html
@@ -2,161 +2,206 @@
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 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<script src="../pkgdown.js"></script>
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-<meta property="og:title" content="Arrhenius scaling — arrhenius.scaling" />
-
-<meta property="og:description" content="Scale temperature dependent trait from measurement temperature to reference temperature" />
-<meta name="twitter:card" content="summary" />
-
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-<![endif]-->
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
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+                <span
+                  class="label label-default"
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+                  >1.6.0</span
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-<div class="row">
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-    <h1>Arrhenius scaling</h1>
-    
-    <div class="hidden name"><code>arrhenius.scaling.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Scale temperature dependent trait from measurement temperature to reference temperature</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>arrhenius.scaling</span>(<span class='no'>observed.value</span>, <span class='no'>old.temp</span>, <span class='kw'>new.temp</span> <span class='kw'>=</span> <span class='fl'>25</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>observed.value</th>
-      <td><p>observed value of temperature dependent trait, e.g. Vcmax, root respiration rate</p></td>
-    </tr>
-    <tr>
-      <th>old.temp</th>
-      <td><p>temperature at which measurement was taken or previously scaled to</p></td>
-    </tr>
-    <tr>
-      <th>new.temp</th>
-      <td><p>temperature to be scaled to, default = 25 C</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>numeric value at reference temperature</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Arrhenius scaling</h1>
+
+            <div class="hidden name"><code>arrhenius.scaling.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Scale temperature dependent trait from measurement temperature to
+              reference temperature
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>arrhenius.scaling</span>(<span class='no'>observed.value</span>, <span class='no'>old.temp</span>, <span class='kw'>new.temp</span> <span class='kw'>=</span> <span class='fl'>25</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>observed.value</th>
+              <td>
+                <p>
+                  observed value of temperature dependent trait, e.g. Vcmax,
+                  root respiration rate
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>old.temp</th>
+              <td>
+                <p>
+                  temperature at which measurement was taken or previously
+                  scaled to
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>new.temp</th>
+              <td><p>temperature to be scaled to, default = 25 C</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>numeric value at reference temperature</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-unknown
+          <h2>Author</h2>
 
-  </div>
-</div>
+          unknown
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/reference/as.sequence.html b/base/utils/docs/reference/as.sequence.html
index bf4240e..2637ed0 100644
--- a/base/utils/docs/reference/as.sequence.html
+++ b/base/utils/docs/reference/as.sequence.html
@@ -2,164 +2,200 @@
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+    ></script>
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+    />
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>as.sequence</h1>
-    
-    <div class="hidden name"><code>as.sequence.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert categorical variable into sequential integers</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>as.sequence</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>categorical variable as vector</p></td>
-    </tr>
-    <tr>
-      <th>na.rm</th>
-      <td><p>logical: return NA's or replace with max(x) + 1</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>sequence from 1:length(unique(x))</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Turns any categorical variable into a sequential integer.
-This transformation is required for using data in BUGS/JAGS</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>as.sequence</h1>
+
+            <div class="hidden name"><code>as.sequence.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert categorical variable into sequential integers</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>as.sequence</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>categorical variable as vector</p></td>
+            </tr>
+            <tr>
+              <th>na.rm</th>
+              <td><p>logical: return NA's or replace with max(x) + 1</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>sequence from 1:length(unique(x))</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Turns any categorical variable into a sequential integer. This
+            transformation is required for using data in BUGS/JAGS
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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+    </div>
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 </html>
-
diff --git a/base/utils/docs/reference/bibtexify.html b/base/utils/docs/reference/bibtexify.html
index c47d7a2..0074042 100644
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+++ b/base/utils/docs/reference/bibtexify.html
@@ -2,167 +2,201 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+
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+
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>bibtexify</h1>
-    
-    <div class="hidden name"><code>bibtexify.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert author, year, title to bibtex citation format</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>bibtexify</span>(<span class='no'>author</span>, <span class='no'>year</span>, <span class='no'>title</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>author</th>
-      <td><p>name of first author</p></td>
-    </tr>
-    <tr>
-      <th>year</th>
-      <td><p>year of publication</p></td>
-    </tr>
-    <tr>
-      <th>title</th>
-      <td><p>manuscript title</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>bibtex citation</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Converts author year title to author1999abc format</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>bibtexify</h1>
+
+            <div class="hidden name"><code>bibtexify.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert author, year, title to bibtex citation format</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>bibtexify</span>(<span class='no'>author</span>, <span class='no'>year</span>, <span class='no'>title</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>author</th>
+              <td><p>name of first author</p></td>
+            </tr>
+            <tr>
+              <th>year</th>
+              <td><p>year of publication</p></td>
+            </tr>
+            <tr>
+              <th>title</th>
+              <td><p>manuscript title</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>bibtex citation</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Converts author year title to author1999abc format</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-unknown
+          <h2>Author</h2>
 
-  </div>
-</div>
+          unknown
+        </div>
+      </div>
 
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diff --git a/base/utils/docs/reference/bugs.rdist.html b/base/utils/docs/reference/bugs.rdist.html
index 00e551f..ef50a56 100644
--- a/base/utils/docs/reference/bugs.rdist.html
+++ b/base/utils/docs/reference/bugs.rdist.html
@@ -2,170 +2,207 @@
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 <html>
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-
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+
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+
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+
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+    />
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+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>bugs.rdist</h1>
-    
-    <div class="hidden name"><code>bugs.rdist.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>bugs.rdist</h1>
 
-    <div class="ref-description">
-    
-    <p>Sample from an R distribution using JAGS</p>
-    
-    </div>
+            <div class="hidden name"><code>bugs.rdist.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Sample from an R distribution using JAGS</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>bugs.rdist</span>(<span class='kw'>prior</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>distn</span> <span class='kw'>=</span> <span class='st'>"norm"</span>, <span class='kw'>parama</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>paramb</span> <span class='kw'>=</span> <span class='fl'>1</span>),
+          <pre
+            class="usage"
+          ><span class='fu'>bugs.rdist</span>(<span class='kw'>prior</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>distn</span> <span class='kw'>=</span> <span class='st'>"norm"</span>, <span class='kw'>parama</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>paramb</span> <span class='kw'>=</span> <span class='fl'>1</span>),
   <span class='kw'>n.iter</span> <span class='kw'>=</span> <span class='fl'>1e+05</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>prior</th>
-      <td><p>dataframe with distribution name and parameters</p></td>
-    </tr>
-    <tr>
-      <th>n.iter</th>
-      <td><p>number of samples, output will have n.iter/4 samples</p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>vector of samples</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Takes a distribution with R parameterization, converts it to a
-BUGS parameterization, and then samples from the distribution using
-JAGS</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>prior</th>
+              <td><p>dataframe with distribution name and parameters</p></td>
+            </tr>
+            <tr>
+              <th>n.iter</th>
+              <td>
+                <p>number of samples, output will have n.iter/4 samples</p>
+              </td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>vector of samples</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Takes a distribution with R parameterization, converts it to a BUGS
+            parameterization, and then samples from the distribution using JAGS
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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   </body>
 </html>
-
diff --git a/base/utils/docs/reference/capitalize.html b/base/utils/docs/reference/capitalize.html
index 7dc5b5f..72d6933 100644
--- a/base/utils/docs/reference/capitalize.html
+++ b/base/utils/docs/reference/capitalize.html
@@ -2,153 +2,182 @@
 <!DOCTYPE html>
 <html>
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <link href="../pkgdown.css" rel="stylesheet" />
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Capitalize a string</h1>
-    
-    <div class="hidden name"><code>capitalize.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Capitalize a string</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>capitalize</span>(<span class='no'>x</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>string</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>x, capitalized</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Capitalize a string</h1>
+
+            <div class="hidden name"><code>capitalize.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Capitalize a string</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>capitalize</span>(<span class='no'>x</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>string</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>x, capitalized</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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diff --git a/base/utils/docs/reference/clear.scratch.html b/base/utils/docs/reference/clear.scratch.html
index 91c49dd..e86b81f 100644
--- a/base/utils/docs/reference/clear.scratch.html
+++ b/base/utils/docs/reference/clear.scratch.html
@@ -2,159 +2,211 @@
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 <html>
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+
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Clear EBI-CLUSTER worker node local scratch directories of old PEcAn output</h1>
-    
-    <div class="hidden name"><code>clear.scratch.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Removes previous model run output from worker node local scratch directories on EBI-CLUSTER</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>clear.scratch</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>list of PEcAn settings. Only <code>settings$host$name</code> is used</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Clear EBI-CLUSTER worker node local scratch directories of old
+              PEcAn output
+            </h1>
+
+            <div class="hidden name"><code>clear.scratch.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Removes previous model run output from worker node local scratch
+              directories on EBI-CLUSTER
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>clear.scratch</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  list of PEcAn settings. Only
+                  <code>settings$host$name</code> is used
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>clear.scratch</span>(<span class='no'>settings</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Shawn Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Shawn Serbin
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/convert.expr.html b/base/utils/docs/reference/convert.expr.html
index 3358401..d2ec180 100644
--- a/base/utils/docs/reference/convert.expr.html
+++ b/base/utils/docs/reference/convert.expr.html
@@ -2,153 +2,185 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<link href="../pkgdown.css" rel="stylesheet">
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>convert.expr — convert.expr • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="convert.expr — convert.expr" />
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+    <meta
+      property="og:description"
+      content="Convert expression to variable names"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
   </head>
 
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-  <a href="../reference/index.html">Reference</a>
-</li>
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-      <ul class="nav navbar-nav navbar-right">
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>convert.expr</h1>
-    
-    <div class="hidden name"><code>convert.expr.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert expression to variable names</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>convert.expr</span>(<span class='no'>expression</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>expression</th>
-      <td><p>expression string</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>convert.expr</h1>
+
+            <div class="hidden name"><code>convert.expr.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert expression to variable names</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>convert.expr</span>(<span class='no'>expression</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>expression</th>
+              <td><p>expression string</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/convert.input.html b/base/utils/docs/reference/convert.input.html
index 38e9b5d..747e5ae 100644
--- a/base/utils/docs/reference/convert.input.html
+++ b/base/utils/docs/reference/convert.input.html
@@ -2,299 +2,465 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-
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-<meta property="og:title" content="Convert between formats, reusing existing files where possible — convert.input" />
-
-<meta property="og:description" content="convert.input is a relatively generic function that applies the function fcn and inserts a record of it into the database. It is primarily designed for converting meteorological data between formats and can be used on observed data, forecasts, and ensembles of forecasts.
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Convert between formats, reusing existing files where possible —
+      convert.input • PEcAn.utils
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert between formats, reusing existing files where possible</h1>
-    
-    <div class="hidden name"><code>convert.input.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p><code>convert.input</code> is a relatively generic function that applies the function <code>fcn</code> and inserts a record of it into the database. It is primarily designed for converting meteorological data between formats and can be used on observed data, forecasts, and ensembles of forecasts.
-To minimize downloading and storing duplicate data, it first checks to see if a given file is already in the
-database before applying <code>fcn</code>.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>convert.input</span>(<span class='no'>input.id</span>, <span class='no'>outfolder</span>, <span class='no'>formatname</span>, <span class='no'>mimetype</span>, <span class='no'>site.id</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Convert between formats, reusing existing files where possible
+            </h1>
+
+            <div class="hidden name"><code>convert.input.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              <code>convert.input</code> is a relatively generic function that
+              applies the function <code>fcn</code> and inserts a record of it
+              into the database. It is primarily designed for converting
+              meteorological data between formats and can be used on observed
+              data, forecasts, and ensembles of forecasts. To minimize
+              downloading and storing duplicate data, it first checks to see if
+              a given file is already in the database before applying
+              <code>fcn</code>.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>convert.input</span>(<span class='no'>input.id</span>, <span class='no'>outfolder</span>, <span class='no'>formatname</span>, <span class='no'>mimetype</span>, <span class='no'>site.id</span>,
   <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>pkg</span>, <span class='no'>fcn</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='no'>con</span>, <span class='no'>host</span>, <span class='no'>browndog</span>,
   <span class='kw'>write</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>format.vars</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>exact.dates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>allow.conflicting.dates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>insert.new.file</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>pattern</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>forecast</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>ensemble</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>ensemble_name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>input.id</th>
-      <td><p>The database id of the input file of the parent of the file being processed here.  The parent will have the same data, but in a different format.</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>The directory where files generated by functions called by convert.input will be placed</p></td>
-    </tr>
-    <tr>
-      <th>formatname</th>
-      <td><p>data product specific format name</p></td>
-    </tr>
-    <tr>
-      <th>mimetype</th>
-      <td><p>data product specific file format</p></td>
-    </tr>
-    <tr>
-      <th>site.id</th>
-      <td><p>The id of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start date of the data being requested or processed</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End date of the data being requested or processed</p></td>
-    </tr>
-    <tr>
-      <th>pkg</th>
-      <td><p>The package that the function being executed is in (as a string)</p></td>
-    </tr>
-    <tr>
-      <th>fcn</th>
-      <td><p>The function to be executed if records of the output file aren't found in the database. (as a string)</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>Database connection object</p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>Named list identifying the machine where conversion should be performed.
-Currently only <code>host$name</code> is used by <code>convert.input</code>, but whole list is passed to other functions</p></td>
-    </tr>
-    <tr>
-      <th>browndog</th>
-      <td><p>List of information related to browndog conversion.  NULL if browndog is not to be used for conversion</p></td>
-    </tr>
-    <tr>
-      <th>write</th>
-      <td><p>Logical: Write new file records to the database?</p></td>
-    </tr>
-    <tr>
-      <th>format.vars</th>
-      <td><p>Passed on as arguments to <code>fcn</code></p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>Logical: If a file already exists, create a fresh copy? Passed along to fcn.</p></td>
-    </tr>
-    <tr>
-      <th>exact.dates</th>
-      <td><p>Ignore time-span appending and enforce exact start and end dates on the database input file? (logical)</p></td>
-    </tr>
-    <tr>
-      <th>allow.conflicting.dates</th>
-      <td><p>Should overlapping years ignore time-span appending and exist as separate input files? (logical)</p></td>
-    </tr>
-    <tr>
-      <th>insert.new.file</th>
-      <td><p>Logical: force creation of a new database record even if one already exists?</p></td>
-    </tr>
-    <tr>
-      <th>pattern</th>
-      <td><p>A regular expression, passed to <code><a href='http://www.rdocumentation.org/packages/PEcAn.DB/topics/dbfile.input.check'>PEcAn.DB::dbfile.input.check</a></code>, used to match the name of the input file.</p></td>
-    </tr>
-    <tr>
-      <th>forecast</th>
-      <td><p>Logical: Is the data product a forecast?</p></td>
-    </tr>
-    <tr>
-      <th>ensemble</th>
-      <td><p>An integer representing the number of ensembles, or FALSE if it data product is not an ensemble.</p></td>
-    </tr>
-    <tr>
-      <th>ensemble_name</th>
-      <td><p>If convert.input is being called iteratively for each ensemble, ensemble_name contains the identifying name/number for that ensemble.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional arguments, passed unchanged to <code>fcn</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A list of two BETY IDs (input.id, dbfile.id) identifying a pre-existing file if one was available, or a newly created file if not.  Each id may be a vector of ids if the function is processing an entire ensemble at once.</p>
-    
-    <h2 class="hasAnchor" id="executing-the-function"><a class="anchor" href="#executing-the-function"></a>Executing the function</h2>
-
-    
-    <p>convert.input executes the function fcn in package pkg via PEcAn.remote::remote.execute.R.  All additional arguments passed to
-convert.input (...) are in turn passed along to fcn as arguments.  In addition, several named arguments to convert.input are passed
-along to fcn.  The command to execute fcn is built as a string.</p>
-    
-    <h2 class="hasAnchor" id="database-files"><a class="anchor" href="#database-files"></a>Database files</h2>
-
-    
-    <p>There are two kinds of database records (in different tables) that represent a given data file in the file system.  An input file
-contains information about the contents of the data file.  A dbfile contains machine spacific information for a given input file, 
-such as the file path.  Because duplicates of data files for a given input can be on multiple different machines, there can be more 
-than one dbfile for a given input file.</p>
-    
-    <h2 class="hasAnchor" id="time-span-appending"><a class="anchor" href="#time-span-appending"></a>Time-span appending</h2>
-
-    
-    <p>By default, convert.input tries to optimize the download of most data products by only downloading the years of data not present on 
-the current machine.  (For example, if files for 2004-2008 exist for a given data product exist on this machine and the user requests
-2006-2010, the function will only download data for 2009 and 2010).  In year-long data files, each year exists as a separate file.
-The database input file contains records of the bounds of the range stored by those years.  The data optimization can be turned off
-by overriding the default values for exact.dates and allow.conflicting.dates.</p>
-    
-    <h2 class="hasAnchor" id="forecast-data"><a class="anchor" href="#forecast-data"></a>Forecast data</h2>
-
-    
-    <p>If the flag forecast is TRUE, convert.input treats data as if it were forecast data.  Forecast data do not undergo time span
-appending.</p>
-    
-    <h2 class="hasAnchor" id="ensembles"><a class="anchor" href="#ensembles"></a>Ensembles</h2>
-
-    
-    <p>convert.input has the capability to handle ensembles of met data.  If ensemble = an integer &gt; 1, convert.input checks the database
-for records of all ensemble members, and calls fcn if at least one is missing.  convert.input assumes that fcn will return records
-for all ensembles. convert.input can also be called iteratevely for each ensemble member.  In this case ensemble_name contains the
-unique identifying name/number of the ensemble to be processed.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#executing-the-function">Executing the function</a></li>
-
-      <li><a href="#database-files">Database files</a></li>
-
-      <li><a href="#time-span-appending">Time-span appending</a></li>
-
-      <li><a href="#forecast-data">Forecast data</a></li>
-
-      <li><a href="#ensembles">Ensembles</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>input.id</th>
+              <td>
+                <p>
+                  The database id of the input file of the parent of the file
+                  being processed here. The parent will have the same data, but
+                  in a different format.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td>
+                <p>
+                  The directory where files generated by functions called by
+                  convert.input will be placed
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>formatname</th>
+              <td><p>data product specific format name</p></td>
+            </tr>
+            <tr>
+              <th>mimetype</th>
+              <td><p>data product specific file format</p></td>
+            </tr>
+            <tr>
+              <th>site.id</th>
+              <td><p>The id of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>Start date of the data being requested or processed</p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End date of the data being requested or processed</p></td>
+            </tr>
+            <tr>
+              <th>pkg</th>
+              <td>
+                <p>
+                  The package that the function being executed is in (as a
+                  string)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>fcn</th>
+              <td>
+                <p>
+                  The function to be executed if records of the output file
+                  aren't found in the database. (as a string)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>Database connection object</p></td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td>
+                <p>
+                  Named list identifying the machine where conversion should be
+                  performed. Currently only <code>host$name</code> is used by
+                  <code>convert.input</code>, but whole list is passed to other
+                  functions
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>browndog</th>
+              <td>
+                <p>
+                  List of information related to browndog conversion. NULL if
+                  browndog is not to be used for conversion
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>write</th>
+              <td><p>Logical: Write new file records to the database?</p></td>
+            </tr>
+            <tr>
+              <th>format.vars</th>
+              <td>
+                <p>Passed on as arguments to <code>fcn</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>
+                  Logical: If a file already exists, create a fresh copy? Passed
+                  along to fcn.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>exact.dates</th>
+              <td>
+                <p>
+                  Ignore time-span appending and enforce exact start and end
+                  dates on the database input file? (logical)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>allow.conflicting.dates</th>
+              <td>
+                <p>
+                  Should overlapping years ignore time-span appending and exist
+                  as separate input files? (logical)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>insert.new.file</th>
+              <td>
+                <p>
+                  Logical: force creation of a new database record even if one
+                  already exists?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pattern</th>
+              <td>
+                <p>
+                  A regular expression, passed to
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/PEcAn.DB/topics/dbfile.input.check"
+                      >PEcAn.DB::dbfile.input.check</a
+                    ></code
+                  >, used to match the name of the input file.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>forecast</th>
+              <td><p>Logical: Is the data product a forecast?</p></td>
+            </tr>
+            <tr>
+              <th>ensemble</th>
+              <td>
+                <p>
+                  An integer representing the number of ensembles, or FALSE if
+                  it data product is not an ensemble.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ensemble_name</th>
+              <td>
+                <p>
+                  If convert.input is being called iteratively for each
+                  ensemble, ensemble_name contains the identifying name/number
+                  for that ensemble.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  Additional arguments, passed unchanged to <code>fcn</code>
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A list of two BETY IDs (input.id, dbfile.id) identifying a
+            pre-existing file if one was available, or a newly created file if
+            not. Each id may be a vector of ids if the function is processing an
+            entire ensemble at once.
+          </p>
+
+          <h2 class="hasAnchor" id="executing-the-function">
+            <a class="anchor" href="#executing-the-function"></a>Executing the
+            function
+          </h2>
+
+          <p>
+            convert.input executes the function fcn in package pkg via
+            PEcAn.remote::remote.execute.R. All additional arguments passed to
+            convert.input (...) are in turn passed along to fcn as arguments. In
+            addition, several named arguments to convert.input are passed along
+            to fcn. The command to execute fcn is built as a string.
+          </p>
+
+          <h2 class="hasAnchor" id="database-files">
+            <a class="anchor" href="#database-files"></a>Database files
+          </h2>
+
+          <p>
+            There are two kinds of database records (in different tables) that
+            represent a given data file in the file system. An input file
+            contains information about the contents of the data file. A dbfile
+            contains machine spacific information for a given input file, such
+            as the file path. Because duplicates of data files for a given input
+            can be on multiple different machines, there can be more than one
+            dbfile for a given input file.
+          </p>
+
+          <h2 class="hasAnchor" id="time-span-appending">
+            <a class="anchor" href="#time-span-appending"></a>Time-span
+            appending
+          </h2>
+
+          <p>
+            By default, convert.input tries to optimize the download of most
+            data products by only downloading the years of data not present on
+            the current machine. (For example, if files for 2004-2008 exist for
+            a given data product exist on this machine and the user requests
+            2006-2010, the function will only download data for 2009 and 2010).
+            In year-long data files, each year exists as a separate file. The
+            database input file contains records of the bounds of the range
+            stored by those years. The data optimization can be turned off by
+            overriding the default values for exact.dates and
+            allow.conflicting.dates.
+          </p>
+
+          <h2 class="hasAnchor" id="forecast-data">
+            <a class="anchor" href="#forecast-data"></a>Forecast data
+          </h2>
+
+          <p>
+            If the flag forecast is TRUE, convert.input treats data as if it
+            were forecast data. Forecast data do not undergo time span
+            appending.
+          </p>
+
+          <h2 class="hasAnchor" id="ensembles">
+            <a class="anchor" href="#ensembles"></a>Ensembles
+          </h2>
+
+          <p>
+            convert.input has the capability to handle ensembles of met data. If
+            ensemble = an integer &gt; 1, convert.input checks the database for
+            records of all ensemble members, and calls fcn if at least one is
+            missing. convert.input assumes that fcn will return records for all
+            ensembles. convert.input can also be called iteratevely for each
+            ensemble member. In this case ensemble_name contains the unique
+            identifying name/number of the ensemble to be processed.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li>
+              <a href="#executing-the-function">Executing the function</a>
+            </li>
+
+            <li><a href="#database-files">Database files</a></li>
+
+            <li><a href="#time-span-appending">Time-span appending</a></li>
+
+            <li><a href="#forecast-data">Forecast data</a></li>
+
+            <li><a href="#ensembles">Ensembles</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Betsy Cowdery, Michael Dietze, Ankur Desai, Tony Gardella, Luke Dramko
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Betsy Cowdery, Michael Dietze, Ankur Desai, Tony Gardella, Luke Dramko
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
-
diff --git a/base/utils/docs/reference/create.base.plot.html b/base/utils/docs/reference/create.base.plot.html
index bebf95f..8c4a759 100644
--- a/base/utils/docs/reference/create.base.plot.html
+++ b/base/utils/docs/reference/create.base.plot.html
@@ -2,151 +2,177 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
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-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>Create Base Plot — create.base.plot • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+
+    <meta property="og:description" content="Creates empty ggplot object" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
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+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create Base Plot</h1>
-    
-    <div class="hidden name"><code>create.base.plot.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create Base Plot</h1>
 
-    <div class="ref-description">
-    
-    <p>Creates empty ggplot object</p>
-    
-    </div>
+            <div class="hidden name"><code>create.base.plot.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>create.base.plot</span>()</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <div class="ref-description">
+            <p>Creates empty ggplot object</p>
+          </div>
 
-    <p>empty ggplot object</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+          <pre class="usage"><span class='fu'>create.base.plot</span>()</pre>
 
-    <p>An empty base plot to which layers created by other functions
-(<code><a href='plot_data.html'>plot_data</a></code>, <code>plot.prior.density</code>,
-<code>plot.posterior.density</code>) can be added.</p>
-    
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <p>empty ggplot object</p>
 
-      <li><a href="#details">Details</a></li>
-          </ul>
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <p>
+            An empty base plot to which layers created by other functions (<code
+              ><a href="plot_data.html">plot_data</a></code
+            >, <code>plot.prior.density</code>,
+            <code>plot.posterior.density</code>) can be added.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
 
-  </div>
-</div>
+            <li><a href="#details">Details</a></li>
+          </ul>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <h2>Author</h2>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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   </body>
 </html>
-
diff --git a/base/utils/docs/reference/days_in_year.html b/base/utils/docs/reference/days_in_year.html
index ae424a7..2429c5b 100644
--- a/base/utils/docs/reference/days_in_year.html
+++ b/base/utils/docs/reference/days_in_year.html
@@ -2,165 +2,208 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
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+      crossorigin="anonymous"
+    ></script>
+
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+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Number of days in a year — days_in_year"
+    />
+
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+      property="og:description"
+      content="Calculate number of days in a year based on whether it is a leap year or not."
+    />
+    <meta name="twitter:card" content="summary" />
+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Number of days in a year</h1>
-    
-    <div class="hidden name"><code>days_in_year.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate number of days in a year based on whether it is a leap year or not.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>days_in_year</span>(<span class='no'>year</span>, <span class='kw'>leap_year</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>year</th>
-      <td><p>Numeric year (can be a vector)</p></td>
-    </tr>
-    <tr>
-      <th>leap_year</th>
-      <td><p>Default = TRUE. If set to FALSE will always return 365</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>integer vector, all either 365 or 366</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Number of days in a year</h1>
+
+            <div class="hidden name"><code>days_in_year.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Calculate number of days in a year based on whether it is a leap
+              year or not.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>days_in_year</span>(<span class='no'>year</span>, <span class='kw'>leap_year</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>year</th>
+              <td><p>Numeric year (can be a vector)</p></td>
+            </tr>
+            <tr>
+              <th>leap_year</th>
+              <td>
+                <p>Default = TRUE. If set to FALSE will always return 365</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>integer vector, all either 365 or 366</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>days_in_year</span>(<span class='fl'>2010</span>)  <span class='co'># Not a leap year -- returns 365</span>
 <span class='fu'>days_in_year</span>(<span class='fl'>2012</span>)  <span class='co'># Leap year -- returns 366</span>
 <span class='fu'>days_in_year</span>(<span class='fl'>2000</span>:<span class='fl'>2008</span>)  <span class='co'># Function is vectorized over years</span>
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Alexey Shiklomanov
+        </div>
+      </div>
 
+      <footer>
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+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index b6877c1..c9ab2fc 100644
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+    ></script>
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-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Diagonally Cut Histogram</h1>
-    
-    <div class="hidden name"><code>dhist.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Diagonally Cut Histogram</h1>
 
-    <div class="ref-description">
-    
-    <p>Variable-width (dagonally cut) histogram</p>
-    
-    </div>
+            <div class="hidden name"><code>dhist.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Variable-width (dagonally cut) histogram</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>dhist</span>(<span class='no'>x</span>, <span class='kw'>a</span> <span class='kw'>=</span> <span class='fl'>5</span> * <span class='fu'><a href='iqr.html'>iqr</a></span>(<span class='no'>x</span>), <span class='kw'>nbins</span> <span class='kw'>=</span> <span class='kw pkg'>grDevices</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/grDevices/topics/nclass'>nclass.Sturges</a></span>(<span class='no'>x</span>),
+          <pre
+            class="usage"
+          ><span class='fu'>dhist</span>(<span class='no'>x</span>, <span class='kw'>a</span> <span class='kw'>=</span> <span class='fl'>5</span> * <span class='fu'><a href='iqr.html'>iqr</a></span>(<span class='no'>x</span>), <span class='kw'>nbins</span> <span class='kw'>=</span> <span class='kw pkg'>grDevices</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/grDevices/topics/nclass'>nclass.Sturges</a></span>(<span class='no'>x</span>),
   <span class='kw'>rx</span> <span class='kw'>=</span> <span class='fu'>range</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>eps</span> <span class='kw'>=</span> <span class='fl'>0.15</span>, <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"x"</span>, <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>lab.spikes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>is a numeric vector (the data)</p></td>
-    </tr>
-    <tr>
-      <th>a</th>
-      <td><p>is the scaling factor, default is 5 * IQR</p></td>
-    </tr>
-    <tr>
-      <th>nbins</th>
-      <td><p>is the number of bins, default is assigned by the Stuges method</p></td>
-    </tr>
-    <tr>
-      <th>rx</th>
-      <td><p>is the range used for the left of the left-most bin to the right of the right-most bin</p></td>
-    </tr>
-    <tr>
-      <th>eps</th>
-      <td><p>used to set artificial bound on min width / max height of bins as described in Denby and Mallows (2009) on page 24.</p></td>
-    </tr>
-    <tr>
-      <th>xlab</th>
-      <td><p>is label for the x axis</p></td>
-    </tr>
-    <tr>
-      <th>plot</th>
-      <td><p>= TRUE produces the plot, FALSE returns the heights, breaks and counts</p></td>
-    </tr>
-    <tr>
-      <th>lab.spikes</th>
-      <td><p>= TRUE labels the % of data in the spikes</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list with two elements, heights of length n and breaks of length n+1 indicating the heights and break points of the histogram bars.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>When constructing a histogram, it is common to make all bars the same width.
-One could also choose to make them all have the same area.
-These two options have complementary strengths and weaknesses; the equal-width histogram oversmooths in regions of high density, and is poor at identifying sharp peaks; the equal-area histogram oversmooths in regions of low density, and so does not identify outliers.
-We describe a compromise approach which avoids both of these defects. We regard the histogram as an exploratory device, rather than as an estimate of a density.</p>
-    
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
-    <p>Lorraine Denby, Colin Mallows. Journal of Computational and Graphical Statistics. March 1, 2009, 18(1): 21-31. doi:10.1198/jcgs.2009.0002.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#references">References</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>is a numeric vector (the data)</p></td>
+            </tr>
+            <tr>
+              <th>a</th>
+              <td><p>is the scaling factor, default is 5 * IQR</p></td>
+            </tr>
+            <tr>
+              <th>nbins</th>
+              <td>
+                <p>
+                  is the number of bins, default is assigned by the Stuges
+                  method
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>rx</th>
+              <td>
+                <p>
+                  is the range used for the left of the left-most bin to the
+                  right of the right-most bin
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>eps</th>
+              <td>
+                <p>
+                  used to set artificial bound on min width / max height of bins
+                  as described in Denby and Mallows (2009) on page 24.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>xlab</th>
+              <td><p>is label for the x axis</p></td>
+            </tr>
+            <tr>
+              <th>plot</th>
+              <td>
+                <p>
+                  = TRUE produces the plot, FALSE returns the heights, breaks
+                  and counts
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lab.spikes</th>
+              <td><p>= TRUE labels the % of data in the spikes</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            list with two elements, heights of length n and breaks of length n+1
+            indicating the heights and break points of the histogram bars.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            When constructing a histogram, it is common to make all bars the
+            same width. One could also choose to make them all have the same
+            area. These two options have complementary strengths and weaknesses;
+            the equal-width histogram oversmooths in regions of high density,
+            and is poor at identifying sharp peaks; the equal-area histogram
+            oversmooths in regions of low density, and so does not identify
+            outliers. We describe a compromise approach which avoids both of
+            these defects. We regard the histogram as an exploratory device,
+            rather than as an estimate of a density.
+          </p>
+
+          <h2 class="hasAnchor" id="references">
+            <a class="anchor" href="#references"></a>References
+          </h2>
+
+          <p>
+            Lorraine Denby, Colin Mallows. Journal of Computational and
+            Graphical Statistics. March 1, 2009, 18(1): 21-31.
+            doi:10.1198/jcgs.2009.0002.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#references">References</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Lorraine Denby, Colin Mallows
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Lorraine Denby, Colin Mallows
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/base/utils/docs/reference/distn.stats.html b/base/utils/docs/reference/distn.stats.html
index 20a41d4..dece196 100644
--- a/base/utils/docs/reference/distn.stats.html
+++ b/base/utils/docs/reference/distn.stats.html
@@ -2,169 +2,215 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+    ></script>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Distribution Stats</h1>
-    
-    <div class="hidden name"><code>distn.stats.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Implementation of standard equations used to calculate mean and sd for a variety of 
-named distributions different</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>distn.stats</span>(<span class='no'>distn</span>, <span class='no'>a</span>, <span class='no'>b</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>distn</th>
-      <td><p>named distribution, one of 'beta', 'exp', 'f', 'gamma', 'lnorm', 'norm', 't',</p></td>
-    </tr>
-    <tr>
-      <th>a</th>
-      <td><p>numeric; first parameter of <code>distn</code></p></td>
-    </tr>
-    <tr>
-      <th>b</th>
-      <td><p>numeric; second parameter of <code>distn</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>vector with mean and standard deviation</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Distribution Stats</h1>
+
+            <div class="hidden name"><code>distn.stats.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Implementation of standard equations used to calculate mean and sd
+              for a variety of named distributions different
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>distn.stats</span>(<span class='no'>distn</span>, <span class='no'>a</span>, <span class='no'>b</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>distn</th>
+              <td>
+                <p>
+                  named distribution, one of 'beta', 'exp', 'f', 'gamma',
+                  'lnorm', 'norm', 't',
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>a</th>
+              <td>
+                <p>numeric; first parameter of <code>distn</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>b</th>
+              <td>
+                <p>numeric; second parameter of <code>distn</code></p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>vector with mean and standard deviation</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>distn.stats</span>(<span class='st'>'norm'</span>, <span class='fl'>0</span>, <span class='fl'>1</span>)
 <span class='co'># }</span></pre>
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-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
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+          <h2>Author</h2>
 
-  
+          David LeBauer
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diff --git a/base/utils/docs/reference/distn.table.stats.html b/base/utils/docs/reference/distn.table.stats.html
index 6227ac3..257f4e4 100644
--- a/base/utils/docs/reference/distn.table.stats.html
+++ b/base/utils/docs/reference/distn.table.stats.html
@@ -2,156 +2,201 @@
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+    <title>
+      return mean and standard deviation of a distribution for each distribution
+      in a table with <code>colnames = c('distn', 'a', 'b')</code>, e.g. in a
+      table of priors — distn.table.stats • PEcAn.utils
+    </title>
+
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      property="og:title"
+      content="return mean and standard deviation of a distribution for each distribution in a table with <code>colnames = c('distn', 'a', 'b')</code>,
+ e.g. in a table of priors — distn.table.stats"
+    />
+
+    <meta
+      property="og:description"
+      content="a helper function for computing summary statistics of a parametric distribution"
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>return mean and standard deviation of a distribution for each distribution in a table with <code>colnames = c('distn', 'a', 'b')</code>,
- e.g. in a table of priors</h1>
-    
-    <div class="hidden name"><code>distn.table.stats.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>a helper function for computing summary statistics of a parametric distribution</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>distn.table.stats</span>(<span class='no'>distns</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>distns</th>
-      <td><p>table of distributions; see examples</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>named vector of mean and SD</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              return mean and standard deviation of a distribution for each
+              distribution in a table with
+              <code>colnames = c('distn', 'a', 'b')</code>, e.g. in a table of
+              priors
+            </h1>
+
+            <div class="hidden name"><code>distn.table.stats.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              a helper function for computing summary statistics of a parametric
+              distribution
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>distn.table.stats</span>(<span class='no'>distns</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>distns</th>
+              <td><p>table of distributions; see examples</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>named vector of mean and SD</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/do_conversions.html b/base/utils/docs/reference/do_conversions.html
index 00cdea1..d20fff2 100644
--- a/base/utils/docs/reference/do_conversions.html
+++ b/base/utils/docs/reference/do_conversions.html
@@ -2,152 +2,179 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>do_conversions — do_conversions • PEcAn.utils</title>
-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="do_conversions — do_conversions" />
+
+    <meta property="og:description" content="Input conversion workflow" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>do_conversions</h1>
-    
-    <div class="hidden name"><code>do_conversions.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>do_conversions</h1>
 
-    <div class="ref-description">
-    
-    <p>Input conversion workflow</p>
-    
-    </div>
+            <div class="hidden name"><code>do_conversions.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>do_conversions</span>(<span class='no'>settings</span>, <span class='kw'>overwrite.met</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>overwrite.fia</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>overwrite.ic</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings list</p></td>
-    </tr>
-    <tr>
-      <th>overwrite.met, overwrite.fia, overwrite.ic</th>
-      <td><p>logical</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Ryan Kelly, Rob Kooper, Betsy Cowdery, Istem Fer
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Input conversion workflow</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>do_conversions</span>(<span class='no'>settings</span>, <span class='kw'>overwrite.met</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>overwrite.fia</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>overwrite.ic</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings list</p></td>
+            </tr>
+            <tr>
+              <th>overwrite.met, overwrite.fia, overwrite.ic</th>
+              <td><p>logical</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Ryan Kelly, Rob Kooper, Betsy Cowdery, Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/download.file.html b/base/utils/docs/reference/download.file.html
index a3aeaff..7e0fdcf 100644
--- a/base/utils/docs/reference/download.file.html
+++ b/base/utils/docs/reference/download.file.html
@@ -2,134 +2,178 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>download.file — download.file • PEcAn.utils</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="download.file — download.file" />
-
-<meta property="og:description" content="Simple function to use ncftpget for FTP downloads behind a firewall.
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>download.file — download.file • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="download.file — download.file" />
+
+    <meta
+      property="og:description"
+      content="Simple function to use ncftpget for FTP downloads behind a firewall.
 Requires ncftpget and a properly formatted config file in the users
-home directory" />
-<meta name="twitter:card" content="summary" />
-
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+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.file</h1>
-    
-    <div class="hidden name"><code>download.file.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Simple function to use ncftpget for FTP downloads behind a firewall.
-Requires ncftpget and a properly formatted config file in the users
-home directory</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>download.file</span>(<span class='no'>url</span>, <span class='no'>filename</span>, <span class='no'>method</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>url</th>
-      <td><p>complete URL for file download</p></td>
-    </tr>
-    <tr>
-      <th>filename</th>
-      <td><p>destination file name</p></td>
-    </tr>
-    <tr>
-      <th>method</th>
-      <td><p>Method of file retrieval. Can set this using the options(download.ftp.method=[method]) in your Rprofile.
-example options(download.ftp.method="ncftpget")</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.file</h1>
+
+            <div class="hidden name"><code>download.file.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Simple function to use ncftpget for FTP downloads behind a
+              firewall. Requires ncftpget and a properly formatted config file
+              in the users home directory
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>download.file</span>(<span class='no'>url</span>, <span class='no'>filename</span>, <span class='no'>method</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>url</th>
+              <td><p>complete URL for file download</p></td>
+            </tr>
+            <tr>
+              <th>filename</th>
+              <td><p>destination file name</p></td>
+            </tr>
+            <tr>
+              <th>method</th>
+              <td>
+                <p>
+                  Method of file retrieval. Can set this using the
+                  options(download.ftp.method=[method]) in your Rprofile.
+                  example options(download.ftp.method="ncftpget")
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>download.file</span>(<span class='st'>"http://lib.stat.cmu.edu/datasets/csb/ch11b.txt"</span>,<span class='st'>"~/test.download.txt"</span>)
 
 <span class='co'># }</span><span class='co'># NOT RUN {</span>
@@ -139,36 +183,32 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Shawn Serbin, Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Shawn Serbin, Rob Kooper
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/download.url.html b/base/utils/docs/reference/download.url.html
index b512585..d4abf0c 100644
--- a/base/utils/docs/reference/download.url.html
+++ b/base/utils/docs/reference/download.url.html
@@ -2,182 +2,225 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-
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-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Download file from the url. — download.url • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Download file from the url. — download.url"
+    />
+
+    <meta property="og:description" content="Try and download a file." />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download file from the url.</h1>
-    
-    <div class="hidden name"><code>download.url.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download file from the url.</h1>
 
-    <div class="ref-description">
-    
-    <p>Try and download a file.</p>
-    
-    </div>
+            <div class="hidden name"><code>download.url.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.url</span>(<span class='no'>url</span>, <span class='no'>file</span>, <span class='kw'>timeout</span> <span class='kw'>=</span> <span class='fl'>600</span>, <span class='kw'>.opts</span> <span class='kw'>=</span> <span class='fu'>list</span>(),
+          <div class="ref-description">
+            <p>Try and download a file.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>download.url</span>(<span class='no'>url</span>, <span class='no'>file</span>, <span class='kw'>timeout</span> <span class='kw'>=</span> <span class='fl'>600</span>, <span class='kw'>.opts</span> <span class='kw'>=</span> <span class='fu'>list</span>(),
   <span class='kw'>retry404</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>url</th>
-      <td><p>the url of the file to download</p></td>
-    </tr>
-    <tr>
-      <th>file</th>
-      <td><p>the filename</p></td>
-    </tr>
-    <tr>
-      <th>timeout</th>
-      <td><p>number of seconds to wait for file (default 600)</p></td>
-    </tr>
-    <tr>
-      <th>.opts</th>
-      <td><p>list of options for curl, for example to download from a
-protected site use list(userpwd=userpass, httpauth = 1L)</p></td>
-    </tr>
-    <tr>
-      <th>retry404</th>
-      <td><p>retry on a 404, this is used by Brown Dog</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>returns name of file if successful or NA if not.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This will download a file, if retry404 and 404 is returned it will
-wait until the file is available. If the file is still not available
-after timeout tries, it will return NA. If the file is downloaded
-it will return the name of the file</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>url</th>
+              <td><p>the url of the file to download</p></td>
+            </tr>
+            <tr>
+              <th>file</th>
+              <td><p>the filename</p></td>
+            </tr>
+            <tr>
+              <th>timeout</th>
+              <td><p>number of seconds to wait for file (default 600)</p></td>
+            </tr>
+            <tr>
+              <th>.opts</th>
+              <td>
+                <p>
+                  list of options for curl, for example to download from a
+                  protected site use list(userpwd=userpass, httpauth = 1L)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>retry404</th>
+              <td><p>retry on a 404, this is used by Brown Dog</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>returns name of file if successful or NA if not.</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This will download a file, if retry404 and 404 is returned it will
+            wait until the file is available. If the file is still not available
+            after timeout tries, it will return NA. If the file is downloaded it
+            will return the name of the file
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>download.url</span>(<span class='st'>'http://localhost/'</span>, <span class='no'>index.html</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#details">Details</a></li>
 
-  
+            <li><a href="#examples">Examples</a></li>
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+      <footer>
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diff --git a/base/utils/docs/reference/ensemble.filename.html b/base/utils/docs/reference/ensemble.filename.html
index fe3ec28..82b9f4c 100644
--- a/base/utils/docs/reference/ensemble.filename.html
+++ b/base/utils/docs/reference/ensemble.filename.html
@@ -2,154 +2,185 @@
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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-    <h1>Generate ensemble filenames</h1>
-    
-    <div class="hidden name"><code>ensemble.filename.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generate ensemble filenames</h1>
 
-    <div class="ref-description">
-    
-    <p>Generate ensemble filenames</p>
-    
-    </div>
+            <div class="hidden name"><code>ensemble.filename.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Generate ensemble filenames</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>ensemble.filename</span>(<span class='no'>settings</span>, <span class='kw'>prefix</span> <span class='kw'>=</span> <span class='st'>"ensemble.samples"</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>ensemble.filename</span>(<span class='no'>settings</span>, <span class='kw'>prefix</span> <span class='kw'>=</span> <span class='st'>"ensemble.samples"</span>,
   <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='st'>"Rdata"</span>, <span class='kw'>all.var.yr</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>ensemble.id</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>ensemble</span>$<span class='no'>ensemble.id</span>,
   <span class='kw'>variable</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>ensemble</span>$<span class='no'>variable</span>,
   <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>ensemble</span>$<span class='no'>start.year</span>,
   <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>ensemble</span>$<span class='no'>end.year</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>a filename</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
 
-    <p>Generally uses values in settings, but can be overwritten for manual uses</p>
-    
+          <p>a filename</p>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
 
-      <li><a href="#details">Details</a></li>
+          <p>
+            Generally uses values in settings, but can be overwritten for manual
+            uses
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/reference/full.path.html b/base/utils/docs/reference/full.path.html
index c2df931..b041ab6 100644
--- a/base/utils/docs/reference/full.path.html
+++ b/base/utils/docs/reference/full.path.html
@@ -2,157 +2,195 @@
 <!DOCTYPE html>
 <html>
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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-    
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-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Creates an absolute path to a folder</h1>
 
-    <div class="ref-description">
-    
-    <p>Creates an absolute path to a folder.</p>
-    
-    </div>
+            <div class="hidden name"><code>full.path.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>full.path</span>(<span class='no'>folder</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <div class="ref-description">
+            <p>Creates an absolute path to a folder.</p>
+          </div>
 
-    <p>absolute path</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+          <pre
+            class="usage"
+          ><span class='fu'>full.path</span>(<span class='no'>folder</span>)</pre>
 
-    <p>This will take a folder and make it into an absolute folder name. It
-will normalize the path and prepend it with the current working folder
-if needed to get an absolute path name.</p>
-    
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
 
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
-<span class='fu'>full.path</span>(<span class='st'>'pecan'</span>)
-<span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <p>absolute path</p>
 
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <p>
+            This will take a folder and make it into an absolute folder name. It
+            will normalize the path and prepend it with the current working
+            folder if needed to get an absolute path name.
+          </p>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='fu'>full.path</span>(<span class='st'>'pecan'</span>)
+<span class='co'># }</span></pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/get.ensemble.inputs.html b/base/utils/docs/reference/get.ensemble.inputs.html
index 8bdeeed..a2beba0 100644
--- a/base/utils/docs/reference/get.ensemble.inputs.html
+++ b/base/utils/docs/reference/get.ensemble.inputs.html
@@ -2,157 +2,189 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>get.ensemble.inputs — get.ensemble.inputs • PEcAn.utils</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="get.ensemble.inputs — get.ensemble.inputs" />
-
-<meta property="og:description" content="Splits climate met for SIPNET" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>get.ensemble.inputs — get.ensemble.inputs • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="get.ensemble.inputs — get.ensemble.inputs"
+    />
+
+    <meta property="og:description" content="Splits climate met for SIPNET" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get.ensemble.inputs</h1>
-    
-    <div class="hidden name"><code>get.ensemble.inputs.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Splits climate met for SIPNET</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.ensemble.inputs</span>(<span class='no'>settings</span>, <span class='kw'>ens</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings list</p></td>
-    </tr>
-    <tr>
-      <th>ens</th>
-      <td><p>ensemble number. default = 1</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>find correct ensemble inputs</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get.ensemble.inputs</h1>
+
+            <div class="hidden name"><code>get.ensemble.inputs.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Splits climate met for SIPNET</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.ensemble.inputs</span>(<span class='no'>settings</span>, <span class='kw'>ens</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings list</p></td>
+            </tr>
+            <tr>
+              <th>ens</th>
+              <td><p>ensemble number. default = 1</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>find correct ensemble inputs</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze and Ann Raiho
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze and Ann Raiho
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/get.ensemble.samples.html b/base/utils/docs/reference/get.ensemble.samples.html
index 31fbc11..68f3f37 100644
--- a/base/utils/docs/reference/get.ensemble.samples.html
+++ b/base/utils/docs/reference/get.ensemble.samples.html
@@ -2,183 +2,251 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Get Ensemble Samples — get.ensemble.samples • PEcAn.utils</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Get Ensemble Samples — get.ensemble.samples" />
-
-<meta property="og:description" content="Get parameter values used in ensemble" />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Get Ensemble Samples — get.ensemble.samples • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Get Ensemble Samples — get.ensemble.samples"
+    />
+
+    <meta
+      property="og:description"
+      content="Get parameter values used in ensemble"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
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-
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-        <li>
-  <a href="../index.html">
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-        
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get Ensemble Samples</h1>
-    
-    <div class="hidden name"><code>get.ensemble.samples.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get Ensemble Samples</h1>
 
-    <div class="ref-description">
-    
-    <p>Get parameter values used in ensemble</p>
-    
-    </div>
+            <div class="hidden name"><code>get.ensemble.samples.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get parameter values used in ensemble</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>get.ensemble.samples</span>(<span class='no'>ensemble.size</span>, <span class='no'>pft.samples</span>, <span class='no'>env.samples</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>get.ensemble.samples</span>(<span class='no'>ensemble.size</span>, <span class='no'>pft.samples</span>, <span class='no'>env.samples</span>,
   <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"uniform"</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ensemble.size</th>
-      <td><p>number of runs in model ensemble</p></td>
-    </tr>
-    <tr>
-      <th>pft.samples</th>
-      <td><p>random samples from parameter distribution, e.g. from a MCMC chain</p></td>
-    </tr>
-    <tr>
-      <th>env.samples</th>
-      <td><p>env samples</p></td>
-    </tr>
-    <tr>
-      <th>method</th>
-      <td><p>the method used to generate the ensemble samples. Random generators: uniform, uniform with latin hypercube permutation. Quasi-random generators: halton, sobol, torus. Random generation draws random variates whereas quasi-random generation is deterministic but well equidistributed. Default is uniform. For small ensemble size with relatively large parameter number (e.g ensemble size &lt; 5 and # of traits &gt; 5) use methods other than halton.</p></td>
-    </tr>
-    <tr>
-      <th>param.names</th>
-      <td><p>a list of parameter names that were fitted either by MA or PDA, important argument, if NULL parameters will be resampled independently</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>matrix of (quasi-)random samples from trait distributions</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>DEPRECATED: This function has been moved to the <code>PEcAn.uncertainty</code> package.
-The version in <code>PEcAn.utils</code> is deprecated, will not be updated to add any new features,
-and will be removed in a future release of PEcAn.
-Please use <code><a href='http://www.rdocumentation.org/packages/PEcAn.uncertainty/topics/get.ensemble.samples'>PEcAn.uncertainty::get.ensemble.samples</a></code> instead.
-Returns a matrix of randomly or quasi-randomly sampled trait values 
-to be assigned to traits over several model runs.
-given the number of model runs and a list of sample distributions for traits
-The model run is indexed first by model run, then by trait</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ensemble.size</th>
+              <td><p>number of runs in model ensemble</p></td>
+            </tr>
+            <tr>
+              <th>pft.samples</th>
+              <td>
+                <p>
+                  random samples from parameter distribution, e.g. from a MCMC
+                  chain
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>env.samples</th>
+              <td><p>env samples</p></td>
+            </tr>
+            <tr>
+              <th>method</th>
+              <td>
+                <p>
+                  the method used to generate the ensemble samples. Random
+                  generators: uniform, uniform with latin hypercube permutation.
+                  Quasi-random generators: halton, sobol, torus. Random
+                  generation draws random variates whereas quasi-random
+                  generation is deterministic but well equidistributed. Default
+                  is uniform. For small ensemble size with relatively large
+                  parameter number (e.g ensemble size &lt; 5 and # of traits
+                  &gt; 5) use methods other than halton.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>param.names</th>
+              <td>
+                <p>
+                  a list of parameter names that were fitted either by MA or
+                  PDA, important argument, if NULL parameters will be resampled
+                  independently
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>matrix of (quasi-)random samples from trait distributions</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            DEPRECATED: This function has been moved to the
+            <code>PEcAn.uncertainty</code> package. The version in
+            <code>PEcAn.utils</code> is deprecated, will not be updated to add
+            any new features, and will be removed in a future release of PEcAn.
+            Please use
+            <code
+              ><a
+                href="http://www.rdocumentation.org/packages/PEcAn.uncertainty/topics/get.ensemble.samples"
+                >PEcAn.uncertainty::get.ensemble.samples</a
+              ></code
+            >
+            instead. Returns a matrix of randomly or quasi-randomly sampled
+            trait values to be assigned to traits over several model runs. given
+            the number of model runs and a list of sample distributions for
+            traits The model run is indexed first by model run, then by trait
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/base/utils/docs/reference/get.model.output.html b/base/utils/docs/reference/get.model.output.html
index 5b5179f..939cc51 100644
--- a/base/utils/docs/reference/get.model.output.html
+++ b/base/utils/docs/reference/get.model.output.html
@@ -2,156 +2,192 @@
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Retrieve model output</h1>
-    
-    <div class="hidden name"><code>get.model.output.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function retrieves model output for further analyses</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.model.output</span>(<span class='no'>model</span>, <span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>model</th>
-      <td><p>the ecosystem model run</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Retrieve model output</h1>
+
+            <div class="hidden name"><code>get.model.output.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>This function retrieves model output for further analyses</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.model.output</span>(<span class='no'>model</span>, <span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>model</th>
+              <td><p>the ecosystem model run</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>get.model.output</span>(<span class='no'>model</span>)
 <span class='fu'>get.model.output</span>(<span class='st'>'ED2'</span>)
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze, Shawn Serbin, David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Michael Dietze, Shawn Serbin, David LeBauer
+        </div>
+      </div>
 
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diff --git a/base/utils/docs/reference/get.parameter.stat.html b/base/utils/docs/reference/get.parameter.stat.html
index 1e318c6..eba1f7f 100644
--- a/base/utils/docs/reference/get.parameter.stat.html
+++ b/base/utils/docs/reference/get.parameter.stat.html
@@ -2,163 +2,211 @@
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-    <h1>Get Parameter Statistics</h1>
-    
-    <div class="hidden name"><code>get.parameter.stat.Rd</code></div>
-    </div>
-
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-    
-    <p>Gets statistics for LaTeX - formatted table</p>
-    
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-
-    <pre class="usage"><span class='fu'>get.parameter.stat</span>(<span class='no'>mcmc.summary</span>, <span class='no'>parameter</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mcmc.summary</th>
-      <td><p>probably produced by <code><a href='http://www.rdocumentation.org/packages/coda/topics/summary.mcmc'>summary.mcmc</a></code></p></td>
-    </tr>
-    <tr>
-      <th>parameter</th>
-      <td><p>name of parameter to extract, as character</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>table with parameter statistics</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get Parameter Statistics</h1>
+
+            <div class="hidden name"><code>get.parameter.stat.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Gets statistics for LaTeX - formatted table</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.parameter.stat</span>(<span class='no'>mcmc.summary</span>, <span class='no'>parameter</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mcmc.summary</th>
+              <td>
+                <p>
+                  probably produced by
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/coda/topics/summary.mcmc"
+                      >summary.mcmc</a
+                    ></code
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>parameter</th>
+              <td><p>name of parameter to extract, as character</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>table with parameter statistics</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>get.parameter.stat</span>(<span class='no'>mcmc.summaries</span><span class='kw'>[[</span><span class='fl'>1</span>]], <span class='st'>'beta.o'</span>)
 <span class='co'># }</span></pre>
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-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
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+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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+            <li><a href="#arguments">Arguments</a></li>
 
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+            <li><a href="#examples">Examples</a></li>
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diff --git a/base/utils/docs/reference/get.quantiles.html b/base/utils/docs/reference/get.quantiles.html
index 00fac10..dace11d 100644
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+++ b/base/utils/docs/reference/get.quantiles.html
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-    <h1>Get Quantiles</h1>
-    
-    <div class="hidden name"><code>get.quantiles.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Returns a vector of quantiles specified by a given &lt;quantiles&gt; xml tag</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.quantiles</span>(<span class='no'>quantiles.tag</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>quantiles.tag</th>
-      <td><p>specifies tag used to specify quantiles</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>vector of quantiles</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get Quantiles</h1>
+
+            <div class="hidden name"><code>get.quantiles.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Returns a vector of quantiles specified by a given
+              &lt;quantiles&gt; xml tag
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.quantiles</span>(<span class='no'>quantiles.tag</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>quantiles.tag</th>
+              <td><p>specifies tag used to specify quantiles</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>vector of quantiles</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
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diff --git a/base/utils/docs/reference/get.results.html b/base/utils/docs/reference/get.results.html
index 76c6b71..1b5b677 100644
--- a/base/utils/docs/reference/get.results.html
+++ b/base/utils/docs/reference/get.results.html
@@ -2,154 +2,198 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
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-<!-- Bootstrap -->
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-
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-
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Generate model output for PEcAn analyses — get.results • PEcAn.utils
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Generate model output for PEcAn analyses — get.results"
+    />
+
+    <meta
+      property="og:description"
+      content="Reads model output and runs sensitivity and ensemble analyses"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
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+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
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+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate model output for PEcAn analyses</h1>
-    
-    <div class="hidden name"><code>get.results.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generate model output for PEcAn analyses</h1>
 
-    <div class="ref-description">
-    
-    <p>Reads model output and runs sensitivity and ensemble analyses</p>
-    
-    </div>
+            <div class="hidden name"><code>get.results.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Reads model output and runs sensitivity and ensemble analyses</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>get.results</span>(<span class='no'>settings</span>, <span class='kw'>sa.ensemble.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>ens.ensemble.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>get.results</span>(<span class='no'>settings</span>, <span class='kw'>sa.ensemble.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>ens.ensemble.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>variable</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>list, read from settings file (xml) using <code>read.settings</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Output is placed in model output directory (settings$modeloutdir).</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  list, read from settings file (xml) using
+                  <code>read.settings</code>
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Output is placed in model output directory (settings$modeloutdir).
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Mike Dietze, Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin, Mike Dietze, Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/get.run.id.html b/base/utils/docs/reference/get.run.id.html
index 72b5939..ac8e731 100644
--- a/base/utils/docs/reference/get.run.id.html
+++ b/base/utils/docs/reference/get.run.id.html
@@ -2,179 +2,233 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Get Run ID — get.run.id • PEcAn.utils</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Get Run ID — get.run.id" />
-
-<meta property="og:description" content="returns an id representing a model run" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Get Run ID — get.run.id • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Get Run ID — get.run.id" />
+
+    <meta
+      property="og:description"
+      content="returns an id representing a model run"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+    <![endif]-->
   </head>
 
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-  <a href="../index.html">
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
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-        
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-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get Run ID</h1>
-    
-    <div class="hidden name"><code>get.run.id.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>returns an id representing a model run</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.run.id</span>(<span class='no'>run.type</span>, <span class='no'>index</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>pft.name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>run.type</th>
-      <td><p>character, can be any character; currently 'SA' is used for sensitivity analysis, 'ENS' for ensemble run.</p></td>
-    </tr>
-    <tr>
-      <th>index</th>
-      <td><p>unique index for different runs, e.g. integer counting members of an
-ensemble or a quantile used to which a trait has been perturbed for sensitivity analysis</p></td>
-    </tr>
-    <tr>
-      <th>trait</th>
-      <td><p>name of trait being sampled (for sensitivity analysis)</p></td>
-    </tr>
-    <tr>
-      <th>pft.name</th>
-      <td><p>name of PFT (value from pfts.names field in database)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>id representing a model run</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Provides a consistent method of naming runs; for use in model input files and indices</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get Run ID</h1>
+
+            <div class="hidden name"><code>get.run.id.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>returns an id representing a model run</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.run.id</span>(<span class='no'>run.type</span>, <span class='no'>index</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>pft.name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>run.type</th>
+              <td>
+                <p>
+                  character, can be any character; currently 'SA' is used for
+                  sensitivity analysis, 'ENS' for ensemble run.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>index</th>
+              <td>
+                <p>
+                  unique index for different runs, e.g. integer counting members
+                  of an ensemble or a quantile used to which a trait has been
+                  perturbed for sensitivity analysis
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>trait</th>
+              <td>
+                <p>name of trait being sampled (for sensitivity analysis)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>pft.name</th>
+              <td>
+                <p>name of PFT (value from pfts.names field in database)</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>id representing a model run</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Provides a consistent method of naming runs; for use in model input
+            files and indices
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>get.run.id</span>(<span class='st'>'ENS'</span>, <span class='fu'><a href='left.pad.zeros.html'>left.pad.zeros</a></span>(<span class='fl'>1</span>, <span class='fl'>5</span>))
 <span class='fu'>get.run.id</span>(<span class='st'>'SA'</span>, <span class='fu'>round</span>(<span class='fu'>qnorm</span>(-<span class='fl'>3</span>),<span class='fl'>3</span>), <span class='kw'>trait</span> <span class='kw'>=</span> <span class='st'>'Vcmax'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Carl Davidson, David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Carl Davidson, David LeBauer
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/get.sa.sample.list.html b/base/utils/docs/reference/get.sa.sample.list.html
index b85497c..e5b110d 100644
--- a/base/utils/docs/reference/get.sa.sample.list.html
+++ b/base/utils/docs/reference/get.sa.sample.list.html
@@ -2,158 +2,197 @@
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 <html>
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="get.sa.sample.list — get.sa.sample.list"
+    />
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+      property="og:description"
+      content="get sensitivity samples as a list"
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../index.html">
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get.sa.sample.list</h1>
-    
-    <div class="hidden name"><code>get.sa.sample.list.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>get sensitivity samples as a list</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.sa.sample.list</span>(<span class='no'>pft</span>, <span class='no'>env</span>, <span class='no'>quantiles</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pft</th>
-      <td><p>Plant Functional Type</p></td>
-    </tr>
-    <tr>
-      <th>env</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>quantiles</th>
-      <td><p>quantiles at which to obtain samples from parameter for
-sensitivity analysis</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>sa.sample.list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get.sa.sample.list</h1>
+
+            <div class="hidden name"><code>get.sa.sample.list.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>get sensitivity samples as a list</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.sa.sample.list</span>(<span class='no'>pft</span>, <span class='no'>env</span>, <span class='no'>quantiles</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pft</th>
+              <td><p>Plant Functional Type</p></td>
+            </tr>
+            <tr>
+              <th>env</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>quantiles</th>
+              <td>
+                <p>
+                  quantiles at which to obtain samples from parameter for
+                  sensitivity analysis
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>sa.sample.list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/get.sa.samples.html b/base/utils/docs/reference/get.sa.samples.html
index 5ff0f3c..f847cc0 100644
--- a/base/utils/docs/reference/get.sa.samples.html
+++ b/base/utils/docs/reference/get.sa.samples.html
@@ -2,166 +2,214 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<div class="row">
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-    <h1>get sensitivity analysis samples</h1>
-    
-    <div class="hidden name"><code>get.sa.samples.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Samples parameters for a model run at specified quantiles.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.sa.samples</span>(<span class='no'>samples</span>, <span class='no'>quantiles</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>samples</th>
-      <td><p>random samples from trait distribution</p></td>
-    </tr>
-    <tr>
-      <th>quantiles</th>
-      <td><p>list of quantiles to at which to sample, set in settings file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a list of lists representing quantile values of trait distributions</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Samples from long (&gt;2000) vectors that represent random samples from a trait distribution.
-Samples are either the MCMC chains output from the Bayesian meta-analysis or are randomly sampled from
-the closed-form distribution of the parameter probability distribution function.
-The list is indexed first by trait, then by quantile.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get sensitivity analysis samples</h1>
+
+            <div class="hidden name"><code>get.sa.samples.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Samples parameters for a model run at specified quantiles.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.sa.samples</span>(<span class='no'>samples</span>, <span class='no'>quantiles</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>samples</th>
+              <td><p>random samples from trait distribution</p></td>
+            </tr>
+            <tr>
+              <th>quantiles</th>
+              <td>
+                <p>
+                  list of quantiles to at which to sample, set in settings file
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            a list of lists representing quantile values of trait distributions
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Samples from long (&gt;2000) vectors that represent random samples
+            from a trait distribution. Samples are either the MCMC chains output
+            from the Bayesian meta-analysis or are randomly sampled from the
+            closed-form distribution of the parameter probability distribution
+            function. The list is indexed first by trait, then by quantile.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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index 74639aa..abcd54c 100644
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-<div class="row">
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-    <div class="page-header">
-    <h1>Get stats for parameters in MCMC output</h1>
-    
-    <div class="hidden name"><code>get.stats.mcmc.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Further summarizes output from summary.mcmc</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.stats.mcmc</span>(<span class='no'>mcmc.summary</span>, <span class='no'>sample.size</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mcmc.summary</th>
-      <td><p>probably produced by <code><a href='http://www.rdocumentation.org/packages/coda/topics/summary.mcmc'>summary.mcmc</a></code></p></td>
-    </tr>
-    <tr>
-      <th>sample.size</th>
-      <td><p>passed as 'n' in returned list</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list with summary statistics for parameters in an MCMC chain</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get stats for parameters in MCMC output</h1>
+
+            <div class="hidden name"><code>get.stats.mcmc.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Further summarizes output from summary.mcmc</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.stats.mcmc</span>(<span class='no'>mcmc.summary</span>, <span class='no'>sample.size</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mcmc.summary</th>
+              <td>
+                <p>
+                  probably produced by
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/coda/topics/summary.mcmc"
+                      >summary.mcmc</a
+                    ></code
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sample.size</th>
+              <td><p>passed as 'n' in returned list</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list with summary statistics for parameters in an MCMC chain</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/reference/grid2netcdf.html b/base/utils/docs/reference/grid2netcdf.html
index 26e509b..0282d1a 100644
--- a/base/utils/docs/reference/grid2netcdf.html
+++ b/base/utils/docs/reference/grid2netcdf.html
@@ -2,153 +2,185 @@
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+
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>grid2netcdf</h1>
-    
-    <div class="hidden name"><code>grid2netcdf.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Write gridded data to netcdf file</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>grid2netcdf</span>(<span class='no'>gdata</span>, <span class='kw'>date</span> <span class='kw'>=</span> <span class='st'>"9999-09-09"</span>, <span class='kw'>outfile</span> <span class='kw'>=</span> <span class='st'>"out.nc"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>grid.data</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>writes netCDF file</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>grid2netcdf</h1>
+
+            <div class="hidden name"><code>grid2netcdf.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Write gridded data to netcdf file</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>grid2netcdf</span>(<span class='no'>gdata</span>, <span class='kw'>date</span> <span class='kw'>=</span> <span class='st'>"9999-09-09"</span>, <span class='kw'>outfile</span> <span class='kw'>=</span> <span class='st'>"out.nc"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>grid.data</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>writes netCDF file</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index db21288..85c199d 100644
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
 
-      
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="PEcAn.html">PEcAn</a></code> </p>
-        </td>
-        <td><p>R package to support PEcAn, the Predictive Ecosystem Analyzer</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="arrhenius.scaling.html">arrhenius.scaling()</a></code> </p>
-        </td>
-        <td><p>Arrhenius scaling</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="as.sequence.html">as.sequence()</a></code> </p>
-        </td>
-        <td><p>as.sequence</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="bibtexify.html">bibtexify()</a></code> </p>
-        </td>
-        <td><p>bibtexify</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="bugs.rdist.html">bugs.rdist()</a></code> </p>
-        </td>
-        <td><p>bugs.rdist</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="capitalize.html">capitalize()</a></code> </p>
-        </td>
-        <td><p>Capitalize a string</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="clear.scratch.html">clear.scratch()</a></code> </p>
-        </td>
-        <td><p>Clear EBI-CLUSTER worker node local scratch directories of old PEcAn output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="convert.expr.html">convert.expr()</a></code> </p>
-        </td>
-        <td><p>convert.expr</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="convert.input.html">convert.input()</a></code> </p>
-        </td>
-        <td><p>Convert between formats, reusing existing files where possible</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="create.base.plot.html">create.base.plot()</a></code> </p>
-        </td>
-        <td><p>Create Base Plot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="days_in_year.html">days_in_year()</a></code> </p>
-        </td>
-        <td><p>Number of days in a year</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dhist.html">dhist()</a></code> </p>
-        </td>
-        <td><p>Diagonally Cut Histogram</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="distn.stats.html">distn.stats()</a></code> </p>
-        </td>
-        <td><p>Distribution Stats</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="distn.table.stats.html">distn.table.stats()</a></code> </p>
-        </td>
-        <td><p>return mean and standard deviation of a distribution for each distribution in a table with <code>colnames = c('distn', 'a', 'b')</code>,
- e.g. in a table of priors</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="do_conversions.html">do_conversions()</a></code> </p>
-        </td>
-        <td><p>do_conversions</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.file.html">download.file()</a></code> </p>
-        </td>
-        <td><p>download.file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.url.html">download.url()</a></code> </p>
-        </td>
-        <td><p>Download file from the url.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ensemble.filename.html">ensemble.filename()</a></code> </p>
-        </td>
-        <td><p>Generate ensemble filenames</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="full.path.html">full.path()</a></code> </p>
-        </td>
-        <td><p>Creates an absolute path to a folder</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.ensemble.inputs.html">get.ensemble.inputs()</a></code> </p>
-        </td>
-        <td><p>get.ensemble.inputs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.ensemble.samples.html">get.ensemble.samples()</a></code> </p>
-        </td>
-        <td><p>Get Ensemble Samples</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.model.output.html">get.model.output()</a></code> </p>
-        </td>
-        <td><p>Retrieve model output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.parameter.stat.html">get.parameter.stat()</a></code> </p>
-        </td>
-        <td><p>Get Parameter Statistics</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.quantiles.html">get.quantiles()</a></code> </p>
-        </td>
-        <td><p>Get Quantiles</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.results.html">get.results()</a></code> </p>
-        </td>
-        <td><p>Generate model output for PEcAn analyses</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.run.id.html">get.run.id()</a></code> </p>
-        </td>
-        <td><p>Get Run ID</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.sa.sample.list.html">get.sa.sample.list()</a></code> </p>
-        </td>
-        <td><p>get.sa.sample.list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.sa.samples.html">get.sa.samples()</a></code> </p>
-        </td>
-        <td><p>get sensitivity analysis samples</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.stats.mcmc.html">get.stats.mcmc()</a></code> </p>
-        </td>
-        <td><p>Get stats for parameters in MCMC output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="grid2netcdf.html">grid2netcdf()</a></code> </p>
-        </td>
-        <td><p>grid2netcdf</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="iqr.html">iqr()</a></code> </p>
-        </td>
-        <td><p>Interquartile range</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="left.pad.zeros.html">left.pad.zeros()</a></code> </p>
-        </td>
-        <td><p>Left Pad Zeros</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="listToArgString.html">listToArgString()</a></code> </p>
-        </td>
-        <td><p>format a list of arguments as one comma-separated string</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load.modelpkg.html">load.modelpkg()</a></code> </p>
-        </td>
-        <td><p>Load model package</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logger.debug.html">logger.debug()</a></code> </p>
-        </td>
-        <td><p>Logger functions (imported temporarily from PEcAn.logger)</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="match_file.html">match_file()</a></code> </p>
-        </td>
-        <td><p>Match a file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="mcmc.list2init.html">mcmc.list2init()</a></code> </p>
-        </td>
-        <td><p>Convert mcmc.list to initial condition list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2model.exists.html">met2model.exists()</a></code> </p>
-        </td>
-        <td><p>met2model.exists</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="misc.are.convertible.html">misc.are.convertible()</a></code> </p>
-        </td>
-        <td><p>misc.are.convertible</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="misc.convert.html">misc.convert()</a></code> </p>
-        </td>
-        <td><p>misc.convert</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="mstmipvar.html">mstmipvar()</a></code> </p>
-        </td>
-        <td><p>MstMIP variable</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="n_leap_day.html">n_leap_day()</a></code> </p>
-        </td>
-        <td><p>n_leap_day</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="newxtable.html">newxtable()</a></code> </p>
-        </td>
-        <td><p>newxtable</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="paste.stats.html">paste.stats()</a></code> </p>
-        </td>
-        <td><p>Paste Stats</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pdf.stats.html">pdf.stats()</a></code> </p>
-        </td>
-        <td><p>Probability Distirbution Function Statistics</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot_data.html">plot_data()</a></code> </p>
-        </td>
-        <td><p>Add data to plot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="r2bugs.distributions.html">r2bugs.distributions()</a></code> </p>
-        </td>
-        <td><p>convert R parameterizations to BUGS paramaterizations</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.ensemble.output.html">read.ensemble.output()</a></code> </p>
-        </td>
-        <td><p>Read ensemble output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.output.html">read.output()</a></code> </p>
-        </td>
-        <td><p>Read model output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.sa.output.html">read.sa.output()</a></code> </p>
-        </td>
-        <td><p>Read Sensitivity Analysis output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_web_config.html">read_web_config()</a></code> </p>
-        </td>
-        <td><p>read_web_config</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="regrid.html">regrid()</a></code> </p>
-        </td>
-        <td><p>regrid</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="retry.func.html">retry.func()</a></code> </p>
-        </td>
-        <td><p>retry.func</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="rsync.html">rsync()</a></code> </p>
-        </td>
-        <td><p>rsync</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="run.write.configs.html">run.write.configs()</a></code> </p>
-        </td>
-        <td><p>Run model specific write configuration functions</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="seconds_in_year.html">seconds_in_year()</a></code> </p>
-        </td>
-        <td><p>Number of seconds in a given year</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sendmail.html">sendmail()</a></code> </p>
-        </td>
-        <td><p>Clear EBI-CLUSTER worker node local scratch directories of old PEcAn output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sensitivity.filename.html">sensitivity.filename()</a></code> </p>
-        </td>
-        <td><p>Generate sensitivity analysis filenames</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ssh.html">ssh()</a></code> </p>
-        </td>
-        <td><p>SSH</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="standard_vars.html">standard_vars</a></code> </p>
-        </td>
-        <td><p>Standardized variable names and units for PEcAn</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="status.check.html">status.check()</a></code> </p>
-        </td>
-        <td><p>status.check</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="status.end.html">status.end()</a></code> </p>
-        </td>
-        <td><p>status.end</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="status.skip.html">status.skip()</a></code> </p>
-        </td>
-        <td><p>status.skip</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="status.start.html">status.start()</a></code> </p>
-        </td>
-        <td><p>status.start</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="summarize.result.html">summarize.result()</a></code> </p>
-        </td>
-        <td><p>Summarize Results</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="tabnum.html">tabnum()</a></code> </p>
-        </td>
-        <td><p>Table numbers</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="temp.settings.html">temp.settings()</a></code> </p>
-        </td>
-        <td><p>temp.settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="theme_border.html">theme_border()</a></code> </p>
-        </td>
-        <td><p>Theme border for plot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="timezone_hour.html">timezone_hour()</a></code> </p>
-        </td>
-        <td><p>timezone_hour</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="to_ncdim.html">to_ncdim()</a></code> </p>
-        </td>
-        <td><p>Make some values into an NCDF dimension variable</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="to_ncvar.html">to_ncvar()</a></code> </p>
-        </td>
-        <td><p>Define an NCDF variable</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="trait.lookup.html">trait.lookup()</a></code> </p>
-        </td>
-        <td><p>Dictionary of terms used to identify traits in ed, filenames, and figures</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="transformstats.html">transformstats()</a></code> </p>
-        </td>
-        <td><p>Transform Stats</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="tryl.html">tryl()</a></code> </p>
-        </td>
-        <td><p>tryl</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="units_are_equivalent.html">units_are_equivalent()</a></code> </p>
-        </td>
-        <td><p>Check if two unit strings are equivalent</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="vecpaste.html">vecpaste()</a></code> </p>
-        </td>
-        <td><p>vecpaste</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.ensemble.configs.html">write.ensemble.configs()</a></code> </p>
-        </td>
-        <td><p>Write ensemble configs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.sa.configs.html">write.sa.configs()</a></code> </p>
-        </td>
-        <td><p>Write sensitivity analysis config files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="zero.bounded.density.html">zero.bounded.density()</a></code> </p>
-        </td>
-        <td><p>Zero Bounded Density</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="zero.truncate.html">zero.truncate()</a></code> </p>
-        </td>
-        <td><p>Zero Truncate</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="PEcAn.html">PEcAn</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    R package to support PEcAn, the Predictive Ecosystem
+                    Analyzer
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="arrhenius.scaling.html"
+                        >arrhenius.scaling()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Arrhenius scaling</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="as.sequence.html">as.sequence()</a></code>
+                  </p>
+                </td>
+                <td><p>as.sequence</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="bibtexify.html">bibtexify()</a></code>
+                  </p>
+                </td>
+                <td><p>bibtexify</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="bugs.rdist.html">bugs.rdist()</a></code>
+                  </p>
+                </td>
+                <td><p>bugs.rdist</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="capitalize.html">capitalize()</a></code>
+                  </p>
+                </td>
+                <td><p>Capitalize a string</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="clear.scratch.html">clear.scratch()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Clear EBI-CLUSTER worker node local scratch directories of
+                    old PEcAn output
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="convert.expr.html">convert.expr()</a></code>
+                  </p>
+                </td>
+                <td><p>convert.expr</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="convert.input.html">convert.input()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Convert between formats, reusing existing files where
+                    possible
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="create.base.plot.html"
+                        >create.base.plot()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create Base Plot</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="days_in_year.html">days_in_year()</a></code>
+                  </p>
+                </td>
+                <td><p>Number of days in a year</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="dhist.html">dhist()</a></code>
+                  </p>
+                </td>
+                <td><p>Diagonally Cut Histogram</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="distn.stats.html">distn.stats()</a></code>
+                  </p>
+                </td>
+                <td><p>Distribution Stats</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="distn.table.stats.html"
+                        >distn.table.stats()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    return mean and standard deviation of a distribution for
+                    each distribution in a table with
+                    <code>colnames = c('distn', 'a', 'b')</code>, e.g. in a
+                    table of priors
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="do_conversions.html">do_conversions()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>do_conversions</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.file.html">download.file()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="download.url.html">download.url()</a></code>
+                  </p>
+                </td>
+                <td><p>Download file from the url.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="ensemble.filename.html"
+                        >ensemble.filename()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Generate ensemble filenames</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="full.path.html">full.path()</a></code>
+                  </p>
+                </td>
+                <td><p>Creates an absolute path to a folder</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.ensemble.inputs.html"
+                        >get.ensemble.inputs()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>get.ensemble.inputs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.ensemble.samples.html"
+                        >get.ensemble.samples()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get Ensemble Samples</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.model.output.html"
+                        >get.model.output()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Retrieve model output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.parameter.stat.html"
+                        >get.parameter.stat()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get Parameter Statistics</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.quantiles.html">get.quantiles()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get Quantiles</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.results.html">get.results()</a></code>
+                  </p>
+                </td>
+                <td><p>Generate model output for PEcAn analyses</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.run.id.html">get.run.id()</a></code>
+                  </p>
+                </td>
+                <td><p>Get Run ID</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.sa.sample.list.html"
+                        >get.sa.sample.list()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>get.sa.sample.list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.sa.samples.html">get.sa.samples()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>get sensitivity analysis samples</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.stats.mcmc.html">get.stats.mcmc()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get stats for parameters in MCMC output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="grid2netcdf.html">grid2netcdf()</a></code>
+                  </p>
+                </td>
+                <td><p>grid2netcdf</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="iqr.html">iqr()</a></code>
+                  </p>
+                </td>
+                <td><p>Interquartile range</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="left.pad.zeros.html">left.pad.zeros()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Left Pad Zeros</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="listToArgString.html"
+                        >listToArgString()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    format a list of arguments as one comma-separated string
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="load.modelpkg.html">load.modelpkg()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Load model package</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="logger.debug.html">logger.debug()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Logger functions (imported temporarily from PEcAn.logger)
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="match_file.html">match_file()</a></code>
+                  </p>
+                </td>
+                <td><p>Match a file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="mcmc.list2init.html">mcmc.list2init()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Convert mcmc.list to initial condition list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.exists.html"
+                        >met2model.exists()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2model.exists</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="misc.are.convertible.html"
+                        >misc.are.convertible()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>misc.are.convertible</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="misc.convert.html">misc.convert()</a></code>
+                  </p>
+                </td>
+                <td><p>misc.convert</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="mstmipvar.html">mstmipvar()</a></code>
+                  </p>
+                </td>
+                <td><p>MstMIP variable</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="n_leap_day.html">n_leap_day()</a></code>
+                  </p>
+                </td>
+                <td><p>n_leap_day</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="newxtable.html">newxtable()</a></code>
+                  </p>
+                </td>
+                <td><p>newxtable</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="paste.stats.html">paste.stats()</a></code>
+                  </p>
+                </td>
+                <td><p>Paste Stats</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pdf.stats.html">pdf.stats()</a></code>
+                  </p>
+                </td>
+                <td><p>Probability Distirbution Function Statistics</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="plot_data.html">plot_data()</a></code>
+                  </p>
+                </td>
+                <td><p>Add data to plot</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="r2bugs.distributions.html"
+                        >r2bugs.distributions()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>convert R parameterizations to BUGS paramaterizations</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.ensemble.output.html"
+                        >read.ensemble.output()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read ensemble output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="read.output.html">read.output()</a></code>
+                  </p>
+                </td>
+                <td><p>Read model output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.sa.output.html">read.sa.output()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read Sensitivity Analysis output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read_web_config.html"
+                        >read_web_config()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>read_web_config</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="regrid.html">regrid()</a></code>
+                  </p>
+                </td>
+                <td><p>regrid</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="retry.func.html">retry.func()</a></code>
+                  </p>
+                </td>
+                <td><p>retry.func</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="rsync.html">rsync()</a></code>
+                  </p>
+                </td>
+                <td><p>rsync</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="run.write.configs.html"
+                        >run.write.configs()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Run model specific write configuration functions</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="seconds_in_year.html"
+                        >seconds_in_year()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Number of seconds in a given year</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sendmail.html">sendmail()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Clear EBI-CLUSTER worker node local scratch directories of
+                    old PEcAn output
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="sensitivity.filename.html"
+                        >sensitivity.filename()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Generate sensitivity analysis filenames</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ssh.html">ssh()</a></code>
+                  </p>
+                </td>
+                <td><p>SSH</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="standard_vars.html">standard_vars</a></code>
+                  </p>
+                </td>
+                <td><p>Standardized variable names and units for PEcAn</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="status.check.html">status.check()</a></code>
+                  </p>
+                </td>
+                <td><p>status.check</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="status.end.html">status.end()</a></code>
+                  </p>
+                </td>
+                <td><p>status.end</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="status.skip.html">status.skip()</a></code>
+                  </p>
+                </td>
+                <td><p>status.skip</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="status.start.html">status.start()</a></code>
+                  </p>
+                </td>
+                <td><p>status.start</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="summarize.result.html"
+                        >summarize.result()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Summarize Results</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="tabnum.html">tabnum()</a></code>
+                  </p>
+                </td>
+                <td><p>Table numbers</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="temp.settings.html">temp.settings()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>temp.settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="theme_border.html">theme_border()</a></code>
+                  </p>
+                </td>
+                <td><p>Theme border for plot</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="timezone_hour.html">timezone_hour()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>timezone_hour</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="to_ncdim.html">to_ncdim()</a></code>
+                  </p>
+                </td>
+                <td><p>Make some values into an NCDF dimension variable</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="to_ncvar.html">to_ncvar()</a></code>
+                  </p>
+                </td>
+                <td><p>Define an NCDF variable</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="trait.lookup.html">trait.lookup()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Dictionary of terms used to identify traits in ed,
+                    filenames, and figures
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="transformstats.html">transformstats()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Transform Stats</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="tryl.html">tryl()</a></code>
+                  </p>
+                </td>
+                <td><p>tryl</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="units_are_equivalent.html"
+                        >units_are_equivalent()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check if two unit strings are equivalent</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="vecpaste.html">vecpaste()</a></code>
+                  </p>
+                </td>
+                <td><p>vecpaste</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.ensemble.configs.html"
+                        >write.ensemble.configs()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write ensemble configs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.sa.configs.html"
+                        >write.sa.configs()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write sensitivity analysis config files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="zero.bounded.density.html"
+                        >zero.bounded.density()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Zero Bounded Density</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="zero.truncate.html">zero.truncate()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Zero Truncate</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
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+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Interquartile range</h1>
-    
-    <div class="hidden name"><code>iqr.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate interquartile range</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>iqr</span>(<span class='no'>x</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>vector</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>numeric vector of length 2, with the 25th and 75th quantiles of input vector x.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Calculates the 25th and 75th quantiles given a vector x; used in function <a href='dhist.html'>dhist</a>.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Interquartile range</h1>
+
+            <div class="hidden name"><code>iqr.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate interquartile range</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>iqr</span>(<span class='no'>x</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>vector</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            numeric vector of length 2, with the 25th and 75th quantiles of
+            input vector x.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Calculates the 25th and 75th quantiles given a vector x; used in
+            function <a href="dhist.html">dhist</a>.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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diff --git a/base/utils/docs/reference/left.pad.zeros.html b/base/utils/docs/reference/left.pad.zeros.html
index e14644c..724607c 100644
--- a/base/utils/docs/reference/left.pad.zeros.html
+++ b/base/utils/docs/reference/left.pad.zeros.html
@@ -2,163 +2,197 @@
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
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+      crossorigin="anonymous"
+    ></script>
+
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Left Pad Zeros</h1>
-    
-    <div class="hidden name"><code>left.pad.zeros.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>left padded by zeros up to a given number of digits.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>left.pad.zeros</span>(<span class='no'>num</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>num</th>
-      <td><p>number to be padded (integer)</p></td>
-    </tr>
-    <tr>
-      <th>digits</th>
-      <td><p>number of digits to add</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>num with zeros to the left</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>returns a string representing a given number</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Left Pad Zeros</h1>
+
+            <div class="hidden name"><code>left.pad.zeros.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>left padded by zeros up to a given number of digits.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>left.pad.zeros</span>(<span class='no'>num</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>num</th>
+              <td><p>number to be padded (integer)</p></td>
+            </tr>
+            <tr>
+              <th>digits</th>
+              <td><p>number of digits to add</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>num with zeros to the left</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>returns a string representing a given number</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Carl Davidson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Carl Davidson
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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-
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
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diff --git a/base/utils/docs/reference/listToArgString.html b/base/utils/docs/reference/listToArgString.html
index acda11e..0e14c56 100644
--- a/base/utils/docs/reference/listToArgString.html
+++ b/base/utils/docs/reference/listToArgString.html
@@ -2,153 +2,193 @@
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+      • PEcAn.utils
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    <script src="../pkgdown.js"></script>
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>format a list of arguments as one comma-separated string</h1>
-    
-    <div class="hidden name"><code>listToArgString.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>format a list of arguments as one comma-separated string</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>listToArgString</span>(<span class='no'>l</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>l</th>
-      <td><p>a named list of function arguments</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A string containing named argument/value pairs separated by commas</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>format a list of arguments as one comma-separated string</h1>
+
+            <div class="hidden name"><code>listToArgString.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>format a list of arguments as one comma-separated string</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>listToArgString</span>(<span class='no'>l</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>l</th>
+              <td><p>a named list of function arguments</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A string containing named argument/value pairs separated by commas
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
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diff --git a/base/utils/docs/reference/load.modelpkg.html b/base/utils/docs/reference/load.modelpkg.html
index 1d1ea4f..723a691 100644
--- a/base/utils/docs/reference/load.modelpkg.html
+++ b/base/utils/docs/reference/load.modelpkg.html
@@ -2,159 +2,191 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+                type="button"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Load model package</h1>
-    
-    <div class="hidden name"><code>load.modelpkg.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>load model package</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>load.modelpkg</span>(<span class='no'>model</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>model</th>
-      <td><p>name of model</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>FALSE if function returns error; else TRUE</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Load model package</h1>
+
+            <div class="hidden name"><code>load.modelpkg.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>load model package</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load.modelpkg</span>(<span class='no'>model</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>model</th>
+              <td><p>name of model</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>FALSE if function returns error; else TRUE</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>require.modelpkg</span>(<span class='no'>BioCro</span>)
 <span class='co'># }</span></pre>
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-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
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+          <h2>Author</h2>
 
-  
+          David LeBauer
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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+
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diff --git a/base/utils/docs/reference/logger.debug.html b/base/utils/docs/reference/logger.debug.html
index a007eaa..e2585a3 100644
--- a/base/utils/docs/reference/logger.debug.html
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@@ -2,133 +2,163 @@
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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-<div class="row">
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-    <div class="page-header">
-    <h1>Logger functions (imported temporarily from PEcAn.logger)</h1>
-    
-    <div class="hidden name"><code>logger.debug.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Logger functions (imported temporarily from PEcAn.logger)</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Logger functions (imported temporarily from PEcAn.logger)</h1>
 
-    <pre class="usage"><span class='fu'>logger.debug</span>(<span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>logger.debug.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Logger functions (imported temporarily from PEcAn.logger)</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>logger.debug</span>(<span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
-
diff --git a/base/utils/docs/reference/match_file.html b/base/utils/docs/reference/match_file.html
index 31c36ae..de6264c 100644
--- a/base/utils/docs/reference/match_file.html
+++ b/base/utils/docs/reference/match_file.html
@@ -2,168 +2,210 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>Match a file — match_file • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Match a file — match_file" />
+
+    <meta
+      property="og:description"
+      content="Return a list of files given a full prefix and optional suffix. Optionally, 
 confirm that the right number of files are returned. If the wrong number of 
-files is returned, throw an error." />
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+files is returned, throw an error."
+    />
+    <meta name="twitter:card" content="summary" />
 
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-    <div class="page-header">
-    <h1>Match a file</h1>
-    
-    <div class="hidden name"><code>match_file.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Return a list of files given a full prefix and optional suffix. Optionally, 
-confirm that the right number of files are returned. If the wrong number of 
-files is returned, throw an error.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>match_file</span>(<span class='no'>path_prefix</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>expect</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>path_prefix</th>
-      <td><p>Full path and file prefix</p></td>
-    </tr>
-    <tr>
-      <th>suffix</th>
-      <td><p>File suffix, as character (default = `NULL`)</p></td>
-    </tr>
-    <tr>
-      <th>expect</th>
-      <td><p>Number of files expected to be returned (default = `NULL`)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Character vector of matched file names, as full paths.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>If `path_prefix` points to a directory, then all files inside that directory 
-that match the suffix (if provided) are returned.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Match a file</h1>
+
+            <div class="hidden name"><code>match_file.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Return a list of files given a full prefix and optional suffix.
+              Optionally, confirm that the right number of files are returned.
+              If the wrong number of files is returned, throw an error.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>match_file</span>(<span class='no'>path_prefix</span>, <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>expect</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>path_prefix</th>
+              <td><p>Full path and file prefix</p></td>
+            </tr>
+            <tr>
+              <th>suffix</th>
+              <td><p>File suffix, as character (default = `NULL`)</p></td>
+            </tr>
+            <tr>
+              <th>expect</th>
+              <td>
+                <p>
+                  Number of files expected to be returned (default = `NULL`)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Character vector of matched file names, as full paths.</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            If `path_prefix` points to a directory, then all files inside that
+            directory that match the suffix (if provided) are returned.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/reference/mcmc.list2init.html b/base/utils/docs/reference/mcmc.list2init.html
index 143f453..12e49ab 100644
--- a/base/utils/docs/reference/mcmc.list2init.html
+++ b/base/utils/docs/reference/mcmc.list2init.html
@@ -2,153 +2,193 @@
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+
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
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+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Convert mcmc.list to initial condition list — mcmc.list2init"
+    />
+
+    <meta
+      property="og:description"
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+    />
+    <meta name="twitter:card" content="summary" />
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+            <div class="navbar-header">
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+                type="button"
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+                <span
+                  class="label label-default"
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+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert mcmc.list to initial condition list</h1>
-    
-    <div class="hidden name"><code>mcmc.list2init.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Used for restarting MCMC code based on last parameters sampled (e.g. in JAGS)</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>mcmc.list2init</span>(<span class='no'>dat</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>mcmc.list object</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert mcmc.list to initial condition list</h1>
+
+            <div class="hidden name"><code>mcmc.list2init.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Used for restarting MCMC code based on last parameters sampled
+              (e.g. in JAGS)
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>mcmc.list2init</span>(<span class='no'>dat</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td><p>mcmc.list object</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/reference/met2model.exists.html b/base/utils/docs/reference/met2model.exists.html
index 319b33b..46d1120 100644
--- a/base/utils/docs/reference/met2model.exists.html
+++ b/base/utils/docs/reference/met2model.exists.html
@@ -2,156 +2,189 @@
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+    <meta property="og:title" content="met2model.exists — met2model.exists" />
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-<div class="row">
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-    <div class="page-header">
-    <h1>met2model.exists</h1>
-    
-    <div class="hidden name"><code>met2model.exists.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>checks that met2model function exists</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>met2model.exists</span>(<span class='no'>model</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>model</th>
-      <td><p>model package name</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>logical</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Checks if met2model.&lt;model&gt; exists for a particular
-model</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2model.exists</h1>
+
+            <div class="hidden name"><code>met2model.exists.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>checks that met2model function exists</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.exists</span>(<span class='no'>model</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>model</th>
+              <td><p>model package name</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>logical</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Checks if met2model.&lt;model&gt; exists for a particular model</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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diff --git a/base/utils/docs/reference/misc.are.convertible.html b/base/utils/docs/reference/misc.are.convertible.html
index 35f3dfe..0ca9400 100644
--- a/base/utils/docs/reference/misc.are.convertible.html
+++ b/base/utils/docs/reference/misc.are.convertible.html
@@ -2,157 +2,195 @@
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 <html>
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <script src="../pkgdown.js"></script>
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+      content="misc.are.convertible — misc.are.convertible"
+    />
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+    />
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+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
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+                  title="Released package"
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>misc.are.convertible</h1>
-    
-    <div class="hidden name"><code>misc.are.convertible.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>function to check whether units are convertible by misc.convert function</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>misc.are.convertible</span>(<span class='no'>u1</span>, <span class='no'>u2</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>u1</th>
-      <td><p>unit to be converted from, character</p></td>
-    </tr>
-    <tr>
-      <th>u2</th>
-      <td><p>unit to be converted to, character</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>logical</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>misc.are.convertible</h1>
+
+            <div class="hidden name"><code>misc.are.convertible.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              function to check whether units are convertible by misc.convert
+              function
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>misc.are.convertible</span>(<span class='no'>u1</span>, <span class='no'>u2</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>u1</th>
+              <td><p>unit to be converted from, character</p></td>
+            </tr>
+            <tr>
+              <th>u2</th>
+              <td><p>unit to be converted to, character</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>logical</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer, Shawn Serbin
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer, Shawn Serbin
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/misc.convert.html b/base/utils/docs/reference/misc.convert.html
index 43fab36..9865a02 100644
--- a/base/utils/docs/reference/misc.convert.html
+++ b/base/utils/docs/reference/misc.convert.html
@@ -2,161 +2,196 @@
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 <html>
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-
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-
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-<div class="row">
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-    <h1>misc.convert</h1>
-    
-    <div class="hidden name"><code>misc.convert.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>conversion function for the unit conversions that udunits cannot handle but often needed in PEcAn calculations</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>misc.convert</span>(<span class='no'>x</span>, <span class='no'>u1</span>, <span class='no'>u2</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>convertible values</p></td>
-    </tr>
-    <tr>
-      <th>u1</th>
-      <td><p>unit to be converted from, character</p></td>
-    </tr>
-    <tr>
-      <th>u2</th>
-      <td><p>unit to be converted to, character</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>val converted values</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>misc.convert</h1>
+
+            <div class="hidden name"><code>misc.convert.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              conversion function for the unit conversions that udunits cannot
+              handle but often needed in PEcAn calculations
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>misc.convert</span>(<span class='no'>x</span>, <span class='no'>u1</span>, <span class='no'>u2</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>convertible values</p></td>
+            </tr>
+            <tr>
+              <th>u1</th>
+              <td><p>unit to be converted from, character</p></td>
+            </tr>
+            <tr>
+              <th>u2</th>
+              <td><p>unit to be converted to, character</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>val converted values</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer, Shawn Serbin
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer, Shawn Serbin
+        </div>
+      </div>
 
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diff --git a/base/utils/docs/reference/mstmipvar.html b/base/utils/docs/reference/mstmipvar.html
index 288ddbb..0862302 100644
--- a/base/utils/docs/reference/mstmipvar.html
+++ b/base/utils/docs/reference/mstmipvar.html
@@ -2,177 +2,210 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>MstMIP variable</h1>
-    
-    <div class="hidden name"><code>mstmipvar.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>MstMIP variable</h1>
 
-    <div class="ref-description">
-    
-    <p>return MstMIP variable as ncvar</p>
-    
-    </div>
+            <div class="hidden name"><code>mstmipvar.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>return MstMIP variable as ncvar</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>mstmipvar</span>(<span class='no'>name</span>, <span class='kw'>lat</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>lon</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>nsoil</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>mstmipvar</span>(<span class='no'>name</span>, <span class='kw'>lat</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>lon</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>nsoil</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
   <span class='kw'>silent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>name</th>
-      <td><p>name of variable</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>latitude if dimension requests it</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>longitude if dimension requests it</p></td>
-    </tr>
-    <tr>
-      <th>time</th>
-      <td><p>time if dimension requests it</p></td>
-    </tr>
-    <tr>
-      <th>nsoil</th>
-      <td><p>nsoil if dimension requests it</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>ncvar based on MstMIP definition</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>returns a MstMIP variable as a ncvar based on name and other parameters
-passed in.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>name</th>
+              <td><p>name of variable</p></td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>latitude if dimension requests it</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>longitude if dimension requests it</p></td>
+            </tr>
+            <tr>
+              <th>time</th>
+              <td><p>time if dimension requests it</p></td>
+            </tr>
+            <tr>
+              <th>nsoil</th>
+              <td><p>nsoil if dimension requests it</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>ncvar based on MstMIP definition</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            returns a MstMIP variable as a ncvar based on name and other
+            parameters passed in.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/base/utils/docs/reference/n_leap_day.html b/base/utils/docs/reference/n_leap_day.html
index 9eda671..ba0a545 100644
--- a/base/utils/docs/reference/n_leap_day.html
+++ b/base/utils/docs/reference/n_leap_day.html
@@ -2,147 +2,187 @@
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 <html>
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <link href="../pkgdown.css" rel="stylesheet" />
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+    />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>n_leap_day</h1>
-    
-    <div class="hidden name"><code>n_leap_day.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>number of leap days between two dates</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>n_leap_day</span>(<span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>start_date, end_date</th>
-      <td><p>dates in any format recognized by <code><a href='http://www.rdocumentation.org/packages/base/topics/as.Date'>as.Date</a></code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>n_leap_day</h1>
+
+            <div class="hidden name"><code>n_leap_day.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>number of leap days between two dates</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>n_leap_day</span>(<span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>start_date, end_date</th>
+              <td>
+                <p>
+                  dates in any format recognized by
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/base/topics/as.Date"
+                      >as.Date</a
+                    ></code
+                  >
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/reference/newxtable.html b/base/utils/docs/reference/newxtable.html
index 1f939f6..554b786 100644
--- a/base/utils/docs/reference/newxtable.html
+++ b/base/utils/docs/reference/newxtable.html
@@ -2,169 +2,215 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>newxtable</h1>
-    
-    <div class="hidden name"><code>newxtable.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>newxtable</h1>
 
-    <div class="ref-description">
-    
-    <p>New xtable</p>
-    
-    </div>
+            <div class="hidden name"><code>newxtable.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>New xtable</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>newxtable</span>(<span class='no'>x</span>, <span class='kw'>environment</span> <span class='kw'>=</span> <span class='st'>"table"</span>, <span class='kw'>table.placement</span> <span class='kw'>=</span> <span class='st'>"ht"</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>newxtable</span>(<span class='no'>x</span>, <span class='kw'>environment</span> <span class='kw'>=</span> <span class='st'>"table"</span>, <span class='kw'>table.placement</span> <span class='kw'>=</span> <span class='st'>"ht"</span>,
   <span class='kw'>label</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>caption</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>caption.placement</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>align</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>data.frame to be converted to latex table</p></td>
-    </tr>
-    <tr>
-      <th>environment</th>
-      <td><p>can be 'table'; 'sidewaystable' if using latex rotating package</p></td>
-    </tr>
-    <tr>
-      <th>table.placement, label, caption, caption.placement, align</th>
-      <td><p>passed to <code><a href='http://www.rdocumentation.org/packages/xtable/topics/xtable'>xtable</a></code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Latex version of table, with percentages properly formatted</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>utility to properly escape the '<!-- %' sign for latex --></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>data.frame to be converted to latex table</p></td>
+            </tr>
+            <tr>
+              <th>environment</th>
+              <td>
+                <p>
+                  can be 'table'; 'sidewaystable' if using latex rotating
+                  package
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>table.placement, label, caption, caption.placement, align</th>
+              <td>
+                <p>
+                  passed to
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/xtable/topics/xtable"
+                      >xtable</a
+                    ></code
+                  >
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Latex version of table, with percentages properly formatted</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>utility to properly escape the '<!-- %' sign for latex --></p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/paste.stats.html b/base/utils/docs/reference/paste.stats.html
index 00367a3..c2c6b35 100644
--- a/base/utils/docs/reference/paste.stats.html
+++ b/base/utils/docs/reference/paste.stats.html
@@ -2,172 +2,216 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Paste Stats — paste.stats • PEcAn.utils</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Paste Stats — paste.stats" />
-
-<meta property="og:description" content="A helper function for building a LaTex table." />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Paste Stats — paste.stats • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Paste Stats — paste.stats" />
+
+    <meta
+      property="og:description"
+      content="A helper function for building a LaTex table."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
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-    <div id="navbar" class="navbar-collapse collapse">
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Paste Stats</h1>
-    
-    <div class="hidden name"><code>paste.stats.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>A helper function for building a LaTex table.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>paste.stats</span>(<span class='no'>median</span>, <span class='no'>lcl</span>, <span class='no'>ucl</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>median</th>
-      <td><p>50-percent quantile</p></td>
-    </tr>
-    <tr>
-      <th>lcl</th>
-      <td><p>lower confidence limit</p></td>
-    </tr>
-    <tr>
-      <th>ucl</th>
-      <td><p>upper confidence limit</p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>significant digits for printing. Passed to <code><a href='tabnum.html'>tabnum</a></code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Used by <code><a href='get.parameter.stat.html'>get.parameter.stat</a></code>.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Paste Stats</h1>
+
+            <div class="hidden name"><code>paste.stats.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>A helper function for building a LaTex table.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>paste.stats</span>(<span class='no'>median</span>, <span class='no'>lcl</span>, <span class='no'>ucl</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>median</th>
+              <td><p>50-percent quantile</p></td>
+            </tr>
+            <tr>
+              <th>lcl</th>
+              <td><p>lower confidence limit</p></td>
+            </tr>
+            <tr>
+              <th>ucl</th>
+              <td><p>upper confidence limit</p></td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td>
+                <p>
+                  significant digits for printing. Passed to
+                  <code><a href="tabnum.html">tabnum</a></code>
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Used by
+            <code><a href="get.parameter.stat.html">get.parameter.stat</a></code
+            >.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>paste.stats</span>(<span class='fl'>3.333333</span>, <span class='fl'>5.00001</span>, <span class='fl'>6.22222</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>3</span>)
 <span class='co'># [1] "$3.33(5,6.22)$"</span>
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          David LeBauer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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 </html>
-
diff --git a/base/utils/docs/reference/pdf.stats.html b/base/utils/docs/reference/pdf.stats.html
index 4f393c7..8eb3886 100644
--- a/base/utils/docs/reference/pdf.stats.html
+++ b/base/utils/docs/reference/pdf.stats.html
@@ -2,161 +2,206 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Probability Distirbution Function Statistics — pdf.stats • PEcAn.utils</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Probability Distirbution Function Statistics — pdf.stats" />
-
-<meta property="og:description" content="Calculate mean, variance statistics, and CI from a known distribution" />
-<meta name="twitter:card" content="summary" />
-
-
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-<div class="row">
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-    <h1>Probability Distirbution Function Statistics</h1>
-    
-    <div class="hidden name"><code>pdf.stats.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate mean, variance statistics, and CI from a known distribution</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pdf.stats</span>(<span class='no'>distn</span>, <span class='no'>A</span>, <span class='no'>B</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>distn</th>
-      <td><p>name of distribution used by R (beta, f, gamma, lnorm, norm, weibull)</p></td>
-    </tr>
-    <tr>
-      <th>A</th>
-      <td><p>first parameter</p></td>
-    </tr>
-    <tr>
-      <th>B</th>
-      <td><p>second parameter</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list with mean, variance, and 95 CI</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Probability Distirbution Function Statistics</h1>
+
+            <div class="hidden name"><code>pdf.stats.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Calculate mean, variance statistics, and CI from a known
+              distribution
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pdf.stats</span>(<span class='no'>distn</span>, <span class='no'>A</span>, <span class='no'>B</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>distn</th>
+              <td>
+                <p>
+                  name of distribution used by R (beta, f, gamma, lnorm, norm,
+                  weibull)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>A</th>
+              <td><p>first parameter</p></td>
+            </tr>
+            <tr>
+              <th>B</th>
+              <td><p>second parameter</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list with mean, variance, and 95 CI</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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diff --git a/base/utils/docs/reference/plot_data.html b/base/utils/docs/reference/plot_data.html
index 437ead0..364f836 100644
--- a/base/utils/docs/reference/plot_data.html
+++ b/base/utils/docs/reference/plot_data.html
@@ -2,182 +2,238 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      property="og:description"
+      content="Add data to an existing plot or create a new one from create.base.plot"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Add data to plot</h1>
-    
-    <div class="hidden name"><code>plot_data.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Add data to an existing plot or create a new one from <code><a href='create.base.plot.html'>create.base.plot</a></code></p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>plot_data</span>(<span class='no'>trait.data</span>, <span class='kw'>base.plot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>ymax</span>, <span class='kw'>color</span> <span class='kw'>=</span> <span class='st'>"black"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.data</th>
-      <td><p>data to be plotted</p></td>
-    </tr>
-    <tr>
-      <th>base.plot</th>
-      <td><p>a ggplot object (grob),
-created by <code><a href='create.base.plot.html'>create.base.plot</a></code> if none provided</p></td>
-    </tr>
-    <tr>
-      <th>ymax</th>
-      <td><p>maximum height of y</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>updated plot object</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Used to add raw data or summary statistics to the plot of a distribution.
-The height of Y is arbitrary, and can be set to optimize visualization.
-If SE estimates are available, tehse wil be plotted</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p><code><a href='create.base.plot.html'>create.base.plot</a></code></p></div>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Add data to plot</h1>
+
+            <div class="hidden name"><code>plot_data.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Add data to an existing plot or create a new one from
+              <code><a href="create.base.plot.html">create.base.plot</a></code>
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>plot_data</span>(<span class='no'>trait.data</span>, <span class='kw'>base.plot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>ymax</span>, <span class='kw'>color</span> <span class='kw'>=</span> <span class='st'>"black"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.data</th>
+              <td><p>data to be plotted</p></td>
+            </tr>
+            <tr>
+              <th>base.plot</th>
+              <td>
+                <p>
+                  a ggplot object (grob), created by
+                  <code
+                    ><a href="create.base.plot.html">create.base.plot</a></code
+                  >
+                  if none provided
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ymax</th>
+              <td><p>maximum height of y</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>updated plot object</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Used to add raw data or summary statistics to the plot of a
+            distribution. The height of Y is arbitrary, and can be set to
+            optimize visualization. If SE estimates are available, tehse wil be
+            plotted
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              <code><a href="create.base.plot.html">create.base.plot</a></code>
+            </p>
+          </div>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>plot_data</span>(<span class='fu'>data.frame</span>(<span class='kw'>Y</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>2</span>), <span class='kw'>se</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>2</span>)), <span class='kw'>base.plot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='fl'>10</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <li><a href="#details">Details</a></li>
+            <li><a href="#value">Value</a></li>
 
-      <li><a href="#see-also">See also</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
+            <li><a href="#details">Details</a></li>
 
-    <h2>Author</h2>
-    
-David LeBauer
+            <li><a href="#see-also">See also</a></li>
 
-  </div>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <h2>Author</h2>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/reference/r2bugs.distributions.html b/base/utils/docs/reference/r2bugs.distributions.html
index d34f86b..6e4bbf9 100644
--- a/base/utils/docs/reference/r2bugs.distributions.html
+++ b/base/utils/docs/reference/r2bugs.distributions.html
@@ -2,168 +2,221 @@
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+    </title>
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>convert R parameterizations to BUGS paramaterizations</h1>
-    
-    <div class="hidden name"><code>r2bugs.distributions.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>convert R parameterizations to BUGS paramaterizations</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>r2bugs.distributions</span>(<span class='no'>priors</span>, <span class='kw'>direction</span> <span class='kw'>=</span> <span class='st'>"r2bugs"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>priors</th>
-      <td><p>data.frame with columns distn = distribution name, parama, paramb using R default parameterizations</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>priors dataframe using JAGS default parameterizations</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>R and BUGS have different parameterizations for some distributions. This function transforms the distributions from R defaults to BUGS defaults. BUGS is an implementation of the BUGS language, and these transformations are expected to work for bugs.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>convert R parameterizations to BUGS paramaterizations</h1>
+
+            <div class="hidden name"><code>r2bugs.distributions.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>convert R parameterizations to BUGS paramaterizations</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>r2bugs.distributions</span>(<span class='no'>priors</span>, <span class='kw'>direction</span> <span class='kw'>=</span> <span class='st'>"r2bugs"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>priors</th>
+              <td>
+                <p>
+                  data.frame with columns distn = distribution name, parama,
+                  paramb using R default parameterizations
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>priors dataframe using JAGS default parameterizations</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            R and BUGS have different parameterizations for some distributions.
+            This function transforms the distributions from R defaults to BUGS
+            defaults. BUGS is an implementation of the BUGS language, and these
+            transformations are expected to work for bugs.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>priors</span> <span class='kw'>&lt;-</span> <span class='fu'>data.frame</span>(<span class='kw'>distn</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>'weibull'</span>, <span class='st'>'lnorm'</span>, <span class='st'>'norm'</span>, <span class='st'>'gamma'</span>),
                      <span class='kw'>parama</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>1</span>, <span class='fl'>1</span>, <span class='fl'>1</span>),
                      <span class='kw'>paramb</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>))
 <span class='fu'>r2bugs.distributions</span>(<span class='no'>priors</span>)
 <span class='co'># }</span></pre>
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Ben Bolker
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          David LeBauer, Ben Bolker
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diff --git a/base/utils/docs/reference/read.ensemble.output.html b/base/utils/docs/reference/read.ensemble.output.html
index 043e261..3137081 100644
--- a/base/utils/docs/reference/read.ensemble.output.html
+++ b/base/utils/docs/reference/read.ensemble.output.html
@@ -2,185 +2,239 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read ensemble output</h1>
-    
-    <div class="hidden name"><code>read.ensemble.output.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read ensemble output</h1>
 
-    <div class="ref-description">
-    
-    <p>Reads output from model ensemble</p>
-    
-    </div>
+            <div class="hidden name"><code>read.ensemble.output.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Reads output from model ensemble</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>read.ensemble.output</span>(<span class='no'>ensemble.size</span>, <span class='no'>pecandir</span>, <span class='no'>outdir</span>, <span class='no'>start.year</span>, <span class='no'>end.year</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>read.ensemble.output</span>(<span class='no'>ensemble.size</span>, <span class='no'>pecandir</span>, <span class='no'>outdir</span>, <span class='no'>start.year</span>, <span class='no'>end.year</span>,
   <span class='no'>variable</span>, <span class='kw'>ens.run.ids</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ensemble.size</th>
-      <td><p>the number of ensemble members run</p></td>
-    </tr>
-    <tr>
-      <th>pecandir</th>
-      <td><p>specifies where pecan writes its configuration files</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>directory with model output to use in ensemble analysis</p></td>
-    </tr>
-    <tr>
-      <th>start.year</th>
-      <td><p>first year to include in ensemble analysis</p></td>
-    </tr>
-    <tr>
-      <th>end.year</th>
-      <td><p>last year to include in ensemble analysis</p></td>
-    </tr>
-    <tr>
-      <th>variables</th>
-      <td><p>target variables for ensemble analysis</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a list of ensemble model output</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Reads output for an ensemble of length specified by <code>ensemble.size</code> and bounded by <code>start.year</code> 
-and <code>end.year</code></p>
-<p>DEPRECATED: This function has been moved to the <code>PEcAn.uncertainty</code> package.
-The version in <code>PEcAn.utils</code> is deprecated, will not be updated to add any new features,
-and will be removed in a future release of PEcAn.
-Please use <code><a href='http://www.rdocumentation.org/packages/PEcAn.uncertainty/topics/read.ensemble.output'>PEcAn.uncertainty::read.ensemble.output</a></code> instead.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ensemble.size</th>
+              <td><p>the number of ensemble members run</p></td>
+            </tr>
+            <tr>
+              <th>pecandir</th>
+              <td>
+                <p>specifies where pecan writes its configuration files</p>
+              </td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td>
+                <p>directory with model output to use in ensemble analysis</p>
+              </td>
+            </tr>
+            <tr>
+              <th>start.year</th>
+              <td><p>first year to include in ensemble analysis</p></td>
+            </tr>
+            <tr>
+              <th>end.year</th>
+              <td><p>last year to include in ensemble analysis</p></td>
+            </tr>
+            <tr>
+              <th>variables</th>
+              <td><p>target variables for ensemble analysis</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>a list of ensemble model output</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Reads output for an ensemble of length specified by
+            <code>ensemble.size</code> and bounded by
+            <code>start.year</code> and <code>end.year</code>
+          </p>
+          <p>
+            DEPRECATED: This function has been moved to the
+            <code>PEcAn.uncertainty</code> package. The version in
+            <code>PEcAn.utils</code> is deprecated, will not be updated to add
+            any new features, and will be removed in a future release of PEcAn.
+            Please use
+            <code
+              ><a
+                href="http://www.rdocumentation.org/packages/PEcAn.uncertainty/topics/read.ensemble.output"
+                >PEcAn.uncertainty::read.ensemble.output</a
+              ></code
+            >
+            instead.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, David LeBauer, Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, David LeBauer, Rob Kooper
+        </div>
+      </div>
 
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index 7fcfec8..06f7733 100644
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+++ b/base/utils/docs/reference/read.output.html
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read model output</h1>
-    
-    <div class="hidden name"><code>read.output.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read model output</h1>
 
-    <div class="ref-description">
-    
-    <p>Reads the output of a single model run</p>
-    
-    </div>
+            <div class="hidden name"><code>read.output.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Reads the output of a single model run</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>read.output</span>(<span class='no'>runid</span>, <span class='no'>outdir</span>, <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>read.output</span>(<span class='no'>runid</span>, <span class='no'>outdir</span>, <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
   <span class='kw'>variables</span> <span class='kw'>=</span> <span class='st'>"GPP"</span>, <span class='kw'>dataframe</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>pft.name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>runid</th>
-      <td><p>the id distiguishing the model run.</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>the directory that the model's output was sent to</p></td>
-    </tr>
-    <tr>
-      <th>start.year, end.year</th>
-      <td><p>first and last year of output to read. Specify as a date-time (only the year portion is used) or as a four-digit number or string. If NA, reads all years found in <code>outdir</code>.</p></td>
-    </tr>
-    <tr>
-      <th>variables</th>
-      <td><p>variables to be read from model output</p></td>
-    </tr>
-    <tr>
-      <th>dataframe</th>
-      <td><p>Logical: if TRUE, will return output in a data.frame format with a posix column. Useful for align.data and plotting.</p></td>
-    </tr>
-    <tr>
-      <th>pft.name</th>
-      <td><p>character string, name of the pft to read pft-specific output. If NULL no pft-specific output will be read even the variable has pft as a dimension.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>If <code>dataframe=FALSE</code>, a vector of output variables. If <code>dataframe=TRUE</code>, a data.frame of output variables with POSIXct timestamps added.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Generic function to convert model output from model-specific format to 
-a common PEcAn format. This function uses MsTMIP variables except that units of
- (kg m-2 d-1)  are converted to kg ha-1 y-1. Currently this function converts
-Carbon fluxes: GPP, NPP, NEE, TotalResp, AutoResp, HeteroResp,
-DOC_flux, Fire_flux, and Stem (Stem is specific to the BioCro model)
-and Water fluxes: Evaporation (Evap), Transpiration(TVeg),
-surface runoff (Qs), subsurface runoff (Qsb), and rainfall (Rainf).
-For more details, see the
-<a href='http://nacp.ornl.gov/MsTMIP_variables.shtml'>MsTMIP variables</a>
-documentation</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>runid</th>
+              <td><p>the id distiguishing the model run.</p></td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>the directory that the model's output was sent to</p></td>
+            </tr>
+            <tr>
+              <th>start.year, end.year</th>
+              <td>
+                <p>
+                  first and last year of output to read. Specify as a date-time
+                  (only the year portion is used) or as a four-digit number or
+                  string. If NA, reads all years found in <code>outdir</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>variables</th>
+              <td><p>variables to be read from model output</p></td>
+            </tr>
+            <tr>
+              <th>dataframe</th>
+              <td>
+                <p>
+                  Logical: if TRUE, will return output in a data.frame format
+                  with a posix column. Useful for align.data and plotting.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pft.name</th>
+              <td>
+                <p>
+                  character string, name of the pft to read pft-specific output.
+                  If NULL no pft-specific output will be read even the variable
+                  has pft as a dimension.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            If <code>dataframe=FALSE</code>, a vector of output variables. If
+            <code>dataframe=TRUE</code>, a data.frame of output variables with
+            POSIXct timestamps added.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Generic function to convert model output from model-specific format
+            to a common PEcAn format. This function uses MsTMIP variables except
+            that units of (kg m-2 d-1) are converted to kg ha-1 y-1. Currently
+            this function converts Carbon fluxes: GPP, NPP, NEE, TotalResp,
+            AutoResp, HeteroResp, DOC_flux, Fire_flux, and Stem (Stem is
+            specific to the BioCro model) and Water fluxes: Evaporation (Evap),
+            Transpiration(TVeg), surface runoff (Qs), subsurface runoff (Qsb),
+            and rainfall (Rainf). For more details, see the
+            <a href="http://nacp.ornl.gov/MsTMIP_variables.shtml"
+              >MsTMIP variables</a
+            >
+            documentation
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze, David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze, David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/base/utils/docs/reference/read.sa.output.html b/base/utils/docs/reference/read.sa.output.html
index 752ba47..927a73f 100644
--- a/base/utils/docs/reference/read.sa.output.html
+++ b/base/utils/docs/reference/read.sa.output.html
@@ -2,189 +2,241 @@
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+    ></script>
+
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+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    />
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read Sensitivity Analysis output</h1>
-    
-    <div class="hidden name"><code>read.sa.output.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read Sensitivity Analysis output</h1>
 
-    <div class="ref-description">
-    
-    <p>Reads output of sensitivity analysis runs</p>
-    
-    </div>
+            <div class="hidden name"><code>read.sa.output.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>read.sa.output</span>(<span class='no'>traits</span>, <span class='no'>quantiles</span>, <span class='no'>pecandir</span>, <span class='no'>outdir</span>, <span class='kw'>pft.name</span> <span class='kw'>=</span> <span class='st'>""</span>,
+          <div class="ref-description">
+            <p>Reads output of sensitivity analysis runs</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read.sa.output</span>(<span class='no'>traits</span>, <span class='no'>quantiles</span>, <span class='no'>pecandir</span>, <span class='no'>outdir</span>, <span class='kw'>pft.name</span> <span class='kw'>=</span> <span class='st'>""</span>,
   <span class='no'>start.year</span>, <span class='no'>end.year</span>, <span class='no'>variable</span>, <span class='kw'>sa.run.ids</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>per.pft</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>traits</th>
-      <td><p>model parameters included in the sensitivity analysis</p></td>
-    </tr>
-    <tr>
-      <th>quantiles</th>
-      <td><p>quantiles selected for sensitivity analysis</p></td>
-    </tr>
-    <tr>
-      <th>pecandir</th>
-      <td><p>specifies where pecan writes its configuration files</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>directory with model output to use in sensitivity analysis</p></td>
-    </tr>
-    <tr>
-      <th>pft.name</th>
-      <td><p>name of PFT used in sensitivity analysis (Optional)</p></td>
-    </tr>
-    <tr>
-      <th>start.year</th>
-      <td><p>first year to include in sensitivity analysis</p></td>
-    </tr>
-    <tr>
-      <th>end.year</th>
-      <td><p>last year to include in sensitivity analysis</p></td>
-    </tr>
-    <tr>
-      <th>per.pft</th>
-      <td><p>flag to determine whether we want SA on pft-specific variables</p></td>
-    </tr>
-    <tr>
-      <th>variables</th>
-      <td><p>variables to be read from model output</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dataframe with one col per quantile analysed and one row per trait,
- each cell is a list of AGB over time</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, David LeBauer, Rob Kooper, Mike Dietze, Istem Fer
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>traits</th>
+              <td>
+                <p>model parameters included in the sensitivity analysis</p>
+              </td>
+            </tr>
+            <tr>
+              <th>quantiles</th>
+              <td><p>quantiles selected for sensitivity analysis</p></td>
+            </tr>
+            <tr>
+              <th>pecandir</th>
+              <td>
+                <p>specifies where pecan writes its configuration files</p>
+              </td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td>
+                <p>
+                  directory with model output to use in sensitivity analysis
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pft.name</th>
+              <td>
+                <p>name of PFT used in sensitivity analysis (Optional)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>start.year</th>
+              <td><p>first year to include in sensitivity analysis</p></td>
+            </tr>
+            <tr>
+              <th>end.year</th>
+              <td><p>last year to include in sensitivity analysis</p></td>
+            </tr>
+            <tr>
+              <th>per.pft</th>
+              <td>
+                <p>
+                  flag to determine whether we want SA on pft-specific variables
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>variables</th>
+              <td><p>variables to be read from model output</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            dataframe with one col per quantile analysed and one row per trait,
+            each cell is a list of AGB over time
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
 
-Ryan Kelly, David LeBauer, Rob Kooper, Mike Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, David LeBauer, Rob Kooper, Mike Dietze, Istem Fer Ryan
+          Kelly, David LeBauer, Rob Kooper, Mike Dietze
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
+        </div>
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index 00617b1..180ac06 100644
--- a/base/utils/docs/reference/read_web_config.html
+++ b/base/utils/docs/reference/read_web_config.html
@@ -2,153 +2,182 @@
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+    ></script>
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+    <!-- sticky kit -->
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+                <span
+                  class="label label-default"
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+        <!--/.navbar -->
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>read_web_config</h1>
-    
-    <div class="hidden name"><code>read_web_config.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>read_web_config</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_web_config</span>(<span class='kw'>php.config</span> <span class='kw'>=</span> <span class='st'>"../../web/config.php"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>php.config</th>
-      <td><p>Path to `config.php`</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>config.list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>read_web_config</h1>
+
+            <div class="hidden name"><code>read_web_config.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>read_web_config</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_web_config</span>(<span class='kw'>php.config</span> <span class='kw'>=</span> <span class='st'>"../../web/config.php"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>php.config</th>
+              <td><p>Path to `config.php`</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>config.list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze and Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze and Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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   </body>
 </html>
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diff --git a/base/utils/docs/reference/regrid.html b/base/utils/docs/reference/regrid.html
index 9f391c3..b555c9f 100644
--- a/base/utils/docs/reference/regrid.html
+++ b/base/utils/docs/reference/regrid.html
@@ -2,153 +2,184 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
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-<script src="../pkgdown.js"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>regrid — regrid • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+
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+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>regrid</h1>
-    
-    <div class="hidden name"><code>regrid.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Regrid dataset to even grid</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>regrid</span>(<span class='no'>latlon.data</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>latlon.data</th>
-      <td><p>dataframe with lat, lon, and some value to be regridded</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dataframe with regridded data</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>regrid</h1>
+
+            <div class="hidden name"><code>regrid.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Regrid dataset to even grid</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>regrid</span>(<span class='no'>latlon.data</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>latlon.data</th>
+              <td>
+                <p>dataframe with lat, lon, and some value to be regridded</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>dataframe with regridded data</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
-
diff --git a/base/utils/docs/reference/retry.func.html b/base/utils/docs/reference/retry.func.html
index 19e29da..ef0aaf2 100644
--- a/base/utils/docs/reference/retry.func.html
+++ b/base/utils/docs/reference/retry.func.html
@@ -2,138 +2,179 @@
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 <html>
   <head>
-  <meta charset="utf-8">
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+    <script
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+      crossorigin="anonymous"
+    ></script>
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    <meta property="og:title" content="retry.func — retry.func" />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>retry.func</h1>
-    
-    <div class="hidden name"><code>retry.func.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>retry.func</h1>
 
-    <div class="ref-description">
-    
-    <p>Retry function X times before stopping in error</p>
-    
-    </div>
+            <div class="hidden name"><code>retry.func.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>retry.func</span>(<span class='no'>expr</span>, <span class='kw'>isError</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='st'>"try-error"</span> <span class='kw'>%in%</span> <span class='fu'>class</span>(<span class='no'>x</span>),
+          <div class="ref-description">
+            <p>Retry function X times before stopping in error</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>retry.func</span>(<span class='no'>expr</span>, <span class='kw'>isError</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='st'>"try-error"</span> <span class='kw'>%in%</span> <span class='fu'>class</span>(<span class='no'>x</span>),
   <span class='kw'>maxErrors</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>sleep</span> <span class='kw'>=</span> <span class='fl'>0</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>expr</th>
-      <td><p>The function to try running</p></td>
-    </tr>
-    <tr>
-      <th>maxErrors</th>
-      <td><p>The number of times to retry the function</p></td>
-    </tr>
-    <tr>
-      <th>sleep</th>
-      <td><p>How long to wait before retrying the function call</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>retval returns the results of the function call</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Retry function X times before stopping in error</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>expr</th>
+              <td><p>The function to try running</p></td>
+            </tr>
+            <tr>
+              <th>maxErrors</th>
+              <td><p>The number of times to retry the function</p></td>
+            </tr>
+            <tr>
+              <th>sleep</th>
+              <td><p>How long to wait before retrying the function call</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>retval returns the results of the function call</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Retry function X times before stopping in error</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>dap</span> <span class='kw'>&lt;-</span> <span class='fu'>retry.func</span>(
   <span class='kw pkg'>ncdf4</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/ncdf4/topics/nc_open'>nc_open</a></span>(<span class='st'>'https://thredds.daac.ornl.gov/thredds/dodsC/ornldaac/1220/mstmip_driver_global_hd_climate_lwdown_1999_v1.nc4'</span>),
   <span class='kw'>maxErrors</span><span class='kw'>=</span><span class='fl'>10</span>,
@@ -141,40 +182,37 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Shawn Serbin &lt;adapted from https://stackoverflow.com/questions/20770497/how-to-retry-a-statement-on-error&gt;
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Shawn Serbin &lt;adapted from
+          https://stackoverflow.com/questions/20770497/how-to-retry-a-statement-on-error&gt;
+        </div>
+      </div>
+
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+        <div class="copyright">
+          <p>Developed by .</p>
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+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/reference/rsync.html b/base/utils/docs/reference/rsync.html
index d48f824..a777477 100644
--- a/base/utils/docs/reference/rsync.html
+++ b/base/utils/docs/reference/rsync.html
@@ -2,173 +2,202 @@
 <!DOCTYPE html>
 <html>
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+
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>rsync</h1>
-    
-    <div class="hidden name"><code>rsync.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>R implementation of rsync</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>rsync</span>(<span class='no'>args</span>, <span class='no'>from</span>, <span class='no'>to</span>, <span class='kw'>pattern</span> <span class='kw'>=</span> <span class='st'>""</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>args</th>
-      <td><p>rsync arguments (see man rsync)</p></td>
-    </tr>
-    <tr>
-      <th>from</th>
-      <td><p>source</p></td>
-    </tr>
-    <tr>
-      <th>to</th>
-      <td><p>destination</p></td>
-    </tr>
-    <tr>
-      <th>pattern</th>
-      <td><p>file pattern to be matched</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing, transfers files as a side effect</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>rsync is a file copying tool in bash</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>rsync</h1>
+
+            <div class="hidden name"><code>rsync.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>R implementation of rsync</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>rsync</span>(<span class='no'>args</span>, <span class='no'>from</span>, <span class='no'>to</span>, <span class='kw'>pattern</span> <span class='kw'>=</span> <span class='st'>""</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>args</th>
+              <td><p>rsync arguments (see man rsync)</p></td>
+            </tr>
+            <tr>
+              <th>from</th>
+              <td><p>source</p></td>
+            </tr>
+            <tr>
+              <th>to</th>
+              <td><p>destination</p></td>
+            </tr>
+            <tr>
+              <th>pattern</th>
+              <td><p>file pattern to be matched</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing, transfers files as a side effect</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>rsync is a file copying tool in bash</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-Shawn Serbin
-
-  </div>
-</div>
+          David LeBauer Shawn Serbin
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/run.write.configs.html b/base/utils/docs/reference/run.write.configs.html
index 466ce30..b304ccc 100644
--- a/base/utils/docs/reference/run.write.configs.html
+++ b/base/utils/docs/reference/run.write.configs.html
@@ -2,179 +2,242 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
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-<script src="../pkgdown.js"></script>
-
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-
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-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Run model specific write configuration functions — run.write.configs •
+      PEcAn.utils
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Run model specific write configuration functions — run.write.configs"
+    />
+
+    <meta
+      property="og:description"
+      content="Main driver function to call the ecosystem model specific (e.g. ED, SiPNET) 
+run and configuration file scripts"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Run model specific write configuration functions</h1>
-    
-    <div class="hidden name"><code>run.write.configs.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Run model specific write configuration functions</h1>
 
-    <div class="ref-description">
-    
-    <p>Main driver function to call the ecosystem model specific (e.g. ED, SiPNET) 
-run and configuration file scripts</p>
-    
-    </div>
+            <div class="hidden name"><code>run.write.configs.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Main driver function to call the ecosystem model specific (e.g.
+              ED, SiPNET) run and configuration file scripts
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>run.write.configs</span>(<span class='no'>settings</span>, <span class='kw'>write</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>run.write.configs</span>(<span class='no'>settings</span>, <span class='kw'>write</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>ens.sample.method</span> <span class='kw'>=</span> <span class='st'>"uniform"</span>, <span class='kw'>posterior.files</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>NA</span>,
   <span class='fu'>length</span>(<span class='no'>settings</span>$<span class='no'>pfts</span>)), <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>write</th>
-      <td><p>should the runs be written to the database</p></td>
-    </tr>
-    <tr>
-      <th>ens.sample.method</th>
-      <td><p>how to sample the ensemble members('halton' sequence or 'uniform' random)</p></td>
-    </tr>
-    <tr>
-      <th>posterior.files</th>
-      <td><p>Filenames for posteriors for drawing samples for ensemble and sensitivity
-analysis (e.g. post.distns.Rdata, or prior.distns.Rdata). Defaults to NA, in which case the 
-most recent posterior or prior (in that order) for the workflow is used. Should be a vector, 
-with one entry for each PFT. File name only; PFT outdirs will be appended (this forces use of only
-files within this workflow, to avoid confusion).</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>the ecosystem model to generate the configuration files for</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>an updated settings list, which includes ensemble IDs for SA and ensemble analysis</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>DEPRECATED: This function has been moved to the PEcAn.workflow package and will be removed from PEcAn.utils.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>write</th>
+              <td><p>should the runs be written to the database</p></td>
+            </tr>
+            <tr>
+              <th>ens.sample.method</th>
+              <td>
+                <p>
+                  how to sample the ensemble members('halton' sequence or
+                  'uniform' random)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>posterior.files</th>
+              <td>
+                <p>
+                  Filenames for posteriors for drawing samples for ensemble and
+                  sensitivity analysis (e.g. post.distns.Rdata, or
+                  prior.distns.Rdata). Defaults to NA, in which case the most
+                  recent posterior or prior (in that order) for the workflow is
+                  used. Should be a vector, with one entry for each PFT. File
+                  name only; PFT outdirs will be appended (this forces use of
+                  only files within this workflow, to avoid confusion).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td>
+                <p>
+                  the ecosystem model to generate the configuration files for
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            an updated settings list, which includes ensemble IDs for SA and
+            ensemble analysis
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            DEPRECATED: This function has been moved to the PEcAn.workflow
+            package and will be removed from PEcAn.utils.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Ryan Kelly, Mike Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin, Ryan Kelly, Mike Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/seconds_in_year.html b/base/utils/docs/reference/seconds_in_year.html
index 51e4ab9..1e912a1 100644
--- a/base/utils/docs/reference/seconds_in_year.html
+++ b/base/utils/docs/reference/seconds_in_year.html
@@ -2,159 +2,201 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-    
-    <div class="hidden name"><code>seconds_in_year.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Number of seconds in a given year</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>seconds_in_year</span>(<span class='no'>year</span>, <span class='kw'>leap_year</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>year</th>
-      <td><p>Numeric year (can be a vector)</p></td>
-    </tr>
-    <tr>
-      <th>leap_year</th>
-      <td><p>Default = TRUE. If set to FALSE will always return 31536000</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Number of seconds in a given year</h1>
+
+            <div class="hidden name"><code>seconds_in_year.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Number of seconds in a given year</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>seconds_in_year</span>(<span class='no'>year</span>, <span class='kw'>leap_year</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>year</th>
+              <td><p>Numeric year (can be a vector)</p></td>
+            </tr>
+            <tr>
+              <th>leap_year</th>
+              <td>
+                <p>
+                  Default = TRUE. If set to FALSE will always return 31536000
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>seconds_in_year</span>(<span class='fl'>2000</span>)  <span class='co'># Leap year -- 366 x 24 x 60 x 60 = 31622400</span>
 <span class='fu'>seconds_in_year</span>(<span class='fl'>2001</span>)  <span class='co'># Regular year -- 365 x 24 x 60 x 60 = 31536000</span>
 <span class='fu'>seconds_in_year</span>(<span class='fl'>2000</span>:<span class='fl'>2005</span>)  <span class='co'># Vectorized over year</span>
 <span class='co'># }</span></pre>
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-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
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+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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diff --git a/base/utils/docs/reference/sendmail.html b/base/utils/docs/reference/sendmail.html
index 6769394..97084bc 100644
--- a/base/utils/docs/reference/sendmail.html
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-<div class="row">
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-    <div class="page-header">
-    <h1>Clear EBI-CLUSTER worker node local scratch directories of old PEcAn output</h1>
-    
-    <div class="hidden name"><code>sendmail.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Sends email. This assumes the program sendmail is installed.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sendmail</span>(<span class='no'>from</span>, <span class='no'>to</span>, <span class='no'>subject</span>, <span class='no'>body</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>from</th>
-      <td><p>the sender of the mail message</p></td>
-    </tr>
-    <tr>
-      <th>to</th>
-      <td><p>the receipient of the mail message</p></td>
-    </tr>
-    <tr>
-      <th>subject</th>
-      <td><p>the subject of the mail message</p></td>
-    </tr>
-    <tr>
-      <th>body</th>
-      <td><p>the body of the mail message</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Clear EBI-CLUSTER worker node local scratch directories of old
+              PEcAn output
+            </h1>
+
+            <div class="hidden name"><code>sendmail.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Sends email. This assumes the program sendmail is installed.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sendmail</span>(<span class='no'>from</span>, <span class='no'>to</span>, <span class='no'>subject</span>, <span class='no'>body</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>from</th>
+              <td><p>the sender of the mail message</p></td>
+            </tr>
+            <tr>
+              <th>to</th>
+              <td><p>the receipient of the mail message</p></td>
+            </tr>
+            <tr>
+              <th>subject</th>
+              <td><p>the subject of the mail message</p></td>
+            </tr>
+            <tr>
+              <th>body</th>
+              <td><p>the body of the mail message</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>sendmail</span>(<span class='st'>'bob@example.com'</span>, <span class='st'>'joe@example.com'</span>, <span class='st'>'Hi'</span>, <span class='st'>'This is R.'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/sensitivity.filename.html b/base/utils/docs/reference/sensitivity.filename.html
index 729a6a8..707f0f6 100644
--- a/base/utils/docs/reference/sensitivity.filename.html
+++ b/base/utils/docs/reference/sensitivity.filename.html
@@ -2,154 +2,191 @@
 <!DOCTYPE html>
 <html>
   <head>
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-
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+      Generate sensitivity analysis filenames — sensitivity.filename •
+      PEcAn.utils
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
   </head>
 
   <body>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate sensitivity analysis filenames</h1>
-    
-    <div class="hidden name"><code>sensitivity.filename.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generate sensitivity analysis filenames</h1>
 
-    <div class="ref-description">
-    
-    <p>Generate sensitivity analysis filenames</p>
-    
-    </div>
+            <div class="hidden name"><code>sensitivity.filename.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Generate sensitivity analysis filenames</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>sensitivity.filename</span>(<span class='no'>settings</span>, <span class='kw'>prefix</span> <span class='kw'>=</span> <span class='st'>"sensitivity.samples"</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>sensitivity.filename</span>(<span class='no'>settings</span>, <span class='kw'>prefix</span> <span class='kw'>=</span> <span class='st'>"sensitivity.samples"</span>,
   <span class='kw'>suffix</span> <span class='kw'>=</span> <span class='st'>"Rdata"</span>, <span class='kw'>all.var.yr</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>pft</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>ensemble.id</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>sensitivity.analysis</span>$<span class='no'>ensemble.id</span>,
   <span class='kw'>variable</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>sensitivity.analysis</span>$<span class='no'>variable</span>,
   <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>sensitivity.analysis</span>$<span class='no'>start.year</span>,
   <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>sensitivity.analysis</span>$<span class='no'>end.year</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>a filename</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
 
-    <p>Generally uses values in settings, but can be overwritten for manual uses</p>
-    
+          <p>a filename</p>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
 
-      <li><a href="#details">Details</a></li>
+          <p>
+            Generally uses values in settings, but can be overwritten for manual
+            uses
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/ssh.html b/base/utils/docs/reference/ssh.html
index 2a745d5..feeb72d 100644
--- a/base/utils/docs/reference/ssh.html
+++ b/base/utils/docs/reference/ssh.html
@@ -2,151 +2,182 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
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+    <script src="../pkgdown.js"></script>
+
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+
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+    <![endif]-->
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>SSH</h1>
-    
-    <div class="hidden name"><code>ssh.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>R implementation of SSH</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>ssh</span>(<span class='no'>host</span>, <span class='no'>...</span>, <span class='kw'>args</span> <span class='kw'>=</span> <span class='st'>""</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>host</th>
-      <td><p>(character) machine to connect to</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Commands to execute. Will be passed as a single quoted string</p></td>
-    </tr>
-    <tr>
-      <th>args</th>
-      <td><p>futher arguments</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>SSH</h1>
+
+            <div class="hidden name"><code>ssh.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>R implementation of SSH</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>ssh</span>(<span class='no'>host</span>, <span class='no'>...</span>, <span class='kw'>args</span> <span class='kw'>=</span> <span class='st'>""</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>host</th>
+              <td><p>(character) machine to connect to</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  Commands to execute. Will be passed as a single quoted string
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>args</th>
+              <td><p>futher arguments</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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@@ -2,158 +2,231 @@
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+      PEcAn.utils
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Standardized variable names and units for PEcAn — standard_vars"
+    />
+
+    <meta
+      property="og:description"
+      content="A lookup table giving standard names, units and descriptions for variables in PEcAn input/output files.
 Originally based on the MsTMIP standards,
 with additions to accomodate a wider range of model inputs and outputs.
 The standard_vars table replaces both mstmip_vars and mstmip_local,
-both of which are now deprecated." />
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Standardized variable names and units for PEcAn</h1>
-    
-    <div class="hidden name"><code>standard_vars.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>A lookup table giving standard names, units and descriptions for variables in PEcAn input/output files.
-Originally based on the <a href='https://nacp.ornl.gov/MsTMIP_variables.shtml'>MsTMIP</a> standards,
-with additions to accomodate a wider range of model inputs and outputs.
-The standard_vars table replaces both <code>mstmip_vars</code> and <code>mstmip_local</code>,
-both of which are now deprecated.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='no'>standard_vars</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>data frame, all columns character</p><dl class='dl-horizontal'>
- <dt>Variable.Name</dt><dd><p>Short name suitable for programming with</p></dd>
- <dt>standard_name</dt><dd><p>Name used in the NetCDF <a href='http://cfconventions.org/standard-names.html'>CF metadata conventions</a></p></dd>
- <dt>Units</dt><dd><p>Standard units for this variable. Do not call variables by these names if they are in different units.
-   See <code>udunits</code> for conversions to and from non-standard units</p></dd>
- <dt>Long.Name</dt><dd><p>Human-readable variable name, suitable for e.g. axis labels</p></dd>
- <dt>Category</dt><dd><p>What kind of variable is it? (Carbon pool, N flux, dimension, input driver, etc)</p></dd>
- <dt>var_type</dt><dd><p>Storage type (character, integer, etc)</p></dd>
- <dt>dim1,dim2,dim3,dim4</dt><dd><p>Dimensions across which is this variable allowed to vary.
-   Dimension names are themselves standard vars and must be present in the table with category "Dimension"</p></dd>
- <dt>Description</dt><dd><p>Further details. For composite measures, list the variables it is calculated from</p></dd>
-</dl>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Standardized variable names and units for PEcAn</h1>
+
+            <div class="hidden name"><code>standard_vars.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              A lookup table giving standard names, units and descriptions for
+              variables in PEcAn input/output files. Originally based on the
+              <a href="https://nacp.ornl.gov/MsTMIP_variables.shtml">MsTMIP</a>
+              standards, with additions to accomodate a wider range of model
+              inputs and outputs. The standard_vars table replaces both
+              <code>mstmip_vars</code> and <code>mstmip_local</code>, both of
+              which are now deprecated.
+            </p>
+          </div>
+
+          <pre class="usage"><span class='no'>standard_vars</span></pre>
+
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
+
+          <p>data frame, all columns character</p>
+          <dl class="dl-horizontal">
+            <dt>Variable.Name</dt>
+            <dd><p>Short name suitable for programming with</p></dd>
+            <dt>standard_name</dt>
+            <dd>
+              <p>
+                Name used in the NetCDF
+                <a href="http://cfconventions.org/standard-names.html"
+                  >CF metadata conventions</a
+                >
+              </p>
+            </dd>
+            <dt>Units</dt>
+            <dd>
+              <p>
+                Standard units for this variable. Do not call variables by these
+                names if they are in different units. See
+                <code>udunits</code> for conversions to and from non-standard
+                units
+              </p>
+            </dd>
+            <dt>Long.Name</dt>
+            <dd>
+              <p>Human-readable variable name, suitable for e.g. axis labels</p>
+            </dd>
+            <dt>Category</dt>
+            <dd>
+              <p>
+                What kind of variable is it? (Carbon pool, N flux, dimension,
+                input driver, etc)
+              </p>
+            </dd>
+            <dt>var_type</dt>
+            <dd><p>Storage type (character, integer, etc)</p></dd>
+            <dt>dim1,dim2,dim3,dim4</dt>
+            <dd>
+              <p>
+                Dimensions across which is this variable allowed to vary.
+                Dimension names are themselves standard vars and must be present
+                in the table with category "Dimension"
+              </p>
+            </dd>
+            <dt>Description</dt>
+            <dd>
+              <p>
+                Further details. For composite measures, list the variables it
+                is calculated from
+              </p>
+            </dd>
+          </dl>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+          <p>Developed by .</p>
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diff --git a/base/utils/docs/reference/status.check.html b/base/utils/docs/reference/status.check.html
index 4999621..402dc86 100644
--- a/base/utils/docs/reference/status.check.html
+++ b/base/utils/docs/reference/status.check.html
@@ -2,137 +2,161 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+    <title>status.check — status.check • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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   </head>
 
   <body>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+            <div class="navbar-header">
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+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>status.check</h1>
-    
-    <div class="hidden name"><code>status.check.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>status.check</h1>
 
-    <div class="ref-description">
-    
-    <p>PEcAn workflow status tracking: check module status</p>
-    
-    </div>
+            <div class="hidden name"><code>status.check.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>status.check</span>(<span class='no'>name</span>)</pre>
-        
+          <div class="ref-description">
+            <p>PEcAn workflow status tracking: check module status</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>status.check</span>(<span class='no'>name</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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   </body>
 </html>
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diff --git a/base/utils/docs/reference/status.end.html b/base/utils/docs/reference/status.end.html
index 2536a46..e2e65d3 100644
--- a/base/utils/docs/reference/status.end.html
+++ b/base/utils/docs/reference/status.end.html
@@ -2,137 +2,161 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>status.end — status.end • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="status.end — status.end" />
+
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+      property="og:description"
+      content="PEcAn workflow status tracking: end module"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <span class="icon-bar"></span>
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-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>status.end</h1>
-    
-    <div class="hidden name"><code>status.end.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>status.end</h1>
 
-    <div class="ref-description">
-    
-    <p>PEcAn workflow status tracking: end module</p>
-    
-    </div>
+            <div class="hidden name"><code>status.end.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>status.end</span>(<span class='kw'>status</span> <span class='kw'>=</span> <span class='st'>"DONE"</span>)</pre>
-        
+          <div class="ref-description">
+            <p>PEcAn workflow status tracking: end module</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>status.end</span>(<span class='kw'>status</span> <span class='kw'>=</span> <span class='st'>"DONE"</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/status.skip.html b/base/utils/docs/reference/status.skip.html
index 478de70..9905777 100644
--- a/base/utils/docs/reference/status.skip.html
+++ b/base/utils/docs/reference/status.skip.html
@@ -2,137 +2,161 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>status.skip — status.skip • PEcAn.utils</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<meta name="twitter:card" content="summary" />
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-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>status.skip</h1>
 
-    <div class="ref-description">
-    
-    <p>PEcAn workflow status tracking: skip module</p>
-    
-    </div>
+            <div class="hidden name"><code>status.skip.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>status.skip</span>(<span class='no'>name</span>)</pre>
-        
+          <div class="ref-description">
+            <p>PEcAn workflow status tracking: skip module</p>
+          </div>
 
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
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+          <pre
+            class="usage"
+          ><span class='fu'>status.skip</span>(<span class='no'>name</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
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diff --git a/base/utils/docs/reference/status.start.html b/base/utils/docs/reference/status.start.html
index 8388804..d6297ed 100644
--- a/base/utils/docs/reference/status.start.html
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@@ -2,137 +2,161 @@
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>status.start</h1>
-    
-    <div class="hidden name"><code>status.start.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>status.start</h1>
 
-    <div class="ref-description">
-    
-    <p>PEcAn workflow status tracking: start module</p>
-    
-    </div>
+            <div class="hidden name"><code>status.start.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>status.start</span>(<span class='no'>name</span>)</pre>
-        
+          <div class="ref-description">
+            <p>PEcAn workflow status tracking: start module</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>status.start</span>(<span class='no'>name</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
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+          <p>Developed by .</p>
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 </html>
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diff --git a/base/utils/docs/reference/summarize.result.html b/base/utils/docs/reference/summarize.result.html
index 560c408..8ee9877 100644
--- a/base/utils/docs/reference/summarize.result.html
+++ b/base/utils/docs/reference/summarize.result.html
@@ -2,153 +2,187 @@
 <!DOCTYPE html>
 <html>
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+
+    <!-- Font Awesome icons -->
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+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
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+    <meta property="og:title" content="Summarize Results — summarize.result" />
+
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+      content="Summarize results of replicate observations in trait data query"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Summarize Results</h1>
-    
-    <div class="hidden name"><code>summarize.result.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Summarize results of replicate observations in trait data query</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>summarize.result</span>(<span class='no'>result</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>result</th>
-      <td><p>dataframe with results of trait data query</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>result with replicate observations summarized</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Summarize Results</h1>
+
+            <div class="hidden name"><code>summarize.result.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Summarize results of replicate observations in trait data query
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>summarize.result</span>(<span class='no'>result</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>result</th>
+              <td><p>dataframe with results of trait data query</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>result with replicate observations summarized</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/base/utils/docs/reference/tabnum.html b/base/utils/docs/reference/tabnum.html
index 4dc1725..8cb30c1 100644
--- a/base/utils/docs/reference/tabnum.html
+++ b/base/utils/docs/reference/tabnum.html
@@ -2,164 +2,199 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- clipboard.js -->
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <title>Table numbers — tabnum • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
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+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Table numbers — tabnum" />
+
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+      property="og:description"
+      content="Convert number to n significant digits"
+    />
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+
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+    <![endif]-->
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+                type="button"
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+              </button>
+              <span class="navbar-brand">
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Table numbers</h1>
-    
-    <div class="hidden name"><code>tabnum.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert number to n significant digits</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>tabnum</span>(<span class='no'>x</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>3</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>numeric value or vector</p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>number of significant figures</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>x rounded to n significant figures</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Table numbers</h1>
+
+            <div class="hidden name"><code>tabnum.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert number to n significant digits</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>tabnum</span>(<span class='no'>x</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>3</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>numeric value or vector</p></td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td><p>number of significant figures</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>x rounded to n significant figures</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>tabnum</span>(<span class='fl'>1.2345</span>)
 <span class='fu'>tabnum</span>(<span class='fl'>1.2345</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>4</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          David LeBauer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/temp.settings.html b/base/utils/docs/reference/temp.settings.html
index 7ce155f..617cc4e 100644
--- a/base/utils/docs/reference/temp.settings.html
+++ b/base/utils/docs/reference/temp.settings.html
@@ -2,161 +2,197 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
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+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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-<div class="row">
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-    <div class="page-header">
-    <h1>temp.settings</h1>
-    
-    <div class="hidden name"><code>temp.settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Create a temporary settings file</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>temp.settings</span>(<span class='no'>settings.txt</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings.txt</th>
-      <td><p>character vector to be written</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>character vector written to and read from a temporary file</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Uses <code>tempfile</code> function to provide a valid temporary file (OS independent)
-Useful for testing functions that depend on settings file
-Reference: http://stackoverflow.com/a/12940705/199217</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>temp.settings</h1>
+
+            <div class="hidden name"><code>temp.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Create a temporary settings file</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>temp.settings</span>(<span class='no'>settings.txt</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings.txt</th>
+              <td><p>character vector to be written</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>character vector written to and read from a temporary file</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Uses <code>tempfile</code> function to provide a valid temporary
+            file (OS independent) Useful for testing functions that depend on
+            settings file Reference: http://stackoverflow.com/a/12940705/199217
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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diff --git a/base/utils/docs/reference/theme_border.html b/base/utils/docs/reference/theme_border.html
index a5dc7b2..e3145fc 100644
--- a/base/utils/docs/reference/theme_border.html
+++ b/base/utils/docs/reference/theme_border.html
@@ -2,187 +2,226 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
-<!-- Font Awesome icons -->
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Theme border for plot — theme_border • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Theme border for plot — theme_border" />
+
+    <meta property="og:description" content="Add borders to plot" />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+
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+              <ul class="nav navbar-nav">
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Theme border for plot</h1>
-    
-    <div class="hidden name"><code>theme_border.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Theme border for plot</h1>
 
-    <div class="ref-description">
-    
-    <p>Add borders to plot</p>
-    
-    </div>
+            <div class="hidden name"><code>theme_border.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Add borders to plot</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>theme_border</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"left"</span>, <span class='st'>"right"</span>, <span class='st'>"bottom"</span>, <span class='st'>"top"</span>, <span class='st'>"none"</span>),
+          <pre
+            class="usage"
+          ><span class='fu'>theme_border</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"left"</span>, <span class='st'>"right"</span>, <span class='st'>"bottom"</span>, <span class='st'>"top"</span>, <span class='st'>"none"</span>),
   <span class='kw'>colour</span> <span class='kw'>=</span> <span class='st'>"black"</span>, <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>linetype</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>type</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>colour</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>size</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>linetype</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>adds borders to ggplot as a side effect</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Has ggplot2 display only specified borders, e.g. ('L'-shaped) borders,
-rather than a rectangle or no border. Note that the order can be significant;
-for example, if you specify the L border option and then a theme, the theme settings
-will override the border option, so you need to specify the theme (if any) before the border option, as above.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>type</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>colour</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>size</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>linetype</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>adds borders to ggplot as a side effect</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Has ggplot2 display only specified borders, e.g. ('L'-shaped)
+            borders, rather than a rectangle or no border. Note that the order
+            can be significant; for example, if you specify the L border option
+            and then a theme, the theme settings will override the border
+            option, so you need to specify the theme (if any) before the border
+            option, as above.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>df</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>( <span class='kw'>x</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>y</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>4</span>,<span class='fl'>5</span>,<span class='fl'>6</span>) )
 <span class='fu'>ggplot</span>(<span class='kw'>data</span><span class='kw'>=</span><span class='no'>df</span>, <span class='fu'>aes</span>(<span class='kw'>x</span><span class='kw'>=</span><span class='no'>x</span>, <span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>)) + <span class='fu'>geom_point</span>() + <span class='fu'>theme_bw</span>() +
        <span class='fu'>opts</span>(<span class='kw'>panel.border</span> <span class='kw'>=</span> <span class='fu'>theme_border</span>(<span class='fu'>c</span>(<span class='st'>'bottom'</span>,<span class='st'>'left'</span>)) )
 <span class='fu'>ggplot</span>(<span class='kw'>data</span><span class='kw'>=</span><span class='no'>df</span>, <span class='fu'>aes</span>(<span class='kw'>x</span><span class='kw'>=</span><span class='no'>x</span>, <span class='kw'>y</span><span class='kw'>=</span><span class='no'>y</span>)) + <span class='fu'>geom_point</span>() + <span class='fu'>theme_bw</span>() +
        <span class='fu'>opts</span>(<span class='kw'>panel.border</span> <span class='kw'>=</span> <span class='fu'>theme_border</span>(<span class='fu'>c</span>(<span class='st'>'b'</span>,<span class='st'>'l'</span>)) )
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
+            <li><a href="#value">Value</a></li>
 
-    <h2>Author</h2>
-    
-Rudolf Cardinal
+            <li><a href="#details">Details</a></li>
 
-<a href='ggplot2 google group'>ggplot2 google group</a>https://groups.google.com/forum/?fromgroups#!topic/ggplot2/-ZjRE2OL8lE
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  </div>
-</div>
+          <h2>Author</h2>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          Rudolf Cardinal
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <a href="ggplot2 google group">ggplot2 google group</a
+          >https://groups.google.com/forum/?fromgroups#!topic/ggplot2/-ZjRE2OL8lE
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/timezone_hour.html b/base/utils/docs/reference/timezone_hour.html
index b795625..4ece10c 100644
--- a/base/utils/docs/reference/timezone_hour.html
+++ b/base/utils/docs/reference/timezone_hour.html
@@ -2,159 +2,194 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="timezone_hour — timezone_hour" />
-
-<meta property="og:description" content="return the number of hours offset to UTC for a timezone." />
-<meta name="twitter:card" content="summary" />
-
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>timezone_hour — timezone_hour • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="timezone_hour — timezone_hour" />
+
+    <meta
+      property="og:description"
+      content="return the number of hours offset to UTC for a timezone."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../index.html">
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-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>timezone_hour</h1>
-    
-    <div class="hidden name"><code>timezone_hour.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>return the number of hours offset to UTC for a timezone.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>timezone_hour</span>(<span class='no'>timezone</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>timezone</th>
-      <td><p>to be converted</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>hours offset of the timezone</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>timezone_hour</h1>
+
+            <div class="hidden name"><code>timezone_hour.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>return the number of hours offset to UTC for a timezone.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>timezone_hour</span>(<span class='no'>timezone</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>timezone</th>
+              <td><p>to be converted</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>hours offset of the timezone</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>timezone_hour</span>(<span class='st'>'America/New_York'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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 </html>
-
diff --git a/base/utils/docs/reference/to_ncdim.html b/base/utils/docs/reference/to_ncdim.html
index 95ca07d..b09daf4 100644
--- a/base/utils/docs/reference/to_ncdim.html
+++ b/base/utils/docs/reference/to_ncdim.html
@@ -2,157 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Make some values into an NCDF dimension variable — to_ncdim • PEcAn.utils
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Make some values into an NCDF dimension variable</h1>
-    
-    <div class="hidden name"><code>to_ncdim.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Units and longnames are looked up from the <code><a href='standard_vars.html'>standard_vars</a></code> table</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>to_ncdim</span>(<span class='no'>dimname</span>, <span class='no'>vals</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dimname</th>
-      <td><p>character vector, standard dimension name (must be in PEcAn.utils::standard_vars)</p></td>
-    </tr>
-    <tr>
-      <th>vals</th>
-      <td><p>values of dimension; can be single value or vector</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>ncdim defined according to standard_vars</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Make some values into an NCDF dimension variable</h1>
+
+            <div class="hidden name"><code>to_ncdim.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Units and longnames are looked up from the
+              <code><a href="standard_vars.html">standard_vars</a></code> table
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>to_ncdim</span>(<span class='no'>dimname</span>, <span class='no'>vals</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dimname</th>
+              <td>
+                <p>
+                  character vector, standard dimension name (must be in
+                  PEcAn.utils::standard_vars)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>vals</th>
+              <td><p>values of dimension; can be single value or vector</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>ncdim defined according to standard_vars</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Anne Thomas
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Anne Thomas
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
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diff --git a/base/utils/docs/reference/to_ncvar.html b/base/utils/docs/reference/to_ncvar.html
index c3ecb59..6a87f50 100644
--- a/base/utils/docs/reference/to_ncvar.html
+++ b/base/utils/docs/reference/to_ncvar.html
@@ -2,157 +2,197 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Define an NCDF variable</h1>
-    
-    <div class="hidden name"><code>to_ncvar.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Define an NCDF variable</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>to_ncvar</span>(<span class='no'>varname</span>, <span class='no'>dims</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>varname</th>
-      <td><p>character vector, standard variable name (must be in PEcAn.utils::standard_vars)</p></td>
-    </tr>
-    <tr>
-      <th>dims</th>
-      <td><p>list of previously defined ncdims (function will match subset of dims for this variable in standard_vars; can include other dims--enables lapply.)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>ncvar defined according to standard_vars</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Define an NCDF variable</h1>
+
+            <div class="hidden name"><code>to_ncvar.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Define an NCDF variable</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>to_ncvar</span>(<span class='no'>varname</span>, <span class='no'>dims</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>varname</th>
+              <td>
+                <p>
+                  character vector, standard variable name (must be in
+                  PEcAn.utils::standard_vars)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>dims</th>
+              <td>
+                <p>
+                  list of previously defined ncdims (function will match subset
+                  of dims for this variable in standard_vars; can include other
+                  dims--enables lapply.)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>ncvar defined according to standard_vars</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Anne Thomas
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Anne Thomas
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/trait.lookup.html b/base/utils/docs/reference/trait.lookup.html
index 8a144af..376ce50 100644
--- a/base/utils/docs/reference/trait.lookup.html
+++ b/base/utils/docs/reference/trait.lookup.html
@@ -2,127 +2,186 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<div class="row">
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-    <h1>Dictionary of terms used to identify traits in ed, filenames, and figures</h1>
-    
-    <div class="hidden name"><code>trait.lookup.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Dictionary of terms used to identify traits in ed, filenames, and figures</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>trait.lookup</span>(<span class='kw'>traits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>traits</th>
-      <td><p>a vector of trait names, if traits = NULL, all of the traits will be returned.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a dataframe with id, the name used by ED and PEcAn database for a parameter; fileid, an abbreviated
-    name used for files; figid, the parameter name written out as best known in english for figures
-    and tables.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"># NOT RUN {
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Dictionary of terms used to identify traits in ed, filenames, and
+              figures
+            </h1>
+
+            <div class="hidden name"><code>trait.lookup.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Dictionary of terms used to identify traits in ed, filenames, and
+              figures
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>trait.lookup</span>(<span class='kw'>traits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>traits</th>
+              <td>
+                <p>
+                  a vector of trait names, if traits = NULL, all of the traits
+                  will be returned.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            a dataframe with id, the name used by ED and PEcAn database for a
+            parameter; fileid, an abbreviated name used for files; figid, the
+            parameter name written out as best known in english for figures and
+            tables.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"># NOT RUN {
 # convert parameter name to a string appropriate for end-use plotting
 # }
 <span class='co'># NOT RUN {</span>
@@ -132,34 +191,30 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># get a list of all traits and units in dictionary</span>
 <span class='fu'>trait.lookup</span>()[,<span class='fu'>c</span>(<span class='st'>'figid'</span>, <span class='st'>'units'</span>)]
 <span class='co'># }</span></pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
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+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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index 17d1900..a802350 100644
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-    <h1>Transform Stats</h1>
-    
-    <div class="hidden name"><code>transformstats.Rd</code></div>
-    </div>
-
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-    
-    <p>Transform misc. statistics to SE</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>transformstats</span>(<span class='no'>data</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data</th>
-      <td><p>data frame with mean, statistic, n, and statistic name: <code>example data &lt;- data.frame(Y=rep(1,5), stat=rep(1,5), n=rep(4,5), statname=c('SD', 'MSE', 'LSD', 'HSD', 'MSD'))</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dataframe with statistics transformed to SE</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Automates transformations of SD, MSE, LSD, 95%CI, HSD, and MSD to conservative estimates of SE.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Transform Stats</h1>
+
+            <div class="hidden name"><code>transformstats.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Transform misc. statistics to SE</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>transformstats</span>(<span class='no'>data</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data</th>
+              <td>
+                <p>
+                  data frame with mean, statistic, n, and statistic name:
+                  <code
+                    >example data &lt;- data.frame(Y=rep(1,5), stat=rep(1,5),
+                    n=rep(4,5), statname=c('SD', 'MSE', 'LSD', 'HSD',
+                    'MSD'))</code
+                  >
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>dataframe with statistics transformed to SE</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Automates transformations of SD, MSE, LSD, 95%CI, HSD, and MSD to
+            conservative estimates of SE.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>statdf</span> <span class='kw'>&lt;-</span> <span class='fu'>data.frame</span>(<span class='kw'>Y</span><span class='kw'>=</span><span class='fu'>rep</span>(<span class='fl'>1</span>,<span class='fl'>5</span>),
                                <span class='kw'>stat</span><span class='kw'>=</span><span class='fu'>rep</span>(<span class='fl'>1</span>,<span class='fl'>5</span>),
                                <span class='kw'>n</span><span class='kw'>=</span><span class='fu'>rep</span>(<span class='fl'>4</span>,<span class='fl'>5</span>),
                                <span class='kw'>statname</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='st'>'SD'</span>, <span class='st'>'MSE'</span>, <span class='st'>'LSD'</span>, <span class='st'>'HSD'</span>, <span class='st'>'MSD'</span>))
 <span class='fu'>transformstats</span>(<span class='no'>statdf</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          David LeBauer
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
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 </html>
-
diff --git a/base/utils/docs/reference/tryl.html b/base/utils/docs/reference/tryl.html
index 64f081a..807fec7 100644
--- a/base/utils/docs/reference/tryl.html
+++ b/base/utils/docs/reference/tryl.html
@@ -2,168 +2,202 @@
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+    ></script>
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      crossorigin="anonymous"
+    ></script>
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+                  class="label label-default"
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>tryl</h1>
-    
-    <div class="hidden name"><code>tryl.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Test if function gives an error</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>tryl</span>(<span class='no'>FUN</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>FUN</th>
-      <td><p>function to be evaluated for error</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>FALSE if function returns error; else TRUE</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>adaptation of try that returns a logical value (FALSE if error)</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>tryl</h1>
+
+            <div class="hidden name"><code>tryl.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Test if function gives an error</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>tryl</span>(<span class='no'>FUN</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>FUN</th>
+              <td><p>function to be evaluated for error</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>FALSE if function returns error; else TRUE</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>adaptation of try that returns a logical value (FALSE if error)</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>tryl</span>(<span class='fl'>1</span>+<span class='fl'>1</span>)
 <span class='co'># TRUE</span>
 <span class='fu'>tryl</span>(<span class='fu'>sum</span>(<span class='st'>'a'</span>))
 <span class='co'># FALSE</span>
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          David LeBauer
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
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-
diff --git a/base/utils/docs/reference/units_are_equivalent.html b/base/utils/docs/reference/units_are_equivalent.html
index de49971..0ce7bfa 100644
--- a/base/utils/docs/reference/units_are_equivalent.html
+++ b/base/utils/docs/reference/units_are_equivalent.html
@@ -2,159 +2,199 @@
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+      PEcAn.utils
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+
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+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+
+    <!-- sticky kit -->
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+    <link href="../pkgdown.css" rel="stylesheet" />
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-<div class="row">
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-    <div class="page-header">
-    <h1>Check if two unit strings are equivalent</h1>
-    
-    <div class="hidden name"><code>units_are_equivalent.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This is to allow multiple forms of the same unit to work, such as
-`m/s` vs. `m s-1` or `K` and `Kelvin`.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>units_are_equivalent</span>(<span class='no'>x</span>, <span class='no'>y</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>A unit string, as character</p></td>
-    </tr>
-    <tr>
-      <th>y</th>
-      <td><p>Another unit string for comparison, as character</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`TRUE` if equivalent, `FALSE` otherwise</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check if two unit strings are equivalent</h1>
+
+            <div class="hidden name"><code>units_are_equivalent.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This is to allow multiple forms of the same unit to work, such as
+              `m/s` vs. `m s-1` or `K` and `Kelvin`.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>units_are_equivalent</span>(<span class='no'>x</span>, <span class='no'>y</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>A unit string, as character</p></td>
+            </tr>
+            <tr>
+              <th>y</th>
+              <td><p>Another unit string for comparison, as character</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>`TRUE` if equivalent, `FALSE` otherwise</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-   </div>
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   </body>
 </html>
-
diff --git a/base/utils/docs/reference/vecpaste.html b/base/utils/docs/reference/vecpaste.html
index 644323d..7ab0a46 100644
--- a/base/utils/docs/reference/vecpaste.html
+++ b/base/utils/docs/reference/vecpaste.html
@@ -2,155 +2,192 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<script src="../pkgdown.js"></script>
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-<meta property="og:title" content="vecpaste — vecpaste" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>vecpaste — vecpaste • PEcAn.utils</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="vecpaste — vecpaste" />
+
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+      property="og:description"
+      content="Convert vector to comma delimited string"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
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+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>vecpaste</h1>
-    
-    <div class="hidden name"><code>vecpaste.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert vector to comma delimited string</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>vecpaste</span>(<span class='no'>x</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>vector</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>comma delimited string</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>vecpaste, turns vector into comma delimited string fit for SQL statements.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>vecpaste</h1>
+
+            <div class="hidden name"><code>vecpaste.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert vector to comma delimited string</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>vecpaste</span>(<span class='no'>x</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>vector</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>comma delimited string</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            vecpaste, turns vector into comma delimited string fit for SQL
+            statements.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/base/utils/docs/reference/write.ensemble.configs.html b/base/utils/docs/reference/write.ensemble.configs.html
index e22ffa4..21e14f7 100644
--- a/base/utils/docs/reference/write.ensemble.configs.html
+++ b/base/utils/docs/reference/write.ensemble.configs.html
@@ -2,182 +2,245 @@
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 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-<div class="row">
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-    <h1>Write ensemble configs</h1>
-    
-    <div class="hidden name"><code>write.ensemble.configs.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write ensemble configs</h1>
 
-    <div class="ref-description">
-    
-    <p>Write ensemble config files</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>write.ensemble.configs.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Write ensemble config files</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>write.ensemble.configs</span>(<span class='no'>defaults</span>, <span class='no'>ensemble.samples</span>, <span class='no'>settings</span>, <span class='no'>model</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>write.ensemble.configs</span>(<span class='no'>defaults</span>, <span class='no'>ensemble.samples</span>, <span class='no'>settings</span>, <span class='no'>model</span>,
   <span class='kw'>clean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>write.to.db</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>pft</p></td>
-    </tr>
-    <tr>
-      <th>ensemble.samples</th>
-      <td><p>list of lists supplied by <a href='get.ensemble.samples.html'>get.ensemble.samples</a></p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of PEcAn settings</p></td>
-    </tr>
-    <tr>
-      <th>clean</th>
-      <td><p>remove old output first?</p></td>
-    </tr>
-    <tr>
-      <th>write.config</th>
-      <td><p>a model-specific function to write config files, e.g. write.config.ED</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list, containing $runs = data frame of runids, and $ensemble.id = the ensemble ID for these runs. Also writes sensitivity analysis configuration files as a side effect</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>DEPRECATED: This function has been moved to the <code>PEcAn.uncertainty</code> package.
-The version in <code>PEcAn.utils</code> is deprecated, will not be updated to add any new features,
-and will be removed in a future release of PEcAn.
-Please use <code><a href='http://www.rdocumentation.org/packages/PEcAn.uncertainty/topics/write.ensemble.configs'>PEcAn.uncertainty::write.ensemble.configs</a></code> instead.</p>
-<p>Writes config files for use in meta-analysis and returns a list of run ids.
-Given a pft.xml object, a list of lists as supplied by get.sa.samples, 
-a name to distinguish the output files, and the directory to place the files.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>pft</p></td>
+            </tr>
+            <tr>
+              <th>ensemble.samples</th>
+              <td>
+                <p>
+                  list of lists supplied by
+                  <a href="get.ensemble.samples.html">get.ensemble.samples</a>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of PEcAn settings</p></td>
+            </tr>
+            <tr>
+              <th>clean</th>
+              <td><p>remove old output first?</p></td>
+            </tr>
+            <tr>
+              <th>write.config</th>
+              <td>
+                <p>
+                  a model-specific function to write config files, e.g.
+                  write.config.ED
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            list, containing $runs = data frame of runids, and $ensemble.id =
+            the ensemble ID for these runs. Also writes sensitivity analysis
+            configuration files as a side effect
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            DEPRECATED: This function has been moved to the
+            <code>PEcAn.uncertainty</code> package. The version in
+            <code>PEcAn.utils</code> is deprecated, will not be updated to add
+            any new features, and will be removed in a future release of PEcAn.
+            Please use
+            <code
+              ><a
+                href="http://www.rdocumentation.org/packages/PEcAn.uncertainty/topics/write.ensemble.configs"
+                >PEcAn.uncertainty::write.ensemble.configs</a
+              ></code
+            >
+            instead.
+          </p>
+          <p>
+            Writes config files for use in meta-analysis and returns a list of
+            run ids. Given a pft.xml object, a list of lists as supplied by
+            get.sa.samples, a name to distinguish the output files, and the
+            directory to place the files.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Carl Davidson
+        </div>
+      </div>
 
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index b9ab3b4..baf879c 100644
--- a/base/utils/docs/reference/write.sa.configs.html
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write sensitivity analysis config files</h1>
-    
-    <div class="hidden name"><code>write.sa.configs.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write sensitivity analysis config files</h1>
 
-    <div class="ref-description">
-    
-    <p>Writes config files for use in sensitivity analysis.</p>
-    
-    </div>
+            <div class="hidden name"><code>write.sa.configs.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes config files for use in sensitivity analysis.</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>write.sa.configs</span>(<span class='no'>defaults</span>, <span class='no'>quantile.samples</span>, <span class='no'>settings</span>, <span class='no'>model</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>write.sa.configs</span>(<span class='no'>defaults</span>, <span class='no'>quantile.samples</span>, <span class='no'>settings</span>, <span class='no'>model</span>,
   <span class='kw'>clean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>write.to.db</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>named list with default parameter values</p></td>
-    </tr>
-    <tr>
-      <th>quantile.samples</th>
-      <td><p>list of lists supplied by <a href='get.sa.samples.html'>get.sa.samples</a></p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>name of model to be run</p></td>
-    </tr>
-    <tr>
-      <th>clean</th>
-      <td><p>logical: Delete any existing contents of the directory specified by <code>settings$rundir</code> before writing to it?</p></td>
-    </tr>
-    <tr>
-      <th>write.to.db</th>
-      <td><p>logical: Record this run to BETY? If TRUE, uses connection settings specified in <code>settings$database</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list, containing $runs = data frame of runids, and $ensemble.id = the ensemble ID for these runs. Also writes sensitivity analysis configuration files as a side effect</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>named list with default parameter values</p></td>
+            </tr>
+            <tr>
+              <th>quantile.samples</th>
+              <td>
+                <p>
+                  list of lists supplied by
+                  <a href="get.sa.samples.html">get.sa.samples</a>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings</p></td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td><p>name of model to be run</p></td>
+            </tr>
+            <tr>
+              <th>clean</th>
+              <td>
+                <p>
+                  logical: Delete any existing contents of the directory
+                  specified by <code>settings$rundir</code> before writing to
+                  it?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>write.to.db</th>
+              <td>
+                <p>
+                  logical: Record this run to BETY? If TRUE, uses connection
+                  settings specified in <code>settings$database</code>
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            list, containing $runs = data frame of runids, and $ensemble.id =
+            the ensemble ID for these runs. Also writes sensitivity analysis
+            configuration files as a side effect
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Carl Davidson
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
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diff --git a/base/utils/docs/reference/zero.bounded.density.html b/base/utils/docs/reference/zero.bounded.density.html
index 37bc7fe..692fa24 100644
--- a/base/utils/docs/reference/zero.bounded.density.html
+++ b/base/utils/docs/reference/zero.bounded.density.html
@@ -2,176 +2,242 @@
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+    />
+
+    <!-- clipboard.js -->
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
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+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Zero Bounded Density — zero.bounded.density"
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     <div class="container template-reference-topic">
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-        <a class="navbar-link" href="../index.html">PEcAn.utils</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../reference/index.html">Reference</a>
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-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
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+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+              </ul>
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+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Zero Bounded Density</h1>
-    
-    <div class="hidden name"><code>zero.bounded.density.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Zero bounded density using log density transform</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>zero.bounded.density</span>(<span class='no'>x</span>, <span class='kw'>bw</span> <span class='kw'>=</span> <span class='st'>"SJ"</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1001</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>data, as a numeric vector</p></td>
-    </tr>
-    <tr>
-      <th>bw</th>
-      <td><p>The smoothing bandwidth to be used. See 'bw.nrd'</p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>number of points to use in kernel density estimate. See <code><a href='http://www.rdocumentation.org/packages/stats/topics/density'>density</a></code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data frame with back-transformed log density estimate</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Provides a zero bounded density estimate of a parameter.
-Kernel Density Estimation used by the <code><a href='http://www.rdocumentation.org/packages/stats/topics/density'>density</a></code> function will cause problems
-at the left hand end because it will put some weight on negative values.
-One useful approach is to transform to logs, estimate the density using KDE, and then transform back.</p>
-    
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
-    <p>M. P. Wand, J. S. Marron and D. Ruppert, 1991. Transformations in Density Estimation. Journal of the American Statistical Association. 86(414):343-353 <a href='http://www.jstor.org/stable/2290569'>http://www.jstor.org/stable/2290569</a></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#references">References</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Zero Bounded Density</h1>
+
+            <div class="hidden name"><code>zero.bounded.density.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Zero bounded density using log density transform</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>zero.bounded.density</span>(<span class='no'>x</span>, <span class='kw'>bw</span> <span class='kw'>=</span> <span class='st'>"SJ"</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1001</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>data, as a numeric vector</p></td>
+            </tr>
+            <tr>
+              <th>bw</th>
+              <td><p>The smoothing bandwidth to be used. See 'bw.nrd'</p></td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td>
+                <p>
+                  number of points to use in kernel density estimate. See
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/stats/topics/density"
+                      >density</a
+                    ></code
+                  >
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>data frame with back-transformed log density estimate</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Provides a zero bounded density estimate of a parameter. Kernel
+            Density Estimation used by the
+            <code
+              ><a
+                href="http://www.rdocumentation.org/packages/stats/topics/density"
+                >density</a
+              ></code
+            >
+            function will cause problems at the left hand end because it will
+            put some weight on negative values. One useful approach is to
+            transform to logs, estimate the density using KDE, and then
+            transform back.
+          </p>
+
+          <h2 class="hasAnchor" id="references">
+            <a class="anchor" href="#references"></a>References
+          </h2>
+
+          <p>
+            M. P. Wand, J. S. Marron and D. Ruppert, 1991. Transformations in
+            Density Estimation. Journal of the American Statistical Association.
+            86(414):343-353
+            <a href="http://www.jstor.org/stable/2290569"
+              >http://www.jstor.org/stable/2290569</a
+            >
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#references">References</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-<a href='http://stats.stackexchange.com/q/6588/2750'>Rob Hyndman</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          <a href="http://stats.stackexchange.com/q/6588/2750">Rob Hyndman</a>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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 </html>
-
diff --git a/base/utils/docs/reference/zero.truncate.html b/base/utils/docs/reference/zero.truncate.html
index 02897c7..5c55942 100644
--- a/base/utils/docs/reference/zero.truncate.html
+++ b/base/utils/docs/reference/zero.truncate.html
@@ -2,153 +2,182 @@
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.utils</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Zero Truncate</h1>
-    
-    <div class="hidden name"><code>zero.truncate.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Truncates vector at 0</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>zero.truncate</span>(<span class='no'>y</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>y</th>
-      <td><p>numeric vector</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>numeric vector with all values less than 0 set to 0</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Zero Truncate</h1>
+
+            <div class="hidden name"><code>zero.truncate.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Truncates vector at 0</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>zero.truncate</span>(<span class='no'>y</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>y</th>
+              <td><p>numeric vector</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>numeric vector with all values less than 0 set to 0</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-&lt;unknown&gt;
+          <h2>Author</h2>
 
-  </div>
-</div>
+          &lt;unknown&gt;
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
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index e798c93..70d3938 100644
--- a/base/visualization/docs/LICENSE-text.html
+++ b/base/visualization/docs/LICENSE-text.html
@@ -2,109 +2,144 @@
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+                  <ul class="dropdown-menu" role="menu">
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-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -138,27 +173,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
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-
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+</pre
+          >
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+      </div>
 
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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index db7aca5..34fb9bd 100644
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@@ -2,133 +2,166 @@
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+                >
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+                  class="label label-default"
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+                  >1.6.0</span
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       </header>
 
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+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Articles</h1>
+          </div>
 
-    <div class="section ">
-      <h3>All vignettes</h3>
-      <p class="section-desc"></p>
+          <div class="section ">
+            <h3>All vignettes</h3>
+            <p class="section-desc"></p>
 
-      <ul>
-        <li><a href="usmap.html">UNKNOWN TITLE</a></li>
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+            </ul>
+          </div>
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+      </div>
 
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diff --git a/base/visualization/docs/articles/usmap.html b/base/visualization/docs/articles/usmap.html
index 036e5f8..0a273c9 100644
--- a/base/visualization/docs/articles/usmap.html
+++ b/base/visualization/docs/articles/usmap.html
@@ -1,88 +1,143 @@
 <!DOCTYPE html>
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-      <h1></h1>
-            
-      
-      
-      <div class="hidden name"><code>usmap.Rmd</code></div>
-
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-
-    
-    
-<div id="map" class="section level1">
-<h1 class="hasAnchor">
-<a href="#map" class="anchor"></a>Map</h1>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">require</span>(raster)
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.visualization</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
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+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/usmap.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
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+            </div>
+            <!--/.nav-collapse -->
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+        <!--/.navbar -->
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+        <div class="col-md-9 contents">
+          <div class="page-header toc-ignore">
+            <h1></h1>
+
+            <div class="hidden name"><code>usmap.Rmd</code></div>
+          </div>
+
+          <div id="map" class="section level1">
+            <h1 class="hasAnchor"><a href="#map" class="anchor"></a>Map</h1>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">require</span>(raster)
 <span class="kw">require</span>(sp)
 <span class="kw">require</span>(ggplot2)
 <span class="kw">require</span>(PEcAn.visualization)
@@ -93,11 +148,17 @@ <h1 class="hasAnchor">
 spdf &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/sp/topics/SpatialPoints">SpatialPointsDataFrame</a></span>( <span class="kw">data.frame</span>( <span class="dt">x =</span> testdf<span class="op">$</span>y , <span class="dt">y =</span> testdf<span class="op">$</span>x ) , <span class="dt">data =</span> <span class="kw">data.frame</span>( <span class="dt">z =</span> testdf<span class="op">$</span>z ) )
 
 <span class="co"># Plotting the points reveals the unevenly spaced nature of the points</span>
-<span class="kw"><a href="http://www.rdocumentation.org/packages/raster/topics/spplot">spplot</a></span>(spdf)</code></pre></div>
-<div id="plot-all-maps-for-betydb" class="section level3">
-<h3 class="hasAnchor">
-<a href="#plot-all-maps-for-betydb" class="anchor"></a>Plot all maps for BETYdb</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">files &lt;-<span class="st"> </span><span class="kw">dir</span>(<span class="st">"~/dev/bety/local/modelout"</span>, <span class="dt">pattern=</span><span class="st">"grid.csv"</span>, <span class="dt">full.names=</span><span class="ot">TRUE</span>)
+<span class="kw"><a href="http://www.rdocumentation.org/packages/raster/topics/spplot">spplot</a></span>(spdf)</code></pre>
+            </div>
+            <div id="plot-all-maps-for-betydb" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#plot-all-maps-for-betydb" class="anchor"></a>Plot all
+                maps for BETYdb
+              </h3>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">files &lt;-<span class="st"> </span><span class="kw">dir</span>(<span class="st">"~/dev/bety/local/modelout"</span>, <span class="dt">pattern=</span><span class="st">"grid.csv"</span>, <span class="dt">full.names=</span><span class="ot">TRUE</span>)
 yieldfiles &lt;-<span class="st"> </span>files[<span class="op">!</span><span class="kw">grepl</span>(<span class="st">"evapotranspiration"</span>, files)]
 etfiles &lt;-<span class="st"> </span>files[<span class="kw">grepl</span>(<span class="st">"evapotranspiration"</span>, files)]
 <span class="cf">for</span>(file <span class="cf">in</span> yieldfiles){
@@ -113,23 +174,34 @@ <h3 class="hasAnchor">
   df.in &lt;-<span class="st"> </span><span class="kw">read.csv</span>(file, <span class="dt">skip =</span> <span class="dv">1</span>)
   outfile &lt;-<span class="st"> </span><span class="kw">gsub</span>(<span class="st">"csv"</span>, <span class="st">"png"</span>, file)
   <span class="co">#pecan.worldmap(df.in, outfile=outfile)</span>
-}</code></pre></div>
-</div>
-<div id="demo-regrid" class="section level3">
-<h3 class="hasAnchor">
-<a href="#demo-regrid" class="anchor"></a>demo Regrid</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">latlon.data &lt;-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">"~/dev/bety/public/temp_models/willow_yield_grid.csv"</span>,
+}</code></pre>
+              </div>
+            </div>
+            <div id="demo-regrid" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#demo-regrid" class="anchor"></a>demo Regrid
+              </h3>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">latlon.data &lt;-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">"~/dev/bety/public/temp_models/willow_yield_grid.csv"</span>,
                         <span class="dt">skip =</span> <span class="dv">1</span>)
 
 regridded &lt;-<span class="st"> </span><span class="kw">regrid</span>(latlon.data)
 
 <span class="kw">library</span>(ggplot2)
-<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(<span class="dt">data =</span> regridded) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_tile">geom_tile</a></span>(<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(lat, lon, <span class="dt">fill =</span> yield))</code></pre></div>
-</div>
-<div id="misc-additional-code" class="section level3">
-<h3 class="hasAnchor">
-<a href="#misc-additional-code" class="anchor"></a>Misc additional code</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Make an evenly spaced raster, the same extent as original data</span>
+<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(<span class="dt">data =</span> regridded) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_tile">geom_tile</a></span>(<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(lat, lon, <span class="dt">fill =</span> yield))</code></pre>
+              </div>
+            </div>
+            <div id="misc-additional-code" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#misc-additional-code" class="anchor"></a>Misc
+                additional code
+              </h3>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="co"># Make an evenly spaced raster, the same extent as original data</span>
 e &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/raster/topics/extent">extent</a></span>( spdf )
 
 <span class="co"># Determine ratio between x and y dimensions</span>
@@ -144,8 +216,12 @@ <h3 class="hasAnchor">
 
 <span class="co"># We can then plot this using `geom_tile()` or `geom_raster()`</span>
 rdf &lt;-<span class="st"> </span><span class="kw">data.frame</span>( <span class="kw"><a href="http://www.rdocumentation.org/packages/raster/topics/rasterToPoints">rasterToPoints</a></span>( rf ) )    
-<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>( <span class="ot">NULL</span> ) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_tile">geom_raster</a></span>( <span class="dt">data =</span> rdf , <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>( x , y , <span class="dt">fill =</span> layer ) )</code></pre></div>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># from http://gis.stackexchange.com/a/20052/3218</span>
+<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>( <span class="ot">NULL</span> ) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_tile">geom_raster</a></span>( <span class="dt">data =</span> rdf , <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>( x , y , <span class="dt">fill =</span> layer ) )</code></pre>
+              </div>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="co"># from http://gis.stackexchange.com/a/20052/3218</span>
 <span class="kw">require</span>(rgdal)
 <span class="kw"><a href="http://www.rdocumentation.org/packages/raster/topics/projection">proj4string</a></span>(spdf) &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rgdal/topics/CRS-class">CRS</a></span>(<span class="st">"+init=epsg:4326"</span>)
 pts &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rgdal/topics/spTransform-methods">spTransform</a></span>(spdf ,<span class="kw"><a href="http://www.rdocumentation.org/packages/rgdal/topics/CRS-class">CRS</a></span>(<span class="st">"+proj=longlat +datum=WGS84"</span>))
@@ -154,13 +230,31 @@ <h3 class="hasAnchor">
 p2g &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/sp/topics/SpatialGrid">points2grid</a></span>(spdf, <span class="dt">tolerance =</span> <span class="fl">0.95</span>)
 
 r &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/raster/topics/raster">raster</a></span>(p2g)
-<span class="kw"><a href="http://www.rdocumentation.org/packages/raster/topics/plot">plot</a></span>(p2g)</code></pre></div>
-</div>
-<div id="code-used-to-extract-and-process-old-biocro-output" class="section level3">
-<h3 class="hasAnchor">
-<a href="#code-used-to-extract-and-process-old-biocro-output" class="anchor"></a>Code used to extract and process old BioCro output</h3>
-<p>this was run in data from Willow manuscript. See <a href="https://ebi-forecast.igb.illinois.edu/redmine/issues/2387">redmine issue 2387</a></p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">files &lt;-<span class="st"> </span><span class="kw">dir</span>(<span class="st">"."</span>, <span class="dt">pattern =</span> <span class="st">".txt"</span>)
+<span class="kw"><a href="http://www.rdocumentation.org/packages/raster/topics/plot">plot</a></span>(p2g)</code></pre>
+              </div>
+            </div>
+            <div
+              id="code-used-to-extract-and-process-old-biocro-output"
+              class="section level3"
+            >
+              <h3 class="hasAnchor">
+                <a
+                  href="#code-used-to-extract-and-process-old-biocro-output"
+                  class="anchor"
+                ></a
+                >Code used to extract and process old BioCro output
+              </h3>
+              <p>
+                this was run in data from Willow manuscript. See
+                <a
+                  href="https://ebi-forecast.igb.illinois.edu/redmine/issues/2387"
+                  >redmine issue 2387</a
+                >
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">files &lt;-<span class="st"> </span><span class="kw">dir</span>(<span class="st">"."</span>, <span class="dt">pattern =</span> <span class="st">".txt"</span>)
 <span class="kw">library</span>(data.table)
 lat &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/fread">fread</a></span>(files[<span class="dv">1</span>])[,<span class="kw">list</span>(<span class="dt">lat =</span> V2)]<span class="op">$</span>lat
 lon &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/fread">fread</a></span>(files[<span class="dv">1</span>])[,<span class="kw">list</span>(<span class="dt">lon =</span> V3)]<span class="op">$</span>lon
@@ -188,36 +282,35 @@ <h3 class="hasAnchor">
 a &lt;-<span class="st"> </span><span class="kw">do.call</span>(<span class="st">"cbind"</span>, y)
 <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/setattr">setnames</a></span>(a,  <span class="kw">as.character</span>(<span class="dv">1979</span><span class="op">:</span><span class="dv">2010</span>))
 b &lt;-<span class="st"> </span>a[,<span class="kw">list</span>(<span class="dt">yield =</span> <span class="kw">rowMeans</span>(.SD))]<span class="op">$</span>yield
-willow &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/data.table">data.table</a></span>(<span class="dt">lat =</span> lat, <span class="dt">lon =</span> lon, <span class="dt">yield =</span> b)[<span class="op">!</span><span class="kw">is.na</span>(yield)]</code></pre></div>
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-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#map">Map</a></li>
-      </ul>
-</div>
+willow &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/data.table">data.table</a></span>(<span class="dt">lat =</span> lat, <span class="dt">lon =</span> lon, <span class="dt">yield =</span> b)[<span class="op">!</span><span class="kw">is.na</span>(yield)]</code></pre>
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index f805c76..c2c4a14 100644
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+++ b/base/visualization/docs/authors.html
@@ -2,158 +2,179 @@
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+    ></script>
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-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Alexey Shiklomanov</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Alexey Shiklomanov</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/visualization/docs/docsearch.css b/base/visualization/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/base/visualization/docs/docsearch.css
+++ b/base/visualization/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/base/visualization/docs/docsearch.js b/base/visualization/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/base/visualization/docs/docsearch.js
+++ b/base/visualization/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/base/visualization/docs/index.html b/base/visualization/docs/index.html
index fa359b0..8d7a3b3 100644
--- a/base/visualization/docs/index.html
+++ b/base/visualization/docs/index.html
@@ -1,127 +1,185 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn visualization functions. • PEcAn.visualization</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn visualization functions.">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn visualization functions. • PEcAn.visualization</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta property="og:title" content="PEcAn visualization functions." />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation.
     This module is used to create more complex visualizations from the data
-    generated by PEcAn code, specifically the models.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    generated by PEcAn code, specifically the models."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.visualization</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/usmap.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
-    This module is used to create more complex visualizations from the data
-    generated by PEcAn code, specifically the models.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.visualization</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/usmap.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation. This module is used
+          to create more complex visualizations from the data generated by PEcAn
+          code, specifically the models.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/base/visualization/docs/pkgdown.css b/base/visualization/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/base/visualization/docs/pkgdown.css
+++ b/base/visualization/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/base/visualization/docs/pkgdown.js b/base/visualization/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/base/visualization/docs/pkgdown.js
+++ b/base/visualization/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/base/visualization/docs/reference/add_icon.html b/base/visualization/docs/reference/add_icon.html
index 60454af..1d6c40d 100644
--- a/base/visualization/docs/reference/add_icon.html
+++ b/base/visualization/docs/reference/add_icon.html
@@ -2,167 +2,204 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>add_icon — add_icon • PEcAn.visualization</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="add_icon — add_icon" />
-
-<meta property="og:description" content="add_icon" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>add_icon — add_icon • PEcAn.visualization</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="add_icon — add_icon" />
+
+    <meta property="og:description" content="add_icon" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.visualization</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/usmap.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.visualization</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/usmap.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>add_icon</h1>
-    
-    <div class="hidden name"><code>add_icon.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>add_icon</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>add_icon</span>(<span class='kw'>id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>id</th>
-      <td><p>additional plot identificaition (URL, database ID, etc)</p></td>
-    </tr>
-    <tr>
-      <th>x</th>
-      <td><p>x-coordinate of logo</p></td>
-    </tr>
-    <tr>
-      <th>y</th>
-      <td><p>y-coordinate of logo</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>add_icon</h1>
+
+            <div class="hidden name"><code>add_icon.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>add_icon</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>add_icon</span>(<span class='kw'>id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>y</span> <span class='kw'>=</span> <span class='fl'>0</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>id</th>
+              <td>
+                <p>additional plot identificaition (URL, database ID, etc)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>x</th>
+              <td><p>x-coordinate of logo</p></td>
+            </tr>
+            <tr>
+              <th>y</th>
+              <td><p>y-coordinate of logo</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/visualization/docs/reference/ciEnvelope.html b/base/visualization/docs/reference/ciEnvelope.html
index d2ffe00..b012753 100644
--- a/base/visualization/docs/reference/ciEnvelope.html
+++ b/base/visualization/docs/reference/ciEnvelope.html
@@ -2,167 +2,215 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>plots a confidence interval around an x-y plot (e.g. a timeseries) — ciEnvelope • PEcAn.visualization</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-
-<meta property="og:title" content="plots a confidence interval around an x-y plot (e.g. a timeseries) — ciEnvelope" />
-
-<meta property="og:description" content="plots a confidence interval around an x-y plot (e.g. a timeseries)" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      plots a confidence interval around an x-y plot (e.g. a timeseries) —
+      ciEnvelope • PEcAn.visualization
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="plots a confidence interval around an x-y plot (e.g. a timeseries) — ciEnvelope"
+    />
+
+    <meta
+      property="og:description"
+      content="plots a confidence interval around an x-y plot (e.g. a timeseries)"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+    <![endif]-->
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.visualization</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
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+                    </li>
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+                </li>
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>plots a confidence interval around an x-y plot (e.g. a timeseries)</h1>
-    
-    <div class="hidden name"><code>ciEnvelope.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>plots a confidence interval around an x-y plot (e.g. a timeseries)</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>ciEnvelope</span>(<span class='no'>x</span>, <span class='no'>ylo</span>, <span class='no'>yhi</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>Vector defining CI center</p></td>
-    </tr>
-    <tr>
-      <th>ylo</th>
-      <td><p>Vector defining bottom of CI envelope</p></td>
-    </tr>
-    <tr>
-      <th>yhi</th>
-      <td><p>Vector defining top of CI envelope</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze, David LeBauer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              plots a confidence interval around an x-y plot (e.g. a timeseries)
+            </h1>
+
+            <div class="hidden name"><code>ciEnvelope.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              plots a confidence interval around an x-y plot (e.g. a timeseries)
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>ciEnvelope</span>(<span class='no'>x</span>, <span class='no'>ylo</span>, <span class='no'>yhi</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>Vector defining CI center</p></td>
+            </tr>
+            <tr>
+              <th>ylo</th>
+              <td><p>Vector defining bottom of CI envelope</p></td>
+            </tr>
+            <tr>
+              <th>yhi</th>
+              <td><p>Vector defining top of CI envelope</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze, David LeBauer
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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+        <div class="copyright">
+          <p>Developed by .</p>
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diff --git a/base/visualization/docs/reference/create_status_page.html b/base/visualization/docs/reference/create_status_page.html
index a528919..1b16fed 100644
--- a/base/visualization/docs/reference/create_status_page.html
+++ b/base/visualization/docs/reference/create_status_page.html
@@ -2,185 +2,232 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Create PEcAn Network status page. — create_status_page • PEcAn.visualization</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Create PEcAn Network status page. — create_status_page" />
-
-<meta property="og:description" content="This will create a webpage (file_prefix.html) as well as an image
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Create PEcAn Network status page. — create_status_page •
+      PEcAn.visualization
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Create PEcAn Network status page. — create_status_page"
+    />
+
+    <meta
+      property="og:description"
+      content="This will create a webpage (file_prefix.html) as well as an image
 (file_prefix.png) that shows the PEcAn Network satus. This will
 save the geo location of each site as well as some additional
 information in a cache file (file_prefix.RData). If an update to
 the BETY schema is detected it will be logged in a file
-(file_prefix.log)." />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+(file_prefix.log)."
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.visualization</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/usmap.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create PEcAn Network status page.</h1>
-    
-    <div class="hidden name"><code>create_status_page.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This will create a webpage (file_prefix.html) as well as an image
-(file_prefix.png) that shows the PEcAn Network satus. This will
-save the geo location of each site as well as some additional
-information in a cache file (file_prefix.RData). If an update to
-the BETY schema is detected it will be logged in a file
-(file_prefix.log).</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>create_status_page</span>(<span class='no'>config_file</span>, <span class='kw'>file_prefix</span> <span class='kw'>=</span> <span class='st'>"status"</span>, <span class='kw'>delta</span> <span class='kw'>=</span> <span class='fl'>3600</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>config_file</th>
-      <td><p>Path to `config.php`</p></td>
-    </tr>
-    <tr>
-      <th>file_prefix</th>
-      <td><p>prefix used for all files saved</p></td>
-    </tr>
-    <tr>
-      <th>delta</th>
-      <td><p>number of seconds before</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create PEcAn Network status page.</h1>
+
+            <div class="hidden name"><code>create_status_page.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This will create a webpage (file_prefix.html) as well as an image
+              (file_prefix.png) that shows the PEcAn Network satus. This will
+              save the geo location of each site as well as some additional
+              information in a cache file (file_prefix.RData). If an update to
+              the BETY schema is detected it will be logged in a file
+              (file_prefix.log).
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>create_status_page</span>(<span class='no'>config_file</span>, <span class='kw'>file_prefix</span> <span class='kw'>=</span> <span class='st'>"status"</span>, <span class='kw'>delta</span> <span class='kw'>=</span> <span class='fl'>3600</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>config_file</th>
+              <td><p>Path to `config.php`</p></td>
+            </tr>
+            <tr>
+              <th>file_prefix</th>
+              <td><p>prefix used for all files saved</p></td>
+            </tr>
+            <tr>
+              <th>delta</th>
+              <td><p>number of seconds before</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>create_status_page</span>(<span class='st'>'/home/carya/pecan/web/config.php'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/base/visualization/docs/reference/index.html b/base/visualization/docs/reference/index.html
index c966abf..049a651 100644
--- a/base/visualization/docs/reference/index.html
+++ b/base/visualization/docs/reference/index.html
@@ -2,192 +2,250 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.visualization</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
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-<!-- mathjax -->
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.visualization</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Function reference" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.visualization</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/usmap.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.visualization</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/usmap.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="add_icon.html">add_icon()</a></code> </p>
-        </td>
-        <td><p>add_icon</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ciEnvelope.html">ciEnvelope()</a></code> </p>
-        </td>
-        <td><p>plots a confidence interval around an x-y plot (e.g. a timeseries)</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="create_status_page.html">create_status_page()</a></code> </p>
-        </td>
-        <td><p>Create PEcAn Network status page.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="map.output.html">map.output()</a></code> </p>
-        </td>
-        <td><p>Map Output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot.hdf5.html">plot.netcdf()</a></code> </p>
-        </td>
-        <td><p>Load the tower dataset and create a plot.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="points2county.html">points2county()</a></code> </p>
-        </td>
-        <td><p>Points To County</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="vwReg.html">vwReg()</a></code> </p>
-        </td>
-        <td><p>PEcAn worldmap</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="add_icon.html">add_icon()</a></code>
+                  </p>
+                </td>
+                <td><p>add_icon</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ciEnvelope.html">ciEnvelope()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    plots a confidence interval around an x-y plot (e.g. a
+                    timeseries)
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="create_status_page.html"
+                        >create_status_page()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create PEcAn Network status page.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="map.output.html">map.output()</a></code>
+                  </p>
+                </td>
+                <td><p>Map Output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="plot.hdf5.html">plot.netcdf()</a></code>
+                  </p>
+                </td>
+                <td><p>Load the tower dataset and create a plot.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="points2county.html">points2county()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Points To County</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="vwReg.html">vwReg()</a></code>
+                  </p>
+                </td>
+                <td><p>PEcAn worldmap</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/base/visualization/docs/reference/map.output.html b/base/visualization/docs/reference/map.output.html
index 3efc967..4aa8a90 100644
--- a/base/visualization/docs/reference/map.output.html
+++ b/base/visualization/docs/reference/map.output.html
@@ -2,169 +2,211 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Map Output — map.output • PEcAn.visualization</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Map Output — map.output" />
-
-<meta property="og:description" content="Map Output" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Map Output — map.output • PEcAn.visualization</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+
+    <!-- sticky kit -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
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+                  >PEcAn.visualization</a
+                >
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+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/usmap.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Map Output</h1>
-    
-    <div class="hidden name"><code>map.output.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Map Output</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>map.output</span>(<span class='no'>table</span>, <span class='no'>variable</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>table</th>
-      <td><p>data.table or data.frame with columns lat, lon, followed by variable names</p></td>
-    </tr>
-    <tr>
-      <th>variable</th>
-      <td><p>name of variable to be mapped</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>plot</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Map Output</h1>
+
+            <div class="hidden name"><code>map.output.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Map Output</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>map.output</span>(<span class='no'>table</span>, <span class='no'>variable</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>table</th>
+              <td>
+                <p>
+                  data.table or data.frame with columns lat, lon, followed by
+                  variable names
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>variable</th>
+              <td><p>name of variable to be mapped</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>plot</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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       </footer>
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+    </div>
   </body>
 </html>
-
diff --git a/base/visualization/docs/reference/plot.hdf5.html b/base/visualization/docs/reference/plot.hdf5.html
index 324c642..66bf734 100644
--- a/base/visualization/docs/reference/plot.hdf5.html
+++ b/base/visualization/docs/reference/plot.hdf5.html
@@ -2,190 +2,250 @@
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 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Load the tower dataset and create a plot. — plot.hdf5 •
+      PEcAn.visualization
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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+    ></script>
+
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+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+      content="Load the tower dataset and create a plot. — plot.hdf5"
+    />
+
+    <meta
+      property="og:description"
+      content="plot.hdf5 loads the tower data from an HDF5 file generated by
 ED and will plot the values against one another. The default is for
-the given variable to be plotted against time." />
-<meta name="twitter:card" content="summary" />
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+the given variable to be plotted against time."
+    />
+    <meta name="twitter:card" content="summary" />
 
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.visualization</a
+                >
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+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+                    data-toggle="dropdown"
+                    role="button"
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+
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+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Load the tower dataset and create a plot.</h1>
-    
-    <div class="hidden name"><code>plot.hdf5.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p><code>plot.hdf5</code> loads the tower data from an HDF5 file generated by
-ED and will plot the values against one another. The default is for
-the given variable to be plotted against time.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>plot.netcdf</span>(<span class='no'>datafile</span>, <span class='no'>yvar</span>, <span class='kw'>xvar</span> <span class='kw'>=</span> <span class='st'>"time"</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>800</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='fl'>600</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Load the tower dataset and create a plot.</h1>
+
+            <div class="hidden name"><code>plot.hdf5.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              <code>plot.hdf5</code> loads the tower data from an HDF5 file
+              generated by ED and will plot the values against one another. The
+              default is for the given variable to be plotted against time.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>plot.netcdf</span>(<span class='no'>datafile</span>, <span class='no'>yvar</span>, <span class='kw'>xvar</span> <span class='kw'>=</span> <span class='st'>"time"</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>800</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='fl'>600</span>,
   <span class='kw'>filename</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>datafile</th>
-      <td><p>the specific datafile to use.</p></td>
-    </tr>
-    <tr>
-      <th>yvar</th>
-      <td><p>the variable to plot along the y-axis.</p></td>
-    </tr>
-    <tr>
-      <th>xvar</th>
-      <td><p>the variable to plot along the x-axis, by default time is
-used.</p></td>
-    </tr>
-    <tr>
-      <th>filename</th>
-      <td><p>is the name of the file name that is geneated, this
-can be null to use existing device, otherwise it will try and</p></td>
-    </tr>
-    <tr>
-      <th>year</th>
-      <td><p>the year this data is for (only used in the title).</p></td>
-    </tr>
-    <tr>
-      <th>the</th>
-      <td><p>width of the image generated, default is 800 pixels.</p></td>
-    </tr>
-    <tr>
-      <th>the</th>
-      <td><p>height of the image generated, default is 600 pixels.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>datafile</th>
+              <td><p>the specific datafile to use.</p></td>
+            </tr>
+            <tr>
+              <th>yvar</th>
+              <td><p>the variable to plot along the y-axis.</p></td>
+            </tr>
+            <tr>
+              <th>xvar</th>
+              <td>
+                <p>
+                  the variable to plot along the x-axis, by default time is
+                  used.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>filename</th>
+              <td>
+                <p>
+                  is the name of the file name that is geneated, this can be
+                  null to use existing device, otherwise it will try and
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>year</th>
+              <td>
+                <p>the year this data is for (only used in the title).</p>
+              </td>
+            </tr>
+            <tr>
+              <th>the</th>
+              <td>
+                <p>width of the image generated, default is 800 pixels.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>the</th>
+              <td>
+                <p>height of the image generated, default is 600 pixels.</p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/base/visualization/docs/reference/points2county.html b/base/visualization/docs/reference/points2county.html
index 1d10fc4..d304c53 100644
--- a/base/visualization/docs/reference/points2county.html
+++ b/base/visualization/docs/reference/points2county.html
@@ -2,181 +2,238 @@
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 <html>
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+    <title>Points To County — points2county • PEcAn.visualization</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Points To County — points2county" />
+
+    <meta
+      property="og:description"
+      content="convert a lat, lon, &amp;lt;value&amp;gt; dataset to county-level values"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Points To County</h1>
-    
-    <div class="hidden name"><code>points2county.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>convert a lat, lon, &lt;value&gt; dataset to county-level values</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>points2county</span>(<span class='no'>griddata</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>griddata</th>
-      <td><p>a data frame with columns <code>lat, lon &lt;some value&gt;</code>.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a data.table with county-level information, including state and county name, state abbreviation,
-lat, lon, county_fips, state_fips, fips, and interpolated output</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Uses the <code>earth</code> function to fit a multivariate spline, and then
-reproject to the (approximate) centroids of US counties, for counties that fall within the
-lat / lon range of the data set</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Points To County</h1>
+
+            <div class="hidden name"><code>points2county.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              convert a lat, lon, &lt;value&gt; dataset to county-level values
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>points2county</span>(<span class='no'>griddata</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>griddata</th>
+              <td>
+                <p>
+                  a data frame with columns
+                  <code>lat, lon &lt;some value&gt;</code>.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            a data.table with county-level information, including state and
+            county name, state abbreviation, lat, lon, county_fips, state_fips,
+            fips, and interpolated output
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Uses the <code>earth</code> function to fit a multivariate spline,
+            and then reproject to the (approximate) centroids of US counties,
+            for counties that fall within the lat / lon range of the data set
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>data</span>(<span class='no'>ozone</span>)
 <span class='fu'>colnames</span>(<span class='no'>ozone</span>) <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>'lon'</span>, <span class='st'>'lat'</span>, <span class='st'>'ozone'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          David LeBauer
+        </div>
+      </div>
+
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index 85cc7c8..7023122 100644
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+++ b/base/visualization/docs/reference/vwReg.html
@@ -2,199 +2,262 @@
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
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+                type="button"
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.visualization</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/usmap.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
 
-    <div id="navbar" class="navbar-collapse collapse">
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-
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+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>PEcAn worldmap</h1>
-    
-    <div class="hidden name"><code>vwReg.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>PEcAn worldmap</h1>
 
-    <div class="ref-description">
+            <div class="hidden name"><code>vwReg.Rd</code></div>
+          </div>
 
-    </div>
+          <div class="ref-description"></div>
 
-    <pre class="usage"><span class='fu'>vwReg</span>(<span class='no'>formula</span>, <span class='no'>data</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>B</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>shade</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>vwReg</span>(<span class='no'>formula</span>, <span class='no'>data</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>B</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>shade</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>shade.alpha</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>spag</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>spag.color</span> <span class='kw'>=</span> <span class='st'>"darkblue"</span>,
   <span class='kw'>mweight</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show.lm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show.median</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>median.col</span> <span class='kw'>=</span> <span class='st'>"white"</span>, <span class='kw'>shape</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>show.CI</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>method</span> <span class='kw'>=</span> <span class='no'>loess</span>, <span class='kw'>bw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>slices</span> <span class='kw'>=</span> <span class='fl'>200</span>,
   <span class='kw'>palette</span> <span class='kw'>=</span> <span class='fu'>colorRampPalette</span>(<span class='fu'>c</span>(<span class='st'>"#FFEDA0"</span>, <span class='st'>"#DD0000"</span>), <span class='kw'>bias</span> <span class='kw'>=</span> <span class='fl'>2</span>)(<span class='fl'>20</span>),
   <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quantize</span> <span class='kw'>=</span> <span class='st'>"continuous"</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>B</th>
-      <td><p>= number bootstrapped smoothers</p></td>
-    </tr>
-    <tr>
-      <th>bw</th>
-      <td><p>= TRUE: define a default b&amp;w-palette</p></td>
-    </tr>
-    <tr>
-      <th>shade:</th>
-      <td><p>plot the shaded confidence region?</p></td>
-    </tr>
-    <tr>
-      <th>shade.alpha:</th>
-      <td><p>should the CI shading fade out at the edges? (by reducing alpha; 0 = no alpha decrease, 0.1 = medium alpha decrease, 0.5 = strong alpha decrease)</p></td>
-    </tr>
-    <tr>
-      <th>spag:</th>
-      <td><p>plot spaghetti lines?</p></td>
-    </tr>
-    <tr>
-      <th>spag.color:</th>
-      <td><p>color of spaghetti lines</p></td>
-    </tr>
-    <tr>
-      <th>mweight:</th>
-      <td><p>should the median smoother be visually weighted?</p></td>
-    </tr>
-    <tr>
-      <th>show.lm:</th>
-      <td><p>should the linear regresison line be plotted?</p></td>
-    </tr>
-    <tr>
-      <th>show.CI:</th>
-      <td><p>should the 95<!-- % CI limits be plotted?} --></p>
-<p>show.median:should the median smoother be plotted?</p>
-<p>median.col:color of the median smoother</p>
-<p>shape:shape of points</p>
-<p>method:the fitting function for the spaghettis; default: loess</p>
-<p>slices:number of slices in x and y direction for the shaded region. Higher numbers make a smoother plot, but takes longer to draw. I wouldn'T go beyond 500</p>
-<p>palette:provide a custom color palette for the watercolors</p>
-<p>ylim:restrict range of the watercoloring</p>
-<p>quantize:either 'continuous', or 'SD'. In the latter case, we get three color regions for 1, 2, and 3 SD (an idea of John Mashey)</p>
-<p>add:if add == FALSE, a new ggplot is returned. If add == TRUE, only the elements are returned, which can be added to an existing ggplot (with the '+' operator)</p>
-<p>...:further parameters passed to the fitting function, in the case of loess, for example, 'span = .9', or 'family = 'symmetric''</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>B</th>
+              <td><p>= number bootstrapped smoothers</p></td>
+            </tr>
+            <tr>
+              <th>bw</th>
+              <td><p>= TRUE: define a default b&amp;w-palette</p></td>
+            </tr>
+            <tr>
+              <th>shade:</th>
+              <td><p>plot the shaded confidence region?</p></td>
+            </tr>
+            <tr>
+              <th>shade.alpha:</th>
+              <td>
+                <p>
+                  should the CI shading fade out at the edges? (by reducing
+                  alpha; 0 = no alpha decrease, 0.1 = medium alpha decrease, 0.5
+                  = strong alpha decrease)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>spag:</th>
+              <td><p>plot spaghetti lines?</p></td>
+            </tr>
+            <tr>
+              <th>spag.color:</th>
+              <td><p>color of spaghetti lines</p></td>
+            </tr>
+            <tr>
+              <th>mweight:</th>
+              <td><p>should the median smoother be visually weighted?</p></td>
+            </tr>
+            <tr>
+              <th>show.lm:</th>
+              <td><p>should the linear regresison line be plotted?</p></td>
+            </tr>
+            <tr>
+              <th>show.CI:</th>
+              <td>
+                <p>should the 95<!-- % CI limits be plotted?} --></p>
+                <p>show.median:should the median smoother be plotted?</p>
+                <p>median.col:color of the median smoother</p>
+                <p>shape:shape of points</p>
+                <p>
+                  method:the fitting function for the spaghettis; default: loess
+                </p>
+                <p>
+                  slices:number of slices in x and y direction for the shaded
+                  region. Higher numbers make a smoother plot, but takes longer
+                  to draw. I wouldn'T go beyond 500
+                </p>
+                <p>
+                  palette:provide a custom color palette for the watercolors
+                </p>
+                <p>ylim:restrict range of the watercoloring</p>
+                <p>
+                  quantize:either 'continuous', or 'SD'. In the latter case, we
+                  get three color regions for 1, 2, and 3 SD (an idea of John
+                  Mashey)
+                </p>
+                <p>
+                  add:if add == FALSE, a new ggplot is returned. If add == TRUE,
+                  only the elements are returned, which can be added to an
+                  existing ggplot (with the '+' operator)
+                </p>
+                <p>
+                  ...:further parameters passed to the fitting function, in the
+                  case of loess, for example, 'span = .9', or 'family =
+                  'symmetric''
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
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diff --git a/base/workflow/docs/LICENSE-text.html b/base/workflow/docs/LICENSE-text.html
index d576c08..f3744b2 100644
--- a/base/workflow/docs/LICENSE-text.html
+++ b/base/workflow/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
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+      crossorigin="anonymous"
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+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
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+    ></script>
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <![endif]-->
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+              <button
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+              >
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+              </button>
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+                <a class="navbar-link" href="index.html">PEcAn.workflow</a>
+                <span
+                  class="label label-default"
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+                  >1.6.0</span
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-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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 </html>
-
diff --git a/base/workflow/docs/authors.html b/base/workflow/docs/authors.html
index cb1afa5..97b38b0 100644
--- a/base/workflow/docs/authors.html
+++ b/base/workflow/docs/authors.html
@@ -2,146 +2,161 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.workflow</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.workflow</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.workflow</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.workflow</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/workflow/docs/docsearch.css b/base/workflow/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/base/workflow/docs/docsearch.css
+++ b/base/workflow/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/base/workflow/docs/docsearch.js b/base/workflow/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/base/workflow/docs/docsearch.js
+++ b/base/workflow/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/base/workflow/docs/index.html b/base/workflow/docs/index.html
index 63eb5c8..f1873be 100644
--- a/base/workflow/docs/index.html
+++ b/base/workflow/docs/index.html
@@ -1,119 +1,175 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for ecological forecasts and
-    reanalysis • PEcAn.workflow</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and
-    reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis •
+      PEcAn.workflow
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and
+    reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer
     (PEcAn) is a scientific workflow management tool that
     is designed to simplify the management of model
     parameterization, execution, and analysis. The goal of
     PEcAn is to streamline the interaction between data and
     models, and to improve the efficacy of scientific
     investigation. This package provides workhorse functions
-    that can be used to run the major steps of a PEcAn analysis.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    that can be used to run the major steps of a PEcAn analysis."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.workflow</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer
-    (PEcAn) is a scientific workflow management tool that
-    is designed to simplify the management of model
-    parameterization, execution, and analysis. The goal of
-    PEcAn is to streamline the interaction between data and
-    models, and to improve the efficacy of scientific
-    investigation. This package provides workhorse functions
-    that can be used to run the major steps of a PEcAn analysis.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
-
-  </div>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.workflow</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PEcAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation. This package
+          provides workhorse functions that can be used to run the major steps
+          of a PEcAn analysis.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/base/workflow/docs/pkgdown.css b/base/workflow/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/base/workflow/docs/pkgdown.css
+++ b/base/workflow/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/base/workflow/docs/pkgdown.js b/base/workflow/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/base/workflow/docs/pkgdown.js
+++ b/base/workflow/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/base/workflow/docs/reference/index.html b/base/workflow/docs/reference/index.html
index f234b45..9c25f2f 100644
--- a/base/workflow/docs/reference/index.html
+++ b/base/workflow/docs/reference/index.html
@@ -2,156 +2,208 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.workflow</title>
-
-<!-- jquery -->
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-<!-- Bootstrap -->
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-
-<!-- clipboard.js -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.workflow</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
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+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+    <!-- sticky kit -->
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Function reference" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <span class="navbar-brand">
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.workflow</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="run.write.configs.html">run.write.configs()</a></code> </p>
-        </td>
-        <td><p>Write model-specific run scripts and configuration files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="runModule.get.trait.data.html">runModule.get.trait.data()</a></code> </p>
-        </td>
-        <td><p>Get trait data for all PFTs in a settings list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="runModule.run.write.configs.html">runModule.run.write.configs()</a></code> </p>
-        </td>
-        <td><p>Generate model-specific run configuration files for one or more PEcAn runs</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="run.write.configs.html"
+                        >run.write.configs()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Write model-specific run scripts and configuration files
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="runModule.get.trait.data.html"
+                        >runModule.get.trait.data()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get trait data for all PFTs in a settings list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="runModule.run.write.configs.html"
+                        >runModule.run.write.configs()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Generate model-specific run configuration files for one or
+                    more PEcAn runs
+                  </p>
+                </td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
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-
diff --git a/base/workflow/docs/reference/run.write.configs.html b/base/workflow/docs/reference/run.write.configs.html
index b567fb0..641465c 100644
--- a/base/workflow/docs/reference/run.write.configs.html
+++ b/base/workflow/docs/reference/run.write.configs.html
@@ -2,188 +2,247 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-
-<meta property="og:title" content="Write model-specific run scripts and configuration files — run.write.configs" />
-
-<meta property="og:description" content="Generates run scripts and configuration files for all analyses specified
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Write model-specific run scripts and configuration files —
+      run.write.configs • PEcAn.workflow
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write model-specific run scripts and configuration files — run.write.configs"
+    />
+
+    <meta
+      property="og:description"
+      content="Generates run scripts and configuration files for all analyses specified
 in the provided settings. Most of the heavy lifting is done by the
 write.config.* function for your specific ecosystem model
-(e.g. write.config.ED2, write.config.SIPNET)." />
-<meta name="twitter:card" content="summary" />
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+(e.g. write.config.ED2, write.config.SIPNET)."
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.workflow</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.workflow</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write model-specific run scripts and configuration files</h1>
-    
-    <div class="hidden name"><code>run.write.configs.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generates run scripts and configuration files for all analyses specified
-in the provided settings. Most of the heavy lifting is done by the
-<code>write.config.*</code> function for your specific ecosystem model
-(e.g. write.config.ED2, write.config.SIPNET).</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>run.write.configs</span>(<span class='no'>settings</span>, <span class='kw'>write</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write model-specific run scripts and configuration files</h1>
+
+            <div class="hidden name"><code>run.write.configs.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Generates run scripts and configuration files for all analyses
+              specified in the provided settings. Most of the heavy lifting is
+              done by the <code>write.config.*</code> function for your specific
+              ecosystem model (e.g. write.config.ED2, write.config.SIPNET).
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>run.write.configs</span>(<span class='no'>settings</span>, <span class='kw'>write</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>ens.sample.method</span> <span class='kw'>=</span> <span class='st'>"uniform"</span>, <span class='kw'>posterior.files</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>NA</span>,
   <span class='fu'>length</span>(<span class='no'>settings</span>$<span class='no'>pfts</span>)), <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>a PEcAn settings list</p></td>
-    </tr>
-    <tr>
-      <th>write</th>
-      <td><p>should the runs be written to the database?</p></td>
-    </tr>
-    <tr>
-      <th>ens.sample.method</th>
-      <td><p>how to sample the ensemble members('halton' sequence or 'uniform' random)</p></td>
-    </tr>
-    <tr>
-      <th>posterior.files</th>
-      <td><p>Filenames for posteriors for drawing samples for ensemble and sensitivity
-analysis (e.g. post.distns.Rdata, or prior.distns.Rdata)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: Replace output files that already exist?</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>an updated settings list, which includes ensemble IDs for SA and ensemble analysis</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>The default value for <code>posterior.files</code> is NA, in which case the
-   most recent posterior or prior (in that order) for the workflow is used.
-   When specified, <code>posterior.files</code> should be a vector of filenames with one entry for each PFT.
-   Specify filenames with no path; PFT outdirs will be appended. This forces use of only
-   files within this workflow, to avoid confusion.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>a PEcAn settings list</p></td>
+            </tr>
+            <tr>
+              <th>write</th>
+              <td><p>should the runs be written to the database?</p></td>
+            </tr>
+            <tr>
+              <th>ens.sample.method</th>
+              <td>
+                <p>
+                  how to sample the ensemble members('halton' sequence or
+                  'uniform' random)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>posterior.files</th>
+              <td>
+                <p>
+                  Filenames for posteriors for drawing samples for ensemble and
+                  sensitivity analysis (e.g. post.distns.Rdata, or
+                  prior.distns.Rdata)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical: Replace output files that already exist?</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            an updated settings list, which includes ensemble IDs for SA and
+            ensemble analysis
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            The default value for <code>posterior.files</code> is NA, in which
+            case the most recent posterior or prior (in that order) for the
+            workflow is used. When specified,
+            <code>posterior.files</code> should be a vector of filenames with
+            one entry for each PFT. Specify filenames with no path; PFT outdirs
+            will be appended. This forces use of only files within this
+            workflow, to avoid confusion.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Ryan Kelly, Mike Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin, Ryan Kelly, Mike Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/base/workflow/docs/reference/runModule.get.trait.data.html b/base/workflow/docs/reference/runModule.get.trait.data.html
index 7bd3e3e..5da1e7a 100644
--- a/base/workflow/docs/reference/runModule.get.trait.data.html
+++ b/base/workflow/docs/reference/runModule.get.trait.data.html
@@ -2,143 +2,186 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Get trait data for all PFTs in a settings list — runModule.get.trait.data • PEcAn.workflow</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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+      • PEcAn.workflow
+    </title>
+
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+                <span
+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get trait data for all PFTs in a settings list</h1>
-    
-    <div class="hidden name"><code>runModule.get.trait.data.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get trait data for all PFTs in a settings list</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>runModule.get.trait.data</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn configuration list. Must have class `Settings` or `MultiSettings`</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get trait data for all PFTs in a settings list</h1>
+
+            <div class="hidden name">
+              <code>runModule.get.trait.data.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get trait data for all PFTs in a settings list</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>runModule.get.trait.data</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  PEcAn configuration list. Must have class `Settings` or
+                  `MultiSettings`
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/base/workflow/docs/reference/runModule.run.write.configs.html b/base/workflow/docs/reference/runModule.run.write.configs.html
index 8d569d9..424b059 100644
--- a/base/workflow/docs/reference/runModule.run.write.configs.html
+++ b/base/workflow/docs/reference/runModule.run.write.configs.html
@@ -2,153 +2,201 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Generate model-specific run configuration files for one or more PEcAn runs
+      — runModule.run.write.configs • PEcAn.workflow
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      content="Generate model-specific run configuration files for one or more PEcAn runs — runModule.run.write.configs"
+    />
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+      content="Generate model-specific run configuration files for one or more PEcAn runs"
+    />
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+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.workflow</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+                type="button"
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.workflow</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate model-specific run configuration files for one or more PEcAn runs</h1>
-    
-    <div class="hidden name"><code>runModule.run.write.configs.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generate model-specific run configuration files for one or more PEcAn runs</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>runModule.run.write.configs</span>(<span class='no'>settings</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>a PEcAn Settings or MultiSettings object</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: Replace config files if they already exist?</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A modified settings object, invisibly</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Generate model-specific run configuration files for one or more
+              PEcAn runs
+            </h1>
+
+            <div class="hidden name">
+              <code>runModule.run.write.configs.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Generate model-specific run configuration files for one or more
+              PEcAn runs
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>runModule.run.write.configs</span>(<span class='no'>settings</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>a PEcAn Settings or MultiSettings object</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>logical: Replace config files if they already exist?</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>A modified settings object, invisibly</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/css/components.css b/css/components.css
index f4eb45d..14a6814 100644
--- a/css/components.css
+++ b/css/components.css
@@ -17,20 +17,24 @@
   display: none;
 }
 .tab-nav > .tab-label {
-  float:left;
+  float: left;
 }
-a.tab-label, a.tab-label:link, a.tab-label:visited, a.tab-label:hover {
+a.tab-label,
+a.tab-label:link,
+a.tab-label:visited,
+a.tab-label:hover {
   background: none repeat scroll 0 0 #262626;
   color: #fff;
   margin-right: 1px;
   padding: 0.625rem 1.25rem;
-  transition: background 0.20s linear 0s;
-  -o-transition: background 0.20s linear 0s;
-  -ms-transition: background 0.20s linear 0s;
-  -moz-transition: background 0.20s linear 0s;
-  -webkit-transition: background 0.20s linear 0s;
+  transition: background 0.2s linear 0s;
+  -o-transition: background 0.2s linear 0s;
+  -ms-transition: background 0.2s linear 0s;
+  -moz-transition: background 0.2s linear 0s;
+  -webkit-transition: background 0.2s linear 0s;
 }
-a.tab-label:hover,a.tab-label.active-btn {
+a.tab-label:hover,
+a.tab-label.active-btn {
   background: none repeat scroll 0 0 #999;
 }
 .tab-label.active-btn {
@@ -39,75 +43,99 @@ a.tab-label:hover,a.tab-label.active-btn {
 .tab-content {
   text-align: left;
 }
-@media screen and (max-width:768px) {    
+@media screen and (max-width: 768px) {
   .tab-nav > .tab-label {
     margin: 0.5px 0;
     width: 100%;
   }
 }
 /* Custom forms */
-form.customform input, form.customform select, form.customform textarea, form.customform button {
- font-size:0.9rem;
- font-family:inherit;
- margin-bottom:1.25rem;
-} 
-form.customform input, form.customform select {height: 2.7rem;}
-form.customform input, form.customform textarea, form.customform select { 
- background: none repeat scroll 0 0 #F5F5F5;
- transition: background 0.20s linear 0s;
- -o-transition: background 0.20s linear 0s;
- -ms-transition: background 0.20s linear 0s;
- -moz-transition: background 0.20s linear 0s;
- -webkit-transition: background 0.20s linear 0s;
-}
-form.customform input:hover, form.customform textarea:hover, form.customform select:hover, form.customform input:focus, form.customform textarea:focus, form.customform select:focus {background: none repeat scroll 0 0 #fff;}
-form.customform input, form.customform textarea, form.customform select {
- background: none repeat scroll 0 0 #F5F5F5;
- border: 1px solid #E0E0E0;
- padding: 0.625rem;
- width: 100%;
+form.customform input,
+form.customform select,
+form.customform textarea,
+form.customform button {
+  font-size: 0.9rem;
+  font-family: inherit;
+  margin-bottom: 1.25rem;
+}
+form.customform input,
+form.customform select {
+  height: 2.7rem;
+}
+form.customform input,
+form.customform textarea,
+form.customform select {
+  background: none repeat scroll 0 0 #f5f5f5;
+  transition: background 0.2s linear 0s;
+  -o-transition: background 0.2s linear 0s;
+  -ms-transition: background 0.2s linear 0s;
+  -moz-transition: background 0.2s linear 0s;
+  -webkit-transition: background 0.2s linear 0s;
+}
+form.customform input:hover,
+form.customform textarea:hover,
+form.customform select:hover,
+form.customform input:focus,
+form.customform textarea:focus,
+form.customform select:focus {
+  background: none repeat scroll 0 0 #fff;
+}
+form.customform input,
+form.customform textarea,
+form.customform select {
+  background: none repeat scroll 0 0 #f5f5f5;
+  border: 1px solid #e0e0e0;
+  padding: 0.625rem;
+  width: 100%;
 }
 form.customform input[type="file"] {
- border: 1px solid #E0E0E0;
- height: auto;
- max-height: 2.7rem;
- min-height: 2.7rem;
- padding: 0.4rem;
- width: 100%;
-}
-form.customform input[type="radio"], form.customform input[type="checkbox"] {
- margin-right: 0.625rem;
- width:auto;
- padding:0;
- height:auto;
-}
-form.customform option {padding: 0.625rem;}
-form.customform select[multiple="multiple"] {height: auto;}
+  border: 1px solid #e0e0e0;
+  height: auto;
+  max-height: 2.7rem;
+  min-height: 2.7rem;
+  padding: 0.4rem;
+  width: 100%;
+}
+form.customform input[type="radio"],
+form.customform input[type="checkbox"] {
+  margin-right: 0.625rem;
+  width: auto;
+  padding: 0;
+  height: auto;
+}
+form.customform option {
+  padding: 0.625rem;
+}
+form.customform select[multiple="multiple"] {
+  height: auto;
+}
 form.customform button {
- width: 100%;
- background: none repeat scroll 0 0 #152732;
- border: 0 none;
- color: #fff;
- height: 2.7rem;
- padding: 0.625rem;
- cursor:pointer;
- width: 100%;
- transition: background 0.20s linear 0s;
- -o-transition: background 0.20s linear 0s;
- -ms-transition: background 0.20s linear 0s;
- -moz-transition: background 0.20s linear 0s;
- -webkit-transition: background 0.20s linear 0s;
+  width: 100%;
+  background: none repeat scroll 0 0 #152732;
+  border: 0 none;
+  color: #fff;
+  height: 2.7rem;
+  padding: 0.625rem;
+  cursor: pointer;
+  width: 100%;
+  transition: background 0.2s linear 0s;
+  -o-transition: background 0.2s linear 0s;
+  -ms-transition: background 0.2s linear 0s;
+  -moz-transition: background 0.2s linear 0s;
+  -webkit-transition: background 0.2s linear 0s;
 }
 /* Tooltip */
-a.tooltip-container,.tooltip-container {
-  border-bottom:1px dotted;
+a.tooltip-container,
+.tooltip-container {
+  border-bottom: 1px dotted;
   border-bottom-color: color;
   cursor: help;
   font-weight: 600;
 }
-a .tooltip-content,.tooltip-content {
+a .tooltip-content,
+.tooltip-content {
   background: #152732 none repeat scroll 0 0;
-  color: #fff!important;
+  color: #fff !important;
   border-radius: 3px;
   display: none;
   font-size: 0.8rem;
@@ -132,7 +160,8 @@ a .tooltip-content,.tooltip-content {
   position: absolute;
   width: 0;
 }
-a.tooltip-content.tooltip-bottom,.tooltip-content.tooltip-bottom {
+a.tooltip-content.tooltip-bottom,
+.tooltip-content.tooltip-bottom {
   margin-top: 1.25rem;
 }
 .tooltip-content.tooltip-bottom::after {
@@ -143,7 +172,11 @@ a.tooltip-content.tooltip-bottom,.tooltip-content.tooltip-bottom {
   top: -5px;
 }
 /* Buttons */
-.button,a.button,a.button:link,a.button:active,a.button:visited {
+.button,
+a.button,
+a.button:link,
+a.button:active,
+a.button:visited {
   background: #777 none repeat scroll 0 0;
   border: 0;
   color: #fff;
@@ -152,11 +185,11 @@ a.tooltip-content.tooltip-bottom,.tooltip-content.tooltip-bottom {
   font-size: 0.85rem;
   padding: 0.825rem 1rem;
   text-align: center;
-  transition: all 0.20s linear 0s;
-  -o-transition: all 0.20s linear 0s;
-  -ms-transition: all 0.20s linear 0s;
-  -moz-transition: all 0.20s linear 0s;
-  -webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
 }
 .button.rounded-btn {
   border-radius: 4px;
@@ -164,42 +197,60 @@ a.tooltip-content.tooltip-bottom,.tooltip-content.tooltip-bottom {
 .button.rounded-full-btn {
   border-radius: 100px;
 }
-.button:hover {box-shadow: 0 0 10px 100px rgba(255,255,255,0.15) inset;}
-.button.secondary-btn,a.button.secondary-btn,a.button.secondary-btn:link,a.button.secondary-btn:active,a.button.secondary-btn:visited {
+.button:hover {
+  box-shadow: 0 0 10px 100px rgba(255, 255, 255, 0.15) inset;
+}
+.button.secondary-btn,
+a.button.secondary-btn,
+a.button.secondary-btn:link,
+a.button.secondary-btn:active,
+a.button.secondary-btn:visited {
   background: #444 none repeat scroll 0 0;
 }
-.button.cancel-btn,a.button.cancel-btn,a.button.cancel-btn:link,a.button.cancel-btn:active,a.button.cancel-btn:visited {
+.button.cancel-btn,
+a.button.cancel-btn,
+a.button.cancel-btn:link,
+a.button.cancel-btn:active,
+a.button.cancel-btn:visited {
   background: #dc003a none repeat scroll 0 0;
 }
-.button.submit-btn,a.button.submit-btn,a.button.submit-btn:link,a.button.submit-btn:active,a.button.submit-btn:visited {
+.button.submit-btn,
+a.button.submit-btn,
+a.button.submit-btn:link,
+a.button.submit-btn:active,
+a.button.submit-btn:visited {
   background: #b4bf04 none repeat scroll 0 0;
 }
-.button.reload-btn,a.button.reload-btn,a.button.reload-btn:link,a.button.reload-btn:active,a.button.reload-btn:visited {
+.button.reload-btn,
+a.button.reload-btn,
+a.button.reload-btn:link,
+a.button.reload-btn:active,
+a.button.reload-btn:visited {
   background: #ff9800 none repeat scroll 0 0;
 }
 .button.disabled-btn {
-  cursor: not-allowed!important;
+  cursor: not-allowed !important;
   opacity: 0.2;
 }
 .button i {
   background: rgba(0, 0, 0, 0.1) none repeat scroll 0 0;
   border-radius: 27px;
-  color: #fff!important;
+  color: #fff !important;
   display: inline-block;
   font-size: 0.8rem;
   height: 27px;
   line-height: 27px;
   margin-right: 5px;
   width: 27px;
-  transition: all 0.20s linear 0s;
-  -o-transition: all 0.20s linear 0s;
-  -ms-transition: all 0.20s linear 0s;
-  -moz-transition: all 0.20s linear 0s;
-  -webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
 }
 .button:hover > i {
   background: rgba(0, 0, 0, 0.06) none repeat scroll 0 0;
 }
 .grid .button {
-    width: 100%;
-}
\ No newline at end of file
+  width: 100%;
+}
diff --git a/css/icons.css b/css/icons.css
index e0b2d64..49fdea7 100644
--- a/css/icons.css
+++ b/css/icons.css
@@ -1,13 +1,14 @@
 /* Icon font - MFG labs */
 @font-face {
-  font-family: 'mfg';
-    src: url('../font/mfglabsiconset-webfont.eot');
-    src: url('../font/mfglabsiconset-webfont.svg#mfg_labs_iconsetregular') format('svg'),
-   		   url('../font/mfglabsiconset-webfont.eot?#iefix') format('embedded-opentype'),
-         url('../font/mfglabsiconset-webfont.woff') format('woff'),
-         url('../font/mfglabsiconset-webfont.ttf') format('truetype');
-    font-weight: normal;
-    font-style: normal;
+  font-family: "mfg";
+  src: url("../font/mfglabsiconset-webfont.eot");
+  src: url("../font/mfglabsiconset-webfont.svg#mfg_labs_iconsetregular")
+      format("svg"),
+    url("../font/mfglabsiconset-webfont.eot?#iefix") format("embedded-opentype"),
+    url("../font/mfglabsiconset-webfont.woff") format("woff"),
+    url("../font/mfglabsiconset-webfont.ttf") format("truetype");
+  font-weight: normal;
+  font-style: normal;
 }
 
 .icon-cloud,
@@ -196,213 +197,593 @@
 .icon-disconnect,
 .icon-graph,
 .icon-new_user {
-  font-family: 'mfg';
+  font-family: "mfg";
   font-style: normal;
   font-variant: normal;
   font-weight: normal;
-  color:#e3e3e3;
-  speak: none; 
+  color: #e3e3e3;
+  speak: none;
   text-transform: none;
   /* Better Font Rendering =========== */
   -webkit-font-smoothing: antialiased;
   -moz-osx-font-smoothing: grayscale;
 }
-.icon2x {font-size: 2rem;}
-.icon3x {font-size: 3rem;}
-
-.icon-cloud:before { content: "\2601"; }
-.icon-at:before { content: "\0040"; }
-.icon-plus:before { content: "\002B"; }
-.icon-minus:before { content: "\2212"; }
-.icon-arrow_up:before { content: "\2191"; }
-.icon-arrow_down:before { content: "\2193"; }
-.icon-arrow_right:before { content: "\2192"; }
-.icon-arrow_left:before { content: "\2190"; }
-.icon-chevron_down:before { content: "\f004"; }
-.icon-chevron_up:before { content: "\f005"; }
-.icon-chevron_right:before { content: "\f006"; }
-.icon-chevron_left:before { content: "\f007"; }
-.icon-reorder:before { content: "\f008"; }
-.icon-list:before { content: "\f009"; }
-.icon-reorder_square:before { content: "\f00a"; }
-.icon-reorder_square_line:before { content: "\f00b"; }
-.icon-coverflow:before { content: "\f00c"; }
-.icon-coverflow_line:before { content: "\f00d"; }
-.icon-pause:before { content: "\f00e"; }
-.icon-play:before { content: "\f00f"; }
-.icon-step_forward:before { content: "\f010"; }
-.icon-step_backward:before { content: "\f011"; }
-.icon-fast_forward:before { content: "\f012"; }
-.icon-fast_backward:before { content: "\f013"; }
-.icon-cloud_upload:before { content: "\f014"; }
-.icon-cloud_download:before { content: "\f015"; }
-.icon-data_science:before { content: "\f016"; }
-.icon-data_science_black:before { content: "\f017"; }
-.icon-globe:before { content: "\f018"; }
-.icon-globe_black:before { content: "\f019"; }
-.icon-math_ico:before { content: "\f01a"; }
-.icon-math:before { content: "\f01b"; }
-.icon-math_black:before { content: "\f01c"; }
-.icon-paperplane_ico:before { content: "\f01d"; }
-.icon-paperplane:before { content: "\f01e"; }
-.icon-paperplane_black:before { content: "\f01f"; }
-.icon-color_balance:before { content: "\f020"; }
-.icon-star:before { content: "\2605"; }
-.icon-star_half:before { content: "\f022"; }
-.icon-star_empty:before { content: "\2606"; }
-.icon-star_half_empty:before { content: "\f024"; }
-.icon-reload:before { content: "\f025"; }
-.icon-heart:before { content: "\2665"; }
-.icon-heart_broken:before { content: "\f028"; }
-.icon-hashtag:before { content: "\f029"; }
-.icon-reply:before { content: "\f02a"; }
-.icon-retweet:before { content: "\f02b"; }
-.icon-signin:before { content: "\f02c"; }
-.icon-signout:before { content: "\f02d"; }
-.icon-download:before { content: "\f02e"; }
-.icon-upload:before { content: "\f02f"; }
-.icon-placepin:before { content: "\f031"; }
-.icon-display_screen:before { content: "\f032"; }
-.icon-tablet:before { content: "\f033"; }
-.icon-smartphone:before { content: "\f034"; }
-.icon-connected_object:before { content: "\f035"; }
-.icon-lock:before { content: "\F512"; }
-.icon-unlock:before { content: "\F513"; }
-.icon-camera:before { content: "\F4F7"; }
-.icon-isight:before { content: "\f039"; }
-.icon-video_camera:before { content: "\f03a"; }
-.icon-random:before { content: "\f03b"; }
-.icon-message:before { content: "\F4AC"; }
-.icon-discussion:before { content: "\f03d"; }
-.icon-calendar:before { content: "\F4C5"; }
-.icon-ringbell:before { content: "\f03f"; }
-.icon-movie:before { content: "\f040"; }
-.icon-mail:before { content: "\2709"; }
-.icon-pen:before { content: "\270F"; }
-.icon-settings:before { content: "\9881"; }
-.icon-measure:before { content: "\f044"; }
-.icon-vector:before { content: "\f045"; }
-.icon-vector_pen:before { content: "\2712"; }
-.icon-mute_on:before { content: "\f047"; }
-.icon-mute_off:before { content: "\f048"; }
-.icon-home:before { content: "\2302"; }
-.icon-sheet:before { content: "\f04a"; }
-.icon-arrow_big_right:before { content: "\21C9"; }
-.icon-arrow_big_left:before { content: "\21C7"; }
-.icon-arrow_big_down:before { content: "\21CA"; }
-.icon-arrow_big_up:before { content: "\21C8"; }
-.icon-dribbble_circle:before { content: "\f04f"; }
-.icon-dribbble:before { content: "\f050"; }
-.icon-facebook_circle:before { content: "\f051"; }
-.icon-facebook:before { content: "\f052"; }
-.icon-git_circle_alt:before { content: "\f053"; }
-.icon-git_circle:before { content: "\f054"; }
-.icon-git:before { content: "\f055"; }
-.icon-octopus:before { content: "\f056"; }
-.icon-twitter_circle:before { content: "\f057"; }
-.icon-twitter:before { content: "\f058"; }
-.icon-google_plus_circle:before { content: "\f059"; }
-.icon-google_plus:before { content: "\f05a"; }
-.icon-linked_in_circle:before { content: "\f05b"; }
-.icon-linked_in:before { content: "\f05c"; }
-.icon-instagram:before { content: "\f05d"; }
-.icon-instagram_circle:before { content: "\f05e"; }
-.icon-mfg_icon:before { content: "\f05f"; }
-.icon-xing:before { content: "\F532"; }
-.icon-xing_circle:before { content: "\F533"; }
-.icon-mfg_icon_circle:before { content: "\f060"; }
-.icon-user:before { content: "\f061"; }
-.icon-user_male:before { content: "\f062"; }
-.icon-user_female:before { content: "\f063"; }
-.icon-users:before { content: "\f064"; }
-.icon-file_open:before { content: "\F4C2"; }
-.icon-file_close:before { content: "\f067"; }
-.icon-file_alt:before { content: "\f068"; }
-.icon-file_close_alt:before { content: "\f069"; }
-.icon-attachment:before { content: "\f06a"; }
-.icon-check:before { content: "\2713"; }
-.icon-cross_mark:before { content: "\274C"; }
-.icon-cancel_circle:before { content: "\F06E"; }
-.icon-check_circle:before { content: "\f06d"; }
-.icon-magnifying:before { content: "\F50D"; }
-.icon-inbox:before { content: "\f070"; }
-.icon-clock:before { content: "\23F2"; }
-.icon-stopwatch:before { content: "\23F1"; }
-.icon-hourglass:before { content: "\231B"; }
-.icon-trophy:before { content: "\f074"; }
-.icon-unlock_alt:before { content: "\F075"; }
-.icon-lock_alt:before { content: "\F510"; }
-.icon-arrow_doubled_right:before { content: "\21D2"; }
-.icon-arrow_doubled_left:before { content: "\21D0"; }
-.icon-arrow_doubled_down:before { content: "\21D3"; }
-.icon-arrow_doubled_up:before { content: "\21D1"; }
-.icon-link:before { content: "\f07B"; }
-.icon-warning:before { content: "\2757"; }
-.icon-warning_alt:before { content: "\2755"; }
-.icon-magnifying_plus:before { content: "\f07E"; }
-.icon-magnifying_minus:before { content: "\f07F"; }
-.icon-white_question:before { content: "\2754"; }
-.icon-black_question:before { content: "\2753"; }
-.icon-stop:before { content: "\f080"; }
-.icon-share:before { content: "\f081"; }
-.icon-eye:before { content: "\f082"; }
-.icon-trash_can:before { content: "\f083"; }
-.icon-hard_drive:before { content: "\f084"; }
-.icon-information_black:before { content: "\f085"; }
-.icon-information_white:before { content: "\f086"; }
-.icon-printer:before { content: "\f087"; }
-.icon-letter:before { content: "\f088"; }
-.icon-soundcloud:before { content: "\f089"; }
-.icon-soundcloud_circle:before { content: "\f08A"; }
-.icon-anchor:before { content: "\2693"; }
-.icon-female_sign:before { content: "\2640"; }
-.icon-male_sign:before { content: "\2642"; }
-.icon-joystick:before { content: "\F514"; }
-.icon-high_voltage:before { content: "\26A1"; }
-.icon-fire:before { content: "\F525"; }
-.icon-newspaper:before { content: "\F4F0"; }
-.icon-chart:before { content: "\F526"; }
-.icon-spread:before { content: "\F527"; }
-.icon-spinner_1:before { content: "\F528"; }
-.icon-spinner_2:before { content: "\F529"; }
-.icon-chart_alt:before { content: "\F530"; }
-.icon-label:before { content: "\F531"; }
-.icon-brush:before { content: "\E000"; }
-.icon-refresh:before { content: "\E001"; }
-.icon-node:before { content: "\E002"; }
-.icon-node_2:before { content: "\E003"; }
-.icon-node_3:before { content: "\E004"; }
-.icon-link_2_nodes:before { content: "\E005"; }
-.icon-link_3_nodes:before { content: "\E006"; }
-.icon-link_loop_nodes:before { content: "\E007"; }
-.icon-node_size:before { content: "\E008"; }
-.icon-node_color:before { content: "\E009"; }
-.icon-layout_directed:before { content: "\E010"; }
-.icon-layout_radial:before { content: "\E011"; }
-.icon-layout_hierarchical:before { content: "\E012"; }
-.icon-node_link_direction:before { content: "\E013"; }
-.icon-node_link_short_path:before { content: "\E014"; }
-.icon-node_cluster:before { content: "\E015"; }
-.icon-display_graph:before { content: "\E016"; }
-.icon-node_link_weight:before { content: "\E017"; }
-.icon-more_node_links:before { content: "\E018"; }
-.icon-node_shape:before { content: "\E00A"; }
-.icon-node_icon:before { content: "\E00B"; }
-.icon-node_text:before { content: "\E00C"; }
-.icon-node_link_text:before { content: "\E00D"; }
-.icon-node_link_color:before { content: "\E00E"; }
-.icon-node_link_shape:before { content: "\E00F"; }
-.icon-credit_card:before { content: "\F4B3"; }
-.icon-disconnect:before { content: "\F534"; }
-.icon-graph:before { content: "\F535"; }
-.icon-new_user:before { content: "\F536"; }
+.icon2x {
+  font-size: 2rem;
+}
+.icon3x {
+  font-size: 3rem;
+}
 
+.icon-cloud:before {
+  content: "\2601";
+}
+.icon-at:before {
+  content: "\0040";
+}
+.icon-plus:before {
+  content: "\002B";
+}
+.icon-minus:before {
+  content: "\2212";
+}
+.icon-arrow_up:before {
+  content: "\2191";
+}
+.icon-arrow_down:before {
+  content: "\2193";
+}
+.icon-arrow_right:before {
+  content: "\2192";
+}
+.icon-arrow_left:before {
+  content: "\2190";
+}
+.icon-chevron_down:before {
+  content: "\f004";
+}
+.icon-chevron_up:before {
+  content: "\f005";
+}
+.icon-chevron_right:before {
+  content: "\f006";
+}
+.icon-chevron_left:before {
+  content: "\f007";
+}
+.icon-reorder:before {
+  content: "\f008";
+}
+.icon-list:before {
+  content: "\f009";
+}
+.icon-reorder_square:before {
+  content: "\f00a";
+}
+.icon-reorder_square_line:before {
+  content: "\f00b";
+}
+.icon-coverflow:before {
+  content: "\f00c";
+}
+.icon-coverflow_line:before {
+  content: "\f00d";
+}
+.icon-pause:before {
+  content: "\f00e";
+}
+.icon-play:before {
+  content: "\f00f";
+}
+.icon-step_forward:before {
+  content: "\f010";
+}
+.icon-step_backward:before {
+  content: "\f011";
+}
+.icon-fast_forward:before {
+  content: "\f012";
+}
+.icon-fast_backward:before {
+  content: "\f013";
+}
+.icon-cloud_upload:before {
+  content: "\f014";
+}
+.icon-cloud_download:before {
+  content: "\f015";
+}
+.icon-data_science:before {
+  content: "\f016";
+}
+.icon-data_science_black:before {
+  content: "\f017";
+}
+.icon-globe:before {
+  content: "\f018";
+}
+.icon-globe_black:before {
+  content: "\f019";
+}
+.icon-math_ico:before {
+  content: "\f01a";
+}
+.icon-math:before {
+  content: "\f01b";
+}
+.icon-math_black:before {
+  content: "\f01c";
+}
+.icon-paperplane_ico:before {
+  content: "\f01d";
+}
+.icon-paperplane:before {
+  content: "\f01e";
+}
+.icon-paperplane_black:before {
+  content: "\f01f";
+}
+.icon-color_balance:before {
+  content: "\f020";
+}
+.icon-star:before {
+  content: "\2605";
+}
+.icon-star_half:before {
+  content: "\f022";
+}
+.icon-star_empty:before {
+  content: "\2606";
+}
+.icon-star_half_empty:before {
+  content: "\f024";
+}
+.icon-reload:before {
+  content: "\f025";
+}
+.icon-heart:before {
+  content: "\2665";
+}
+.icon-heart_broken:before {
+  content: "\f028";
+}
+.icon-hashtag:before {
+  content: "\f029";
+}
+.icon-reply:before {
+  content: "\f02a";
+}
+.icon-retweet:before {
+  content: "\f02b";
+}
+.icon-signin:before {
+  content: "\f02c";
+}
+.icon-signout:before {
+  content: "\f02d";
+}
+.icon-download:before {
+  content: "\f02e";
+}
+.icon-upload:before {
+  content: "\f02f";
+}
+.icon-placepin:before {
+  content: "\f031";
+}
+.icon-display_screen:before {
+  content: "\f032";
+}
+.icon-tablet:before {
+  content: "\f033";
+}
+.icon-smartphone:before {
+  content: "\f034";
+}
+.icon-connected_object:before {
+  content: "\f035";
+}
+.icon-lock:before {
+  content: "\F512";
+}
+.icon-unlock:before {
+  content: "\F513";
+}
+.icon-camera:before {
+  content: "\F4F7";
+}
+.icon-isight:before {
+  content: "\f039";
+}
+.icon-video_camera:before {
+  content: "\f03a";
+}
+.icon-random:before {
+  content: "\f03b";
+}
+.icon-message:before {
+  content: "\F4AC";
+}
+.icon-discussion:before {
+  content: "\f03d";
+}
+.icon-calendar:before {
+  content: "\F4C5";
+}
+.icon-ringbell:before {
+  content: "\f03f";
+}
+.icon-movie:before {
+  content: "\f040";
+}
+.icon-mail:before {
+  content: "\2709";
+}
+.icon-pen:before {
+  content: "\270F";
+}
+.icon-settings:before {
+  content: "\9881";
+}
+.icon-measure:before {
+  content: "\f044";
+}
+.icon-vector:before {
+  content: "\f045";
+}
+.icon-vector_pen:before {
+  content: "\2712";
+}
+.icon-mute_on:before {
+  content: "\f047";
+}
+.icon-mute_off:before {
+  content: "\f048";
+}
+.icon-home:before {
+  content: "\2302";
+}
+.icon-sheet:before {
+  content: "\f04a";
+}
+.icon-arrow_big_right:before {
+  content: "\21C9";
+}
+.icon-arrow_big_left:before {
+  content: "\21C7";
+}
+.icon-arrow_big_down:before {
+  content: "\21CA";
+}
+.icon-arrow_big_up:before {
+  content: "\21C8";
+}
+.icon-dribbble_circle:before {
+  content: "\f04f";
+}
+.icon-dribbble:before {
+  content: "\f050";
+}
+.icon-facebook_circle:before {
+  content: "\f051";
+}
+.icon-facebook:before {
+  content: "\f052";
+}
+.icon-git_circle_alt:before {
+  content: "\f053";
+}
+.icon-git_circle:before {
+  content: "\f054";
+}
+.icon-git:before {
+  content: "\f055";
+}
+.icon-octopus:before {
+  content: "\f056";
+}
+.icon-twitter_circle:before {
+  content: "\f057";
+}
+.icon-twitter:before {
+  content: "\f058";
+}
+.icon-google_plus_circle:before {
+  content: "\f059";
+}
+.icon-google_plus:before {
+  content: "\f05a";
+}
+.icon-linked_in_circle:before {
+  content: "\f05b";
+}
+.icon-linked_in:before {
+  content: "\f05c";
+}
+.icon-instagram:before {
+  content: "\f05d";
+}
+.icon-instagram_circle:before {
+  content: "\f05e";
+}
+.icon-mfg_icon:before {
+  content: "\f05f";
+}
+.icon-xing:before {
+  content: "\F532";
+}
+.icon-xing_circle:before {
+  content: "\F533";
+}
+.icon-mfg_icon_circle:before {
+  content: "\f060";
+}
+.icon-user:before {
+  content: "\f061";
+}
+.icon-user_male:before {
+  content: "\f062";
+}
+.icon-user_female:before {
+  content: "\f063";
+}
+.icon-users:before {
+  content: "\f064";
+}
+.icon-file_open:before {
+  content: "\F4C2";
+}
+.icon-file_close:before {
+  content: "\f067";
+}
+.icon-file_alt:before {
+  content: "\f068";
+}
+.icon-file_close_alt:before {
+  content: "\f069";
+}
+.icon-attachment:before {
+  content: "\f06a";
+}
+.icon-check:before {
+  content: "\2713";
+}
+.icon-cross_mark:before {
+  content: "\274C";
+}
+.icon-cancel_circle:before {
+  content: "\F06E";
+}
+.icon-check_circle:before {
+  content: "\f06d";
+}
+.icon-magnifying:before {
+  content: "\F50D";
+}
+.icon-inbox:before {
+  content: "\f070";
+}
+.icon-clock:before {
+  content: "\23F2";
+}
+.icon-stopwatch:before {
+  content: "\23F1";
+}
+.icon-hourglass:before {
+  content: "\231B";
+}
+.icon-trophy:before {
+  content: "\f074";
+}
+.icon-unlock_alt:before {
+  content: "\F075";
+}
+.icon-lock_alt:before {
+  content: "\F510";
+}
+.icon-arrow_doubled_right:before {
+  content: "\21D2";
+}
+.icon-arrow_doubled_left:before {
+  content: "\21D0";
+}
+.icon-arrow_doubled_down:before {
+  content: "\21D3";
+}
+.icon-arrow_doubled_up:before {
+  content: "\21D1";
+}
+.icon-link:before {
+  content: "\f07B";
+}
+.icon-warning:before {
+  content: "\2757";
+}
+.icon-warning_alt:before {
+  content: "\2755";
+}
+.icon-magnifying_plus:before {
+  content: "\f07E";
+}
+.icon-magnifying_minus:before {
+  content: "\f07F";
+}
+.icon-white_question:before {
+  content: "\2754";
+}
+.icon-black_question:before {
+  content: "\2753";
+}
+.icon-stop:before {
+  content: "\f080";
+}
+.icon-share:before {
+  content: "\f081";
+}
+.icon-eye:before {
+  content: "\f082";
+}
+.icon-trash_can:before {
+  content: "\f083";
+}
+.icon-hard_drive:before {
+  content: "\f084";
+}
+.icon-information_black:before {
+  content: "\f085";
+}
+.icon-information_white:before {
+  content: "\f086";
+}
+.icon-printer:before {
+  content: "\f087";
+}
+.icon-letter:before {
+  content: "\f088";
+}
+.icon-soundcloud:before {
+  content: "\f089";
+}
+.icon-soundcloud_circle:before {
+  content: "\f08A";
+}
+.icon-anchor:before {
+  content: "\2693";
+}
+.icon-female_sign:before {
+  content: "\2640";
+}
+.icon-male_sign:before {
+  content: "\2642";
+}
+.icon-joystick:before {
+  content: "\F514";
+}
+.icon-high_voltage:before {
+  content: "\26A1";
+}
+.icon-fire:before {
+  content: "\F525";
+}
+.icon-newspaper:before {
+  content: "\F4F0";
+}
+.icon-chart:before {
+  content: "\F526";
+}
+.icon-spread:before {
+  content: "\F527";
+}
+.icon-spinner_1:before {
+  content: "\F528";
+}
+.icon-spinner_2:before {
+  content: "\F529";
+}
+.icon-chart_alt:before {
+  content: "\F530";
+}
+.icon-label:before {
+  content: "\F531";
+}
+.icon-brush:before {
+  content: "\E000";
+}
+.icon-refresh:before {
+  content: "\E001";
+}
+.icon-node:before {
+  content: "\E002";
+}
+.icon-node_2:before {
+  content: "\E003";
+}
+.icon-node_3:before {
+  content: "\E004";
+}
+.icon-link_2_nodes:before {
+  content: "\E005";
+}
+.icon-link_3_nodes:before {
+  content: "\E006";
+}
+.icon-link_loop_nodes:before {
+  content: "\E007";
+}
+.icon-node_size:before {
+  content: "\E008";
+}
+.icon-node_color:before {
+  content: "\E009";
+}
+.icon-layout_directed:before {
+  content: "\E010";
+}
+.icon-layout_radial:before {
+  content: "\E011";
+}
+.icon-layout_hierarchical:before {
+  content: "\E012";
+}
+.icon-node_link_direction:before {
+  content: "\E013";
+}
+.icon-node_link_short_path:before {
+  content: "\E014";
+}
+.icon-node_cluster:before {
+  content: "\E015";
+}
+.icon-display_graph:before {
+  content: "\E016";
+}
+.icon-node_link_weight:before {
+  content: "\E017";
+}
+.icon-more_node_links:before {
+  content: "\E018";
+}
+.icon-node_shape:before {
+  content: "\E00A";
+}
+.icon-node_icon:before {
+  content: "\E00B";
+}
+.icon-node_text:before {
+  content: "\E00C";
+}
+.icon-node_link_text:before {
+  content: "\E00D";
+}
+.icon-node_link_color:before {
+  content: "\E00E";
+}
+.icon-node_link_shape:before {
+  content: "\E00F";
+}
+.icon-credit_card:before {
+  content: "\F4B3";
+}
+.icon-disconnect:before {
+  content: "\F534";
+}
+.icon-graph:before {
+  content: "\F535";
+}
+.icon-new_user:before {
+  content: "\F536";
+}
 
 /* Icon font - Simple Line Icons */
 @font-face {
-  font-family: 'sli';
-  src: url('../font/Simple-Line-Icons.eot?v=2.2.2');
-  src: url('../font/Simple-Line-Icons.eot?v=2.2.2#iefix') format('embedded-opentype'), url('../font/Simple-Line-Icons.ttf?v=2.2.2') format('truetype'), url('../font/Simple-Line-Icons.woff2?v=2.2.2') format('woff2'), url('../font/Simple-Line-Icons.woff?v=2.2.2') format('woff'), url('../font/Simple-Line-Icons.svg?v=2.2.2#simple-line-icons') format('svg');
+  font-family: "sli";
+  src: url("../font/Simple-Line-Icons.eot?v=2.2.2");
+  src: url("../font/Simple-Line-Icons.eot?v=2.2.2#iefix")
+      format("embedded-opentype"),
+    url("../font/Simple-Line-Icons.ttf?v=2.2.2") format("truetype"),
+    url("../font/Simple-Line-Icons.woff2?v=2.2.2") format("woff2"),
+    url("../font/Simple-Line-Icons.woff?v=2.2.2") format("woff"),
+    url("../font/Simple-Line-Icons.svg?v=2.2.2#simple-line-icons") format("svg");
   font-weight: normal;
   font-style: normal;
 }
@@ -592,200 +973,570 @@
 .icon-sli-social-stumbleupon,
 .icon-sli-social-youtube,
 .icon-sli-social-dropbox {
-  font-family: 'sli';
-  font-style: normal;  
+  font-family: "sli";
+  font-style: normal;
   font-variant: normal;
   font-weight: normal;
-  color:#e3e3e3;
+  color: #e3e3e3;
   speak: none;
   text-transform: none;
   /* Better Font Rendering =========== */
   -webkit-font-smoothing: antialiased;
   -moz-osx-font-smoothing: grayscale;
 }
-.icon-sli-user:before { content: "\e005"; }
-.icon-sli-people:before { content: "\e001"; }
-.icon-sli-user-female:before { content: "\e000"; }
-.icon-sli-user-follow:before { content: "\e002"; }
-.icon-sli-user-following:before { content: "\e003"; }
-.icon-sli-user-unfollow:before { content: "\e004"; }
-.icon-sli-login:before { content: "\e066"; }
-.icon-sli-logout:before { content: "\e065"; }
-.icon-sli-emotsmile:before { content: "\e021"; }
-.icon-sli-phone:before { content: "\e600"; }
-.icon-sli-call-end:before { content: "\e048"; }
-.icon-sli-call-in:before { content: "\e047"; }
-.icon-sli-call-out:before { content: "\e046"; }
-.icon-sli-map:before { content: "\e033"; }
-.icon-sli-location-pin:before { content: "\e096"; }
-.icon-sli-direction:before { content: "\e042"; }
-.icon-sli-directions:before { content: "\e041"; }
-.icon-sli-compass:before { content: "\e045"; }
-.icon-sli-layers:before { content: "\e034"; }
-.icon-sli-menu:before { content: "\e601"; }
-.icon-sli-list:before { content: "\e067"; }
-.icon-sli-options-vertical:before { content: "\e602"; }
-.icon-sli-options:before { content: "\e603"; }
-.icon-sli-arrow-down:before { content: "\e604"; }
-.icon-sli-arrow-left:before { content: "\e605"; }
-.icon-sli-arrow-right:before { content: "\e606"; }
-.icon-sli-arrow-up:before { content: "\e607"; }
-.icon-sli-arrow-up-circle:before { content: "\e078"; }
-.icon-sli-arrow-left-circle:before { content: "\e07a"; }
-.icon-sli-arrow-right-circle:before { content: "\e079"; }
-.icon-sli-arrow-down-circle:before { content: "\e07b"; }
-.icon-sli-check:before { content: "\e080"; }
-.icon-sli-clock:before { content: "\e081"; }
-.icon-sli-plus:before { content: "\e095"; }
-.icon-sli-minus:before { content: "\e615"; }
-.icon-sli-close:before { content: "\e082"; }
-.icon-sli-organization:before { content: "\e616"; }
+.icon-sli-user:before {
+  content: "\e005";
+}
+.icon-sli-people:before {
+  content: "\e001";
+}
+.icon-sli-user-female:before {
+  content: "\e000";
+}
+.icon-sli-user-follow:before {
+  content: "\e002";
+}
+.icon-sli-user-following:before {
+  content: "\e003";
+}
+.icon-sli-user-unfollow:before {
+  content: "\e004";
+}
+.icon-sli-login:before {
+  content: "\e066";
+}
+.icon-sli-logout:before {
+  content: "\e065";
+}
+.icon-sli-emotsmile:before {
+  content: "\e021";
+}
+.icon-sli-phone:before {
+  content: "\e600";
+}
+.icon-sli-call-end:before {
+  content: "\e048";
+}
+.icon-sli-call-in:before {
+  content: "\e047";
+}
+.icon-sli-call-out:before {
+  content: "\e046";
+}
+.icon-sli-map:before {
+  content: "\e033";
+}
+.icon-sli-location-pin:before {
+  content: "\e096";
+}
+.icon-sli-direction:before {
+  content: "\e042";
+}
+.icon-sli-directions:before {
+  content: "\e041";
+}
+.icon-sli-compass:before {
+  content: "\e045";
+}
+.icon-sli-layers:before {
+  content: "\e034";
+}
+.icon-sli-menu:before {
+  content: "\e601";
+}
+.icon-sli-list:before {
+  content: "\e067";
+}
+.icon-sli-options-vertical:before {
+  content: "\e602";
+}
+.icon-sli-options:before {
+  content: "\e603";
+}
+.icon-sli-arrow-down:before {
+  content: "\e604";
+}
+.icon-sli-arrow-left:before {
+  content: "\e605";
+}
+.icon-sli-arrow-right:before {
+  content: "\e606";
+}
+.icon-sli-arrow-up:before {
+  content: "\e607";
+}
+.icon-sli-arrow-up-circle:before {
+  content: "\e078";
+}
+.icon-sli-arrow-left-circle:before {
+  content: "\e07a";
+}
+.icon-sli-arrow-right-circle:before {
+  content: "\e079";
+}
+.icon-sli-arrow-down-circle:before {
+  content: "\e07b";
+}
+.icon-sli-check:before {
+  content: "\e080";
+}
+.icon-sli-clock:before {
+  content: "\e081";
+}
+.icon-sli-plus:before {
+  content: "\e095";
+}
+.icon-sli-minus:before {
+  content: "\e615";
+}
+.icon-sli-close:before {
+  content: "\e082";
+}
+.icon-sli-organization:before {
+  content: "\e616";
+}
 
-.icon-sli-trophy:before { content: "\e006"; }
-.icon-sli-screen-smartphone:before { content: "\e010"; }
-.icon-sli-screen-desktop:before { content: "\e011"; }
-.icon-sli-plane:before { content: "\e012"; }
-.icon-sli-notebook:before { content: "\e013"; }
-.icon-sli-mustache:before { content: "\e014"; }
-.icon-sli-mouse:before { content: "\e015"; }
-.icon-sli-magnet:before { content: "\e016"; }
-.icon-sli-energy:before { content: "\e020"; }
-.icon-sli-disc:before { content: "\e022"; }
-.icon-sli-cursor:before { content: "\e06e"; }
-.icon-sli-cursor-move:before { content: "\e023"; }
-.icon-sli-crop:before { content: "\e024"; }
-.icon-sli-chemistry:before { content: "\e026"; }
-.icon-sli-speedometer:before { content: "\e007"; }
-.icon-sli-shield:before { content: "\e00e"; }
-.icon-sli-screen-tablet:before { content: "\e00f"; }
-.icon-sli-magic-wand:before { content: "\e017"; }
-.icon-sli-hourglass:before { content: "\e018"; }
-.icon-sli-graduation:before { content: "\e019"; }
-.icon-sli-ghost:before { content: "\e01a"; }
-.icon-sli-game-controller:before { content: "\e01b"; }
-.icon-sli-fire:before { content: "\e01c"; }
-.icon-sli-eyeglass:before { content: "\e01d"; }
-.icon-sli-envelope-open:before { content: "\e01e"; }
-.icon-sli-envelope-letter:before { content: "\e01f"; }
-.icon-sli-bell:before { content: "\e027"; }
-.icon-sli-badge:before { content: "\e028"; }
-.icon-sli-anchor:before { content: "\e029"; }
-.icon-sli-wallet:before { content: "\e02a"; }
-.icon-sli-vector:before { content: "\e02b"; }
-.icon-sli-speech:before { content: "\e02c"; }
-.icon-sli-puzzle:before { content: "\e02d"; }
-.icon-sli-printer:before { content: "\e02e"; }
-.icon-sli-present:before { content: "\e02f"; }
-.icon-sli-playlist:before { content: "\e030"; }
-.icon-sli-pin:before { content: "\e031"; }
-.icon-sli-picture:before { content: "\e032"; }
-.icon-sli-handbag:before { content: "\e035"; }
-.icon-sli-globe-alt:before { content: "\e036"; }
-.icon-sli-globe:before { content: "\e037"; }
-.icon-sli-folder-alt:before { content: "\e039"; }
-.icon-sli-folder:before { content: "\e089"; }
-.icon-sli-film:before { content: "\e03a"; }
-.icon-sli-feed:before { content: "\e03b"; }
-.icon-sli-drop:before { content: "\e03e"; }
-.icon-sli-drawer:before { content: "\e03f"; }
-.icon-sli-docs:before { content: "\e040"; }
-.icon-sli-doc:before { content: "\e085"; }
-.icon-sli-diamond:before { content: "\e043"; }
-.icon-sli-cup:before { content: "\e044"; }
-.icon-sli-calculator:before { content: "\e049"; }
-.icon-sli-bubbles:before { content: "\e04a"; }
-.icon-sli-briefcase:before { content: "\e04b"; }
-.icon-sli-book-open:before { content: "\e04c"; }
-.icon-sli-basket-loaded:before { content: "\e04d"; }
-.icon-sli-basket:before { content: "\e04e"; }
-.icon-sli-bag:before { content: "\e04f"; }
-.icon-sli-action-undo:before { content: "\e050"; }
-.icon-sli-action-redo:before { content: "\e051"; }
-.icon-sli-wrench:before { content: "\e052"; }
-.icon-sli-umbrella:before { content: "\e053"; }
-.icon-sli-trash:before { content: "\e054"; }
-.icon-sli-tag:before { content: "\e055"; }
-.icon-sli-support:before { content: "\e056"; }
-.icon-sli-frame:before { content: "\e038"; }
-.icon-sli-size-fullscreen:before { content: "\e057"; }
-.icon-sli-size-actual:before { content: "\e058"; }
-.icon-sli-shuffle:before { content: "\e059"; }
-.icon-sli-share-alt:before { content: "\e05a"; }
-.icon-sli-share:before { content: "\e05b"; }
-.icon-sli-rocket:before { content: "\e05c"; }
-.icon-sli-question:before { content: "\e05d"; }
-.icon-sli-pie-chart:before { content: "\e05e"; }
-.icon-sli-pencil:before { content: "\e05f"; }
-.icon-sli-note:before { content: "\e060"; }
-.icon-sli-loop:before { content: "\e064"; }
-.icon-sli-home:before { content: "\e069"; }
-.icon-sli-grid:before { content: "\e06a"; }
-.icon-sli-graph:before { content: "\e06b"; }
-.icon-sli-microphone:before { content: "\e063"; }
-.icon-sli-music-tone-alt:before { content: "\e061"; }
-.icon-sli-music-tone:before { content: "\e062"; }
-.icon-sli-earphones-alt:before { content: "\e03c"; }
-.icon-sli-earphones:before { content: "\e03d"; }
-.icon-sli-equalizer:before { content: "\e06c"; }
-.icon-sli-like:before { content: "\e068"; }
-.icon-sli-dislike:before { content: "\e06d"; }
-.icon-sli-control-start:before { content: "\e06f"; }
-.icon-sli-control-rewind:before { content: "\e070"; }
-.icon-sli-control-play:before { content: "\e071"; }
-.icon-sli-control-pause:before { content: "\e072"; }
-.icon-sli-control-forward:before { content: "\e073"; }
-.icon-sli-control-end:before { content: "\e074"; }
-.icon-sli-volume-1:before { content: "\e09f"; }
-.icon-sli-volume-2:before { content: "\e0a0"; }
-.icon-sli-volume-off:before { content: "\e0a1"; }
-.icon-sli-calendar:before { content: "\e075"; }
-.icon-sli-bulb:before { content: "\e076"; }
-.icon-sli-chart:before { content: "\e077"; }
-.icon-sli-ban:before { content: "\e07c"; }
-.icon-sli-bubble:before { content: "\e07d"; }
-.icon-sli-camrecorder:before { content: "\e07e"; }
-.icon-sli-camera:before { content: "\e07f"; }
-.icon-sli-cloud-download:before { content: "\e083"; }
-.icon-sli-cloud-upload:before { content: "\e084"; }
-.icon-sli-envelope:before { content: "\e086"; }
-.icon-sli-eye:before { content: "\e087"; }
-.icon-sli-flag:before { content: "\e088"; }
-.icon-sli-heart:before { content: "\e08a"; }
-.icon-sli-info:before { content: "\e08b"; }
-.icon-sli-key:before { content: "\e08c"; }
-.icon-sli-link:before { content: "\e08d"; }
-.icon-sli-lock:before { content: "\e08e"; }
-.icon-sli-lock-open:before { content: "\e08f"; }
-.icon-sli-magnifier:before { content: "\e090"; }
-.icon-sli-magnifier-add:before { content: "\e091"; }
-.icon-sli-magnifier-remove:before { content: "\e092"; }
-.icon-sli-paper-clip:before { content: "\e093"; }
-.icon-sli-paper-plane:before { content: "\e094"; }
-.icon-sli-power:before { content: "\e097"; }
-.icon-sli-refresh:before { content: "\e098"; }
-.icon-sli-reload:before { content: "\e099"; }
-.icon-sli-settings:before { content: "\e09a"; }
-.icon-sli-star:before { content: "\e09b"; }
-.icon-sli-symbol-female:before { content: "\e09c"; }
-.icon-sli-symbol-male:before { content: "\e09d"; }
-.icon-sli-target:before { content: "\e09e"; }
-.icon-sli-credit-card:before { content: "\e025"; }
-.icon-sli-paypal:before { content: "\e608"; }
-.icon-sli-social-tumblr:before { content: "\e00a"; }
-.icon-sli-social-twitter:before { content: "\e009"; }
-.icon-sli-social-facebook:before { content: "\e00b"; }
-.icon-sli-social-instagram:before { content: "\e609"; }
-.icon-sli-social-linkedin:before { content: "\e60a"; }
-.icon-sli-social-pinterest:before { content: "\e60b"; }
-.icon-sli-social-github:before { content: "\e60c"; }
-.icon-sli-social-google:before { content: "\e60d"; }
-.icon-sli-social-reddit:before { content: "\e60e"; }
-.icon-sli-social-skype:before { content: "\e60f"; }
-.icon-sli-social-dribbble:before { content: "\e00d"; }
-.icon-sli-social-behance:before { content: "\e610"; }
-.icon-sli-social-foursqare:before { content: "\e611"; }
-.icon-sli-social-soundcloud:before { content: "\e612"; }
-.icon-sli-social-spotify:before { content: "\e613"; }
-.icon-sli-social-stumbleupon:before { content: "\e614"; }
-.icon-sli-social-youtube:before { content: "\e008"; }
-.icon-sli-social-dropbox:before { content: "\e00c"; }
\ No newline at end of file
+.icon-sli-trophy:before {
+  content: "\e006";
+}
+.icon-sli-screen-smartphone:before {
+  content: "\e010";
+}
+.icon-sli-screen-desktop:before {
+  content: "\e011";
+}
+.icon-sli-plane:before {
+  content: "\e012";
+}
+.icon-sli-notebook:before {
+  content: "\e013";
+}
+.icon-sli-mustache:before {
+  content: "\e014";
+}
+.icon-sli-mouse:before {
+  content: "\e015";
+}
+.icon-sli-magnet:before {
+  content: "\e016";
+}
+.icon-sli-energy:before {
+  content: "\e020";
+}
+.icon-sli-disc:before {
+  content: "\e022";
+}
+.icon-sli-cursor:before {
+  content: "\e06e";
+}
+.icon-sli-cursor-move:before {
+  content: "\e023";
+}
+.icon-sli-crop:before {
+  content: "\e024";
+}
+.icon-sli-chemistry:before {
+  content: "\e026";
+}
+.icon-sli-speedometer:before {
+  content: "\e007";
+}
+.icon-sli-shield:before {
+  content: "\e00e";
+}
+.icon-sli-screen-tablet:before {
+  content: "\e00f";
+}
+.icon-sli-magic-wand:before {
+  content: "\e017";
+}
+.icon-sli-hourglass:before {
+  content: "\e018";
+}
+.icon-sli-graduation:before {
+  content: "\e019";
+}
+.icon-sli-ghost:before {
+  content: "\e01a";
+}
+.icon-sli-game-controller:before {
+  content: "\e01b";
+}
+.icon-sli-fire:before {
+  content: "\e01c";
+}
+.icon-sli-eyeglass:before {
+  content: "\e01d";
+}
+.icon-sli-envelope-open:before {
+  content: "\e01e";
+}
+.icon-sli-envelope-letter:before {
+  content: "\e01f";
+}
+.icon-sli-bell:before {
+  content: "\e027";
+}
+.icon-sli-badge:before {
+  content: "\e028";
+}
+.icon-sli-anchor:before {
+  content: "\e029";
+}
+.icon-sli-wallet:before {
+  content: "\e02a";
+}
+.icon-sli-vector:before {
+  content: "\e02b";
+}
+.icon-sli-speech:before {
+  content: "\e02c";
+}
+.icon-sli-puzzle:before {
+  content: "\e02d";
+}
+.icon-sli-printer:before {
+  content: "\e02e";
+}
+.icon-sli-present:before {
+  content: "\e02f";
+}
+.icon-sli-playlist:before {
+  content: "\e030";
+}
+.icon-sli-pin:before {
+  content: "\e031";
+}
+.icon-sli-picture:before {
+  content: "\e032";
+}
+.icon-sli-handbag:before {
+  content: "\e035";
+}
+.icon-sli-globe-alt:before {
+  content: "\e036";
+}
+.icon-sli-globe:before {
+  content: "\e037";
+}
+.icon-sli-folder-alt:before {
+  content: "\e039";
+}
+.icon-sli-folder:before {
+  content: "\e089";
+}
+.icon-sli-film:before {
+  content: "\e03a";
+}
+.icon-sli-feed:before {
+  content: "\e03b";
+}
+.icon-sli-drop:before {
+  content: "\e03e";
+}
+.icon-sli-drawer:before {
+  content: "\e03f";
+}
+.icon-sli-docs:before {
+  content: "\e040";
+}
+.icon-sli-doc:before {
+  content: "\e085";
+}
+.icon-sli-diamond:before {
+  content: "\e043";
+}
+.icon-sli-cup:before {
+  content: "\e044";
+}
+.icon-sli-calculator:before {
+  content: "\e049";
+}
+.icon-sli-bubbles:before {
+  content: "\e04a";
+}
+.icon-sli-briefcase:before {
+  content: "\e04b";
+}
+.icon-sli-book-open:before {
+  content: "\e04c";
+}
+.icon-sli-basket-loaded:before {
+  content: "\e04d";
+}
+.icon-sli-basket:before {
+  content: "\e04e";
+}
+.icon-sli-bag:before {
+  content: "\e04f";
+}
+.icon-sli-action-undo:before {
+  content: "\e050";
+}
+.icon-sli-action-redo:before {
+  content: "\e051";
+}
+.icon-sli-wrench:before {
+  content: "\e052";
+}
+.icon-sli-umbrella:before {
+  content: "\e053";
+}
+.icon-sli-trash:before {
+  content: "\e054";
+}
+.icon-sli-tag:before {
+  content: "\e055";
+}
+.icon-sli-support:before {
+  content: "\e056";
+}
+.icon-sli-frame:before {
+  content: "\e038";
+}
+.icon-sli-size-fullscreen:before {
+  content: "\e057";
+}
+.icon-sli-size-actual:before {
+  content: "\e058";
+}
+.icon-sli-shuffle:before {
+  content: "\e059";
+}
+.icon-sli-share-alt:before {
+  content: "\e05a";
+}
+.icon-sli-share:before {
+  content: "\e05b";
+}
+.icon-sli-rocket:before {
+  content: "\e05c";
+}
+.icon-sli-question:before {
+  content: "\e05d";
+}
+.icon-sli-pie-chart:before {
+  content: "\e05e";
+}
+.icon-sli-pencil:before {
+  content: "\e05f";
+}
+.icon-sli-note:before {
+  content: "\e060";
+}
+.icon-sli-loop:before {
+  content: "\e064";
+}
+.icon-sli-home:before {
+  content: "\e069";
+}
+.icon-sli-grid:before {
+  content: "\e06a";
+}
+.icon-sli-graph:before {
+  content: "\e06b";
+}
+.icon-sli-microphone:before {
+  content: "\e063";
+}
+.icon-sli-music-tone-alt:before {
+  content: "\e061";
+}
+.icon-sli-music-tone:before {
+  content: "\e062";
+}
+.icon-sli-earphones-alt:before {
+  content: "\e03c";
+}
+.icon-sli-earphones:before {
+  content: "\e03d";
+}
+.icon-sli-equalizer:before {
+  content: "\e06c";
+}
+.icon-sli-like:before {
+  content: "\e068";
+}
+.icon-sli-dislike:before {
+  content: "\e06d";
+}
+.icon-sli-control-start:before {
+  content: "\e06f";
+}
+.icon-sli-control-rewind:before {
+  content: "\e070";
+}
+.icon-sli-control-play:before {
+  content: "\e071";
+}
+.icon-sli-control-pause:before {
+  content: "\e072";
+}
+.icon-sli-control-forward:before {
+  content: "\e073";
+}
+.icon-sli-control-end:before {
+  content: "\e074";
+}
+.icon-sli-volume-1:before {
+  content: "\e09f";
+}
+.icon-sli-volume-2:before {
+  content: "\e0a0";
+}
+.icon-sli-volume-off:before {
+  content: "\e0a1";
+}
+.icon-sli-calendar:before {
+  content: "\e075";
+}
+.icon-sli-bulb:before {
+  content: "\e076";
+}
+.icon-sli-chart:before {
+  content: "\e077";
+}
+.icon-sli-ban:before {
+  content: "\e07c";
+}
+.icon-sli-bubble:before {
+  content: "\e07d";
+}
+.icon-sli-camrecorder:before {
+  content: "\e07e";
+}
+.icon-sli-camera:before {
+  content: "\e07f";
+}
+.icon-sli-cloud-download:before {
+  content: "\e083";
+}
+.icon-sli-cloud-upload:before {
+  content: "\e084";
+}
+.icon-sli-envelope:before {
+  content: "\e086";
+}
+.icon-sli-eye:before {
+  content: "\e087";
+}
+.icon-sli-flag:before {
+  content: "\e088";
+}
+.icon-sli-heart:before {
+  content: "\e08a";
+}
+.icon-sli-info:before {
+  content: "\e08b";
+}
+.icon-sli-key:before {
+  content: "\e08c";
+}
+.icon-sli-link:before {
+  content: "\e08d";
+}
+.icon-sli-lock:before {
+  content: "\e08e";
+}
+.icon-sli-lock-open:before {
+  content: "\e08f";
+}
+.icon-sli-magnifier:before {
+  content: "\e090";
+}
+.icon-sli-magnifier-add:before {
+  content: "\e091";
+}
+.icon-sli-magnifier-remove:before {
+  content: "\e092";
+}
+.icon-sli-paper-clip:before {
+  content: "\e093";
+}
+.icon-sli-paper-plane:before {
+  content: "\e094";
+}
+.icon-sli-power:before {
+  content: "\e097";
+}
+.icon-sli-refresh:before {
+  content: "\e098";
+}
+.icon-sli-reload:before {
+  content: "\e099";
+}
+.icon-sli-settings:before {
+  content: "\e09a";
+}
+.icon-sli-star:before {
+  content: "\e09b";
+}
+.icon-sli-symbol-female:before {
+  content: "\e09c";
+}
+.icon-sli-symbol-male:before {
+  content: "\e09d";
+}
+.icon-sli-target:before {
+  content: "\e09e";
+}
+.icon-sli-credit-card:before {
+  content: "\e025";
+}
+.icon-sli-paypal:before {
+  content: "\e608";
+}
+.icon-sli-social-tumblr:before {
+  content: "\e00a";
+}
+.icon-sli-social-twitter:before {
+  content: "\e009";
+}
+.icon-sli-social-facebook:before {
+  content: "\e00b";
+}
+.icon-sli-social-instagram:before {
+  content: "\e609";
+}
+.icon-sli-social-linkedin:before {
+  content: "\e60a";
+}
+.icon-sli-social-pinterest:before {
+  content: "\e60b";
+}
+.icon-sli-social-github:before {
+  content: "\e60c";
+}
+.icon-sli-social-google:before {
+  content: "\e60d";
+}
+.icon-sli-social-reddit:before {
+  content: "\e60e";
+}
+.icon-sli-social-skype:before {
+  content: "\e60f";
+}
+.icon-sli-social-dribbble:before {
+  content: "\e00d";
+}
+.icon-sli-social-behance:before {
+  content: "\e610";
+}
+.icon-sli-social-foursqare:before {
+  content: "\e611";
+}
+.icon-sli-social-soundcloud:before {
+  content: "\e612";
+}
+.icon-sli-social-spotify:before {
+  content: "\e613";
+}
+.icon-sli-social-stumbleupon:before {
+  content: "\e614";
+}
+.icon-sli-social-youtube:before {
+  content: "\e008";
+}
+.icon-sli-social-dropbox:before {
+  content: "\e00c";
+}
diff --git a/css/responsee.css b/css/responsee.css
index 6ce3d24..468a6b3 100644
--- a/css/responsee.css
+++ b/css/responsee.css
@@ -4,208 +4,323 @@
  * Copyright 2019, Vision Design - graphic zoo
  * Free to use under the MIT license.
 */
-* {  
-  -webkit-box-sizing:border-box;
-  -moz-box-sizing:border-box;
-  box-sizing:border-box;
-  margin:0;	
+* {
+  -webkit-box-sizing: border-box;
+  -moz-box-sizing: border-box;
+  box-sizing: border-box;
+  margin: 0;
 }
 body {
-  background:none repeat scroll 0 0 #eeeeee;
-  font-size:16px;
-  font-family:"Open Sans",Arial,sans-serif;
-  color:#444;
-}
-h1,h2,h3,h4,h5,h6 {
-  color:#152732;
+  background: none repeat scroll 0 0 #eeeeee;
+  font-size: 16px;
+  font-family: "Open Sans", Arial, sans-serif;
+  color: #444;
+}
+h1,
+h2,
+h3,
+h4,
+h5,
+h6 {
+  color: #152732;
   font-weight: bold;
   line-height: 1.3;
-  margin:0.5rem 0;  
-}
-h1 {font-size:2.7rem;}
-h2 {font-size:2.2rem;}  
-h3 {font-size:1.8rem;}  
-h4 {font-size:1.4rem;}  
-h5 {font-size:1.1rem;}  
-h6 {font-size:0.9rem;}    
-a, a:link, a:visited, a:hover, a:active {
-  text-decoration:none;
-  color:#9BB800;
-  transition:color 0.20s linear 0s;
-  -o-transition:color 0.20s linear 0s;
-  -ms-transition:color 0.20s linear 0s;
-  -moz-transition:color 0.20s linear 0s;
-  -webkit-transition:color 0.20s linear 0s;
-}  
-a:hover {color:#B6C900;}
-p,li,dl,blockquote,table,kbd {
+  margin: 0.5rem 0;
+}
+h1 {
+  font-size: 2.7rem;
+}
+h2 {
+  font-size: 2.2rem;
+}
+h3 {
+  font-size: 1.8rem;
+}
+h4 {
+  font-size: 1.4rem;
+}
+h5 {
+  font-size: 1.1rem;
+}
+h6 {
+  font-size: 0.9rem;
+}
+a,
+a:link,
+a:visited,
+a:hover,
+a:active {
+  text-decoration: none;
+  color: #9bb800;
+  transition: color 0.2s linear 0s;
+  -o-transition: color 0.2s linear 0s;
+  -ms-transition: color 0.2s linear 0s;
+  -moz-transition: color 0.2s linear 0s;
+  -webkit-transition: color 0.2s linear 0s;
+}
+a:hover {
+  color: #b6c900;
+}
+p,
+li,
+dl,
+blockquote,
+table,
+kbd {
   font-size: 0.85rem;
   line-height: 1.6;
 }
-b,strong {font-weight:700;}
-.text-center {text-align:center!important;}
-.text-right {text-align:right!important;}
+b,
+strong {
+  font-weight: 700;
+}
+.text-center {
+  text-align: center !important;
+}
+.text-right {
+  text-align: right !important;
+}
 img {
-  border:0;
-  display:block;
-  height:auto;
-  max-width:100%;
-  width:auto;
+  border: 0;
+  display: block;
+  height: auto;
+  max-width: 100%;
+  width: auto;
 }
-.owl-item img, .full-img {
-  max-width:none;
-  width:100%;
+.owl-item img,
+.full-img {
+  max-width: none;
+  width: 100%;
+}
+.owl-nav div {
+  font-family: "mfg";
 }
-.owl-nav div {font-family:"mfg";}
 .grid .owl-carousel {
-  width:100% !important;
-}  
+  width: 100% !important;
+}
 table {
-  background:none repeat scroll 0 0 #fff;
-  border:1px solid #f0f0f0;
-  border-collapse:collapse;
-  border-spacing:0;
-  text-align:left;
-  width:100%;
-}
-table tr td, table tr th {padding:0.625rem;}
-table tfoot, table thead,table tr:nth-of-type(2n) {background:none repeat scroll 0 0 #f0f0f0;}
-th,table tr:nth-of-type(2n) td {border-right:1px solid #fff;}
-td {border-right:1px solid #f0f0f0;}
-.size-960 .line,.size-1140 .line,.size-1280 .line,.size-1520 .line {
-  margin:0 auto;
-  padding:0 0.625rem;
+  background: none repeat scroll 0 0 #fff;
+  border: 1px solid #f0f0f0;
+  border-collapse: collapse;
+  border-spacing: 0;
+  text-align: left;
+  width: 100%;
+}
+table tr td,
+table tr th {
+  padding: 0.625rem;
+}
+table tfoot,
+table thead,
+table tr:nth-of-type(2n) {
+  background: none repeat scroll 0 0 #f0f0f0;
+}
+th,
+table tr:nth-of-type(2n) td {
+  border-right: 1px solid #fff;
+}
+td {
+  border-right: 1px solid #f0f0f0;
+}
+.size-960 .line,
+.size-1140 .line,
+.size-1280 .line,
+.size-1520 .line {
+  margin: 0 auto;
+  padding: 0 0.625rem;
 }
 .grid {
-  display:grid;
-  grid-template-columns:repeat(12, 1fr);
-  width:100%;
-  margin:0 auto;
-} 
+  display: grid;
+  grid-template-columns: repeat(12, 1fr);
+  width: 100%;
+  margin: 0 auto;
+}
 hr {
   border: 0;
   border-top: 1px solid #e5e5e5;
-  clear:both;  
-  height:0; 
-  margin:2.5rem auto;
+  clear: both;
+  height: 0;
+  margin: 2.5rem auto;
+}
+li {
+  padding: 0;
+}
+ul,
+ol {
+  padding-left: 1.25rem;
 }
-li {padding:0;}
-ul,ol {padding-left:1.25rem;}
 blockquote {
-  border:2px solid #f0f0f0;
-  padding:1.25rem;
+  border: 2px solid #f0f0f0;
+  padding: 1.25rem;
 }
 cite {
-  color:#999;
-  display:block;
-  font-size:0.8rem;
-}
-cite:before {content:"— ";}
-dl dt {font-weight:700;}
-dl dd {margin-bottom:0.625rem;}
-dl dd:last-child {margin-bottom:0;}
-abbr {cursor:help;}
-abbr[title] {border-bottom:1px dotted;}
+  color: #999;
+  display: block;
+  font-size: 0.8rem;
+}
+cite:before {
+  content: "— ";
+}
+dl dt {
+  font-weight: 700;
+}
+dl dd {
+  margin-bottom: 0.625rem;
+}
+dl dd:last-child {
+  margin-bottom: 0;
+}
+abbr {
+  cursor: help;
+}
+abbr[title] {
+  border-bottom: 1px dotted;
+}
 kbd {
   background: #152732 none repeat scroll 0 0;
   color: #fff;
   padding: 0.125rem 0.3125rem;
 }
-code, kbd, pre, samp {font-family: Menlo,Monaco,Consolas,"Courier New",monospace;}
+code,
+kbd,
+pre,
+samp {
+  font-family: Menlo, Monaco, Consolas, "Courier New", monospace;
+}
 mark {
-  background: #F3F8A9 none repeat scroll 0 0;
+  background: #f3f8a9 none repeat scroll 0 0;
   padding: 0.125rem 0.3125rem;
 }
-.size-960 .line,.size-960 .grid {max-width:59.75rem;}
-.size-1140 .line,.size-1140 .grid {max-width:71rem;}
-.size-1280 .line,.size-1280 .grid {max-width:80rem;}
-.size-1520 .line,.size-1520 .grid {max-width:95rem;}
+.size-960 .line,
+.size-960 .grid {
+  max-width: 59.75rem;
+}
+.size-1140 .line,
+.size-1140 .grid {
+  max-width: 71rem;
+}
+.size-1280 .line,
+.size-1280 .grid {
+  max-width: 80rem;
+}
+.size-1520 .line,
+.size-1520 .grid {
+  max-width: 95rem;
+}
 .grid.full {
-  max-width:100%!important;
+  max-width: 100% !important;
   padding: 0;
 }
-.vertical-center {display: inline-grid!important;}
+.vertical-center {
+  display: inline-grid !important;
+}
 .vertical-center * {
-    align-items: center;
-    display: flex!important;
+  align-items: center;
+  display: flex !important;
+}
+.text-center .vertical-center * {
+  justify-content: center;
 }
-.text-center .vertical-center * {justify-content: center;}
 
-.size-960.align-content-left .line,.size-1140.align-content-left .line,.size-1280.align-content-left .line,.size-1520.align-content-left .line {margin-left:0;}
-form {line-height:1.4;}
-nav {
-  display:block;
-  width:100%;
-  background:#152732;
+.size-960.align-content-left .line,
+.size-1140.align-content-left .line,
+.size-1280.align-content-left .line,
+.size-1520.align-content-left .line {
+  margin-left: 0;
 }
-.line::after, nav::after, .center::after, .box::after, .margin::after, .margin2x::after, .grid.full::after {
-  clear:both;
+form {
+  line-height: 1.4;
+}
+nav {
+  display: block;
+  width: 100%;
+  background: #152732;
+}
+.line::after,
+nav::after,
+.center::after,
+.box::after,
+.margin::after,
+.margin2x::after,
+.grid.full::after {
+  clear: both;
   content: ".";
-  display:block;
-  height:0;
-  line-height:0;
-  overflow:hidden;
-  visibility:hidden;
+  display: block;
+  height: 0;
+  line-height: 0;
+  overflow: hidden;
+  visibility: hidden;
+}
+.grid.margin::after,
+.grid.margin2x::after {
+  content: "";
+  display: none;
 }
-.grid.margin::after, .grid.margin2x::after {
+.nav-text:after,
+.nav-text:before,
+.nav-text span {
+  background-color: #fff;
+  border-radius: 3px;
   content: "";
-  display:none;
-}
-.nav-text:after,.nav-text:before,.nav-text span {
-  background-color:#fff;
-  border-radius:3px;
-  content:'';
-  display:block;
-  height:3px;
-  margin:6px auto;
+  display: block;
+  height: 3px;
+  margin: 6px auto;
   width: 30px;
-  transition:all 0.2s ease-in-out;
-  -moz-transition:all 0.2s ease-in-out;
-  -webkit-transition:all 0.2s ease-in-out;
+  transition: all 0.2s ease-in-out;
+  -moz-transition: all 0.2s ease-in-out;
+  -webkit-transition: all 0.2s ease-in-out;
 }
 .show-menu .nav-text:before {
-  transform:translateY(9px) rotate(135deg);
-  -moz-transform:translateY(9px) rotate(135deg);
-  -webkit-transform:translateY(9px) rotate(135deg);
+  transform: translateY(9px) rotate(135deg);
+  -moz-transform: translateY(9px) rotate(135deg);
+  -webkit-transform: translateY(9px) rotate(135deg);
 }
 .show-menu .nav-text:after {
-  transform:translateY(-9px) rotate(-135deg);
-  -moz-transform:translateY(-9px) rotate(-135deg);
-  -webkit-transform:translateY(-9px) rotate(-135deg);
+  transform: translateY(-9px) rotate(-135deg);
+  -moz-transform: translateY(-9px) rotate(-135deg);
+  -webkit-transform: translateY(-9px) rotate(-135deg);
 }
 .show-menu .nav-text span {
-  transform:scale(0);
-  -moz-transform:scale(0);
-  -webkit-transform:scale(0);  
+  transform: scale(0);
+  -moz-transform: scale(0);
+  -webkit-transform: scale(0);
+}
+.top-nav ul {
+  padding: 0;
 }
-.top-nav ul {padding:0;}
 .top-nav ul ul {
-  position:absolute;
-  background:#152732;
+  position: absolute;
+  background: #152732;
 }
 .top-nav li {
-  float:left;
-  list-style:none outside none;
-  cursor:pointer;
+  float: left;
+  list-style: none outside none;
+  cursor: pointer;
 }
 .top-nav li a {
-  color:#fff; 
-  display:block;
-  font-size:1rem;
-  padding:1.25rem; 
+  color: #fff;
+  display: block;
+  font-size: 1rem;
+  padding: 1.25rem;
 }
 .top-nav li ul li a {
-  background:none repeat scroll 0 0 #152732;
-  min-width:100%;
-  padding:0.625rem;
-}
-.top-nav li a:hover, .aside-nav li a:hover {background:#2b4c61;}
-.top-nav li ul {display:none;}
-.top-nav li ul li,.top-nav li ul li ul li {
-  float:none;
-  list-style:none outside none;
-  min-width:100%;
-  padding:0;
+  background: none repeat scroll 0 0 #152732;
+  min-width: 100%;
+  padding: 0.625rem;
+}
+.top-nav li a:hover,
+.aside-nav li a:hover {
+  background: #2b4c61;
+}
+.top-nav li ul {
+  display: none;
+}
+.top-nav li ul li,
+.top-nav li ul li ul li {
+  float: none;
+  list-style: none outside none;
+  min-width: 100%;
+  padding: 0;
 }
 .count-number {
   background: rgba(153, 153, 153, 0.25) none repeat scroll 0 0;
@@ -214,899 +329,2632 @@ nav {
   display: inline-block;
   font-size: 0.7rem;
   height: 1.3rem;
-  line-height: 1.3rem; 
+  line-height: 1.3rem;
   margin: 0 0 -0.3125rem 0.3125rem;
   text-align: center;
   width: 1.3rem;
 }
-ul.chevron .count-number {display:none;}
-ul.chevron .submenu > a:after, ul.chevron .sub-submenu > a:after,ul.chevron .aside-submenu > a:after, ul.chevron .aside-sub-submenu > a:after {
-  content:"\f004";
-  display:inline-block;
-  font-family:"mfg";
-  font-size:0.7rem;
-  margin:0 0.625rem;
+ul.chevron .count-number {
+  display: none;
+}
+ul.chevron .submenu > a:after,
+ul.chevron .sub-submenu > a:after,
+ul.chevron .aside-submenu > a:after,
+ul.chevron .aside-sub-submenu > a:after {
+  content: "\f004";
+  display: inline-block;
+  font-family: "mfg";
+  font-size: 0.7rem;
+  margin: 0 0.625rem;
 }
-.top-nav .active-item a {background:#2b4c61;}
-.aside-nav > ul > li.active-item > a:link,.aside-nav > ul > li.active-item > a:visited {
-  background:#2b4c61;
-  color:#fff;
+.top-nav .active-item a {
+  background: #2b4c61;
+}
+.aside-nav > ul > li.active-item > a:link,
+.aside-nav > ul > li.active-item > a:visited {
+  background: #2b4c61;
+  color: #fff;
 }
-@media screen and (min-width:769px) {
+@media screen and (min-width: 769px) {
   .aside-nav .count-number {
-	  margin-left:-1.25rem;	
-	  float:right;	
+    margin-left: -1.25rem;
+    float: right;
   }
   .top-nav li:hover > ul {
-	  display:block;
-	  z-index:10;
-  }  
+    display: block;
+    z-index: 10;
+  }
   .top-nav li:hover > ul ul {
-    left:100%;
-    margin:-2.5rem 0;
-    width:100%;
-  } 
-}
-.nav-text,.aside-nav-text {display:none;}
-.aside-nav a,.aside-nav a:link,.aside-nav a:visited,.aside-nav li > ul,.top-nav a,.top-nav a:link,.top-nav a:visited {
-  transition:background 0.20s linear 0s;
-  -o-transition:background 0.20s linear 0s;
-  -ms-transition:background 0.20s linear 0s;
-  -moz-transition:background 0.20s linear 0s;
-  -webkit-transition:background 0.20s linear 0s;
+    left: 100%;
+    margin: -2.5rem 0;
+    width: 100%;
+  }
+}
+.nav-text,
+.aside-nav-text {
+  display: none;
+}
+.aside-nav a,
+.aside-nav a:link,
+.aside-nav a:visited,
+.aside-nav li > ul,
+.top-nav a,
+.top-nav a:link,
+.top-nav a:visited {
+  transition: background 0.2s linear 0s;
+  -o-transition: background 0.2s linear 0s;
+  -ms-transition: background 0.2s linear 0s;
+  -moz-transition: background 0.2s linear 0s;
+  -webkit-transition: background 0.2s linear 0s;
 }
 .aside-nav ul {
-  background:#e8e8e8; 
-  padding:0;
+  background: #e8e8e8;
+  padding: 0;
 }
 .aside-nav li {
-  list-style:none outside none;
-  cursor:pointer;
+  list-style: none outside none;
+  cursor: pointer;
 }
-.aside-nav li a,.aside-nav li a:link,.aside-nav li a:visited {
-  color:#444;
-  display:block;
-  font-size:1rem;
-  padding:1.25rem;
+.aside-nav li a,
+.aside-nav li a:link,
+.aside-nav li a:visited {
+  color: #444;
+  display: block;
+  font-size: 1rem;
+  padding: 1.25rem;
+}
+.aside-nav > ul > li:last-child a {
+  border-bottom: 0 none;
 }
-.aside-nav > ul > li:last-child a {border-bottom:0 none;}
 .aside-nav li > ul {
-  height:0;
-  display:block;
-  position:relative;
-  background:#f4f4f4;
-  border-left:solid 1px #f2f2f2;
-  border-right:solid 1px #f2f2f2;
-  overflow:hidden;
+  height: 0;
+  display: block;
+  position: relative;
+  background: #f4f4f4;
+  border-left: solid 1px #f2f2f2;
+  border-right: solid 1px #f2f2f2;
+  overflow: hidden;
 }
 .aside-nav li ul ul {
-  border:0;
-  background:#fff;
-}
-.aside-nav ul ul a {padding:0.625rem 1.25rem;}
-.aside-nav li a:link, .aside-nav li a:visited {color:#333;}
-.aside-nav li li a:hover, .aside-nav li li.active-item > a, .aside-nav li li.aside-sub-submenu li a:hover {
-  color:#fff;
-  background:#2b4c61;
-}
-.aside-nav > ul > li > a:hover {color:#fff;}
-.aside-nav li li a:link, .aside-nav li li a:visited {background:none;}
-.aside-nav .show-aside-ul, .aside-nav .active-aside-item {height:auto;} 
+  border: 0;
+  background: #fff;
+}
+.aside-nav ul ul a {
+  padding: 0.625rem 1.25rem;
+}
+.aside-nav li a:link,
+.aside-nav li a:visited {
+  color: #333;
+}
+.aside-nav li li a:hover,
+.aside-nav li li.active-item > a,
+.aside-nav li li.aside-sub-submenu li a:hover {
+  color: #fff;
+  background: #2b4c61;
+}
+.aside-nav > ul > li > a:hover {
+  color: #fff;
+}
+.aside-nav li li a:link,
+.aside-nav li li a:visited {
+  background: none;
+}
+.aside-nav .show-aside-ul,
+.aside-nav .active-aside-item {
+  height: auto;
+}
 nav.breadcrumb-nav {
-  background:#fff;
-  margin:0.625rem 0;
+  background: #fff;
+  margin: 0.625rem 0;
 }
 nav.breadcrumb-nav ul {
-  list-style:none;
-  padding:0;
+  list-style: none;
+  padding: 0;
+}
+nav.breadcrumb-nav ul li {
+  float: left;
+}
+nav.breadcrumb-nav ul li a:hover {
+  text-decoration: underline;
+}
+.breadcrumb-nav i {
+  color: #b6c900;
 }
-nav.breadcrumb-nav ul li {float:left;}
-nav.breadcrumb-nav ul li a:hover {text-decoration:underline;}
-.breadcrumb-nav i {color:#B6C900;}
 nav.breadcrumb-nav ul li:after {
-  content:"/";
-  margin:0 9px;
-  color:#c8c7c7;
-}
-nav.breadcrumb-nav ul li:last-child:after {content:"";}
-.slide-content, .slide-nav {
-  transition:all 0.10s linear 0s;
-  -o-transition:all 0.10s linear 0s;
-  -ms-transition:all 0.10s linear 0s;
-  -moz-transition:all 0.10s linear 0s;
-  -webkit-transition:all 0.10s linear 0s;
+  content: "/";
+  margin: 0 9px;
+  color: #c8c7c7;
+}
+nav.breadcrumb-nav ul li:last-child:after {
+  content: "";
+}
+.slide-content,
+.slide-nav {
+  transition: all 0.1s linear 0s;
+  -o-transition: all 0.1s linear 0s;
+  -ms-transition: all 0.1s linear 0s;
+  -moz-transition: all 0.1s linear 0s;
+  -webkit-transition: all 0.1s linear 0s;
 }
 .slide-content {
-  float:left;
-  width:calc(100% - 60px);  
+  float: left;
+  width: calc(100% - 60px);
 }
 .aside-nav.slide-nav {
-  background:#1c3849;
-  bottom:0; 
-  right:0;
-  top:0;
-  margin-right:-180px;     
-  overflow-y:auto;
-  padding-top:0.625rem;
-  position:fixed;
-  width:240px;
-  z-index:2;
+  background: #1c3849;
+  bottom: 0;
+  right: 0;
+  top: 0;
+  margin-right: -180px;
+  overflow-y: auto;
+  padding-top: 0.625rem;
+  position: fixed;
+  width: 240px;
+  z-index: 2;
 }
 .aside-nav.slide-nav > ul {
-  background:#1c3849;
-  opacity:0;
-  transition:all 0.20s linear 0s;
-  -o-transition:all 0.20s linear 0s;
-  -ms-transition:all 0.20s linear 0s;
-  -moz-transition:all 0.20s linear 0s;
-  -webkit-transition:all 0.20s linear 0s;
-}
-.aside-nav.slide-nav li a, .aside-nav.slide-nav li a:link, .aside-nav.slide-nav li a:visited {
-  color:#fff;
-  display:block;
-  font-size:0.9rem;
-  padding:0.625rem 1.25rem;
-  border-bottom:0;
+  background: #1c3849;
+  opacity: 0;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
+}
+.aside-nav.slide-nav li a,
+.aside-nav.slide-nav li a:link,
+.aside-nav.slide-nav li a:visited {
+  color: #fff;
+  display: block;
+  font-size: 0.9rem;
+  padding: 0.625rem 1.25rem;
+  border-bottom: 0;
 }
 .aside-nav.slide-nav li a:hover {
-  background:#152732!important;
-  color:#fff!important;
+  background: #152732 !important;
+  color: #fff !important;
 }
 .aside-nav.slide-nav li > ul {
-  background:#2b4c61;
-  border-left:0;
-  border-right:0;
+  background: #2b4c61;
+  border-left: 0;
+  border-right: 0;
 }
 .aside-nav.slide-nav li > ul ul {
-  background:#456274;
-  border-left:0;
-  border-right:0;
+  background: #456274;
+  border-left: 0;
+  border-right: 0;
 }
 .slide-nav-button {
-  background:#152732;
-  cursor:pointer;
-  position:fixed;
-  top:0;
-  right:0;
-  bottom:0;
-  width:60px;
-  z-index:3;
-}
-.active-slide-nav .slide-content {margin-left:-240px;}
-.active-slide-nav .slide-nav {margin-right:60px;}
-.slide-to-left .slide-content {float:right;}
+  background: #152732;
+  cursor: pointer;
+  position: fixed;
+  top: 0;
+  right: 0;
+  bottom: 0;
+  width: 60px;
+  z-index: 3;
+}
+.active-slide-nav .slide-content {
+  margin-left: -240px;
+}
+.active-slide-nav .slide-nav {
+  margin-right: 60px;
+}
+.slide-to-left .slide-content {
+  float: right;
+}
 .slide-to-left .slide-nav {
-  left:0;
-  margin-right:0; 
-  margin-left:-180px;    
+  left: 0;
+  margin-right: 0;
+  margin-left: -180px;
+}
+.slide-to-left .slide-nav-button {
+  left: 0;
 }
-.slide-to-left .slide-nav-button {left:0;}
 .slide-to-left.active-slide-nav .slide-content {
-  margin-right:-240px;
-  margin-left:0;
+  margin-right: -240px;
+  margin-left: 0;
 }
 .slide-to-left.active-slide-nav .slide-nav {
-  margin-right:0;
-  margin-left:60px;
+  margin-right: 0;
+  margin-left: 60px;
+}
+.active-slide-nav .slide-nav ul {
+  opacity: 1;
 }
-.active-slide-nav .slide-nav ul {opacity:1;}
 .nav-icon {
-  padding:0.9rem;
-  width:100%;
-}
-.nav-icon:after,.nav-icon:before,.nav-icon div {
-  background-color:#fff;
-  border-radius:3px;
-  content:"";
-  display:block;
-  height:3px;
-  margin:6px 0;
-  transition:all 0.2s ease-in-out;
-  -moz-transition:all 0.2s ease-in-out;
-  -webkit-transition:all 0.2s ease-in-out;
+  padding: 0.9rem;
+  width: 100%;
+}
+.nav-icon:after,
+.nav-icon:before,
+.nav-icon div {
+  background-color: #fff;
+  border-radius: 3px;
+  content: "";
+  display: block;
+  height: 3px;
+  margin: 6px 0;
+  transition: all 0.2s ease-in-out;
+  -moz-transition: all 0.2s ease-in-out;
+  -webkit-transition: all 0.2s ease-in-out;
 }
 .active-slide-nav .nav-icon:before {
-  transform:translateY(9px) rotate(135deg);
-  -moz-transform:translateY(9px) rotate(135deg);
-  -webkit-transform:translateY(9px) rotate(135deg);
+  transform: translateY(9px) rotate(135deg);
+  -moz-transform: translateY(9px) rotate(135deg);
+  -webkit-transform: translateY(9px) rotate(135deg);
 }
 .active-slide-nav .nav-icon:after {
-  transform:translateY(-9px) rotate(-135deg);
-  -moz-transform:translateY(-9px) rotate(-135deg);
-  -webkit-transform:translateY(-9px) rotate(-135deg);
+  transform: translateY(-9px) rotate(-135deg);
+  -moz-transform: translateY(-9px) rotate(-135deg);
+  -webkit-transform: translateY(-9px) rotate(-135deg);
 }
 .active-slide-nav .nav-icon div {
-  transform:scale(0);
-  -moz-transform:scale(0);
-  -webkit-transform:scale(0);  
+  transform: scale(0);
+  -moz-transform: scale(0);
+  -webkit-transform: scale(0);
+}
+.active-slide-nav {
+  overflow-x: hidden;
 }
-.active-slide-nav {overflow-x:hidden;} 
 .padding {
-  display:list-item;
-  list-style:none outside none;
-  padding:0.625rem;
+  display: list-item;
+  list-style: none outside none;
+  padding: 0.625rem;
+}
+.margin,
+.margin2x {
+  display: block;
+}
+.margin {
+  margin: 0 -0.625rem;
+}
+.margin2x {
+  margin: 0 -1.25rem;
 }
-.margin,.margin2x {display: block;}
-.margin {margin:0 -0.625rem;}
-.margin2x {margin:0 -1.25rem;}
 .grid.margin {
   display: grid;
-  grid-column-gap:20px;
-  margin:0 auto;	
+  grid-column-gap: 20px;
+  margin: 0 auto;
 }
 .grid.margin2x {
   display: grid;
-  grid-column-gap:40px;
-  margin:0 auto;	
+  grid-column-gap: 40px;
+  margin: 0 auto;
+}
+.line {
+  clear: left;
+}
+.line .line {
+  padding: 0;
+}
+.hide-xxl {
+  display: none !important;
 }
-.line {clear:left;}
-.line .line {padding:0;}
-.hide-xxl {display:none!important;}
 .box {
-  background:none repeat scroll 0 0 #fff;
-  display:block;
-  padding:1.25rem;
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-  .xl-order-6 {order:6;}
-  .xl-order-7 {order:7;}
-  .xl-order-8 {order:8;}
-  .xl-order-9 {order:9;}
-  .xl-order-10 {order:10;}
-  .xl-order-11 {order:11;}
-  .xl-order-12 {order:12;} 
-  .xl-order-last {order:99999999;} 
-  .xl-1, .grid .xl-1.center {width:8.3333%;}
-  .xl-2, .grid .xl-2.center {width:16.6666%;}
-  .xl-five {width:20%;}
-  .xl-3, .grid .xl-3.center {width:25%;}
-  .xl-4, .grid .xl-4.center {width:33.3333%;}
-  .xl-5, .grid .xl-5.center {width:41.6666%;}
-  .xl-6, .grid .xl-6.center {width:50%;}
-  .xl-7, .grid .xl-7.center {width:58.3333%;}
-  .xl-8, .grid .xl-8.center {width:66.6666%;}
-  .xl-9, .grid .xl-9.center {width:75%;}
-  .xl-10, .grid .xl-10.center {width:83.3333%;}
-  .xl-11, .grid .xl-11.center {width:91.6666%;}
-  .xl-12, .grid .xl-12.center {width:100%}
-  .grid .xl-1 {grid-column:span 1;}
-  .grid .xl-2 {grid-column:span 2;}
-  .grid .xl-3 {grid-column:span 3;}
-  .grid .xl-4 {grid-column:span 4;}
-  .grid .xl-5 {grid-column:span 5;}
-  .grid .xl-6 {grid-column:span 6;}
-  .grid .xl-7 {grid-column:span 7;}
-  .grid .xl-8 {grid-column:span 8;}
-  .grid .xl-9 {grid-column:span 9;}
-  .grid .xl-10 {grid-column:span 10;}
-  .grid .xl-11 {grid-column:span 11;}
-  .grid .xl-12 {grid-column:span 12;}
-  .grid .xl-row-1 {grid-row:span 1;}
-  .grid .xl-row-2 {grid-row:span 2;}
-  .grid .xl-row-3 {grid-row:span 3;}
-  .grid .xl-row-4 {grid-row:span 4;}
-  .grid .xl-row-5 {grid-row:span 5;}
-  .grid .xl-row-6 {grid-row:span 6;}
-  .grid .xl-row-7 {grid-row:span 7;}
-  .grid .xl-row-8 {grid-row:span 8;}
-  .grid .xl-row-9 {grid-row:span 9;}
-  .grid .xl-row-10 {grid-row:span 10;}
-  .grid .xl-row-11 {grid-row:span 11;}
-  .grid .xl-row-12 {grid-row:span 12;}  
+  background: none repeat scroll 0 0 #fff;
+  display: block;
+  padding: 1.25rem;
+  width: 100%;
+}
+.margin-bottom {
+  margin-bottom: 1.25rem !important;
+}
+.margin-bottom2x {
+  margin-bottom: 2.5rem !important;
+}
+.s-1,
+.s-2,
+.s-five,
+.s-3,
+.s-4,
+.s-5,
+.s-6,
+.s-7,
+.s-8,
+.s-9,
+.s-10,
+.s-11,
+.s-12,
+.m-1,
+.m-2,
+.m-five,
+.m-3,
+.m-4,
+.m-5,
+.m-6,
+.m-7,
+.m-8,
+.m-9,
+.m-10,
+.m-11,
+.m-12,
+.l-1,
+.l-2,
+.l-five,
+.l-3,
+.l-4,
+.l-5,
+.l-6,
+.l-7,
+.l-8,
+.l-9,
+.l-10,
+.l-11,
+.l-12,
+.xl-1,
+.xl-2,
+.xl-five,
+.xl-3,
+.xl-4,
+.xl-5,
+.xl-6,
+.xl-7,
+.xl-8,
+.xl-9,
+.xl-10,
+.xl-11,
+.xl-12,
+.xxl-1,
+.xxl-2,
+.xxl-five,
+.xxl-3,
+.xxl-4,
+.xxl-5,
+.xxl-6,
+.xxl-7,
+.xxl-8,
+.xxl-9,
+.xxl-10,
+.xxl-11,
+.xxl-12 {
+  float: left;
+  position: static;
+}
+.xxl-offset-1 {
+  margin-left: 8.3333%;
+}
+.xxl-offset-2 {
+  margin-left: 16.6666%;
+}
+.xxl-offset-five {
+  margin-left: 20%;
+}
+.xxl-offset-3 {
+  margin-left: 25%;
+}
+.xxl-offset-4 {
+  margin-left: 33.3333%;
+}
+.xxl-offset-5 {
+  margin-left: 41.6666%;
+}
+.xxl-offset-6 {
+  margin-left: 50%;
+}
+.xxl-offset-7 {
+  margin-left: 58.3333%;
+}
+.xxl-offset-8 {
+  margin-left: 66.6666%;
+}
+.xxl-offset-9 {
+  margin-left: 75%;
+}
+.xxl-offset-10 {
+  margin-left: 83.3333%;
+}
+.xxl-offset-11 {
+  margin-left: 91.6666%;
+}
+.xxl-offset-12 {
+  margin-left: 100%;
+}
+.xxl-order-1 {
+  order: -1;
+}
+.xxl-order-2 {
+  order: 2;
+}
+.xxl-order-3 {
+  order: 3;
+}
+.xxl-order-4 {
+  order: 4;
+}
+.xxl-order-5 {
+  order: 5;
+}
+.xxl-order-6 {
+  order: 6;
+}
+.xxl-order-7 {
+  order: 7;
+}
+.xxl-order-8 {
+  order: 8;
+}
+.xxl-order-9 {
+  order: 9;
+}
+.xxl-order-10 {
+  order: 10;
+}
+.xxl-order-11 {
+  order: 11;
+}
+.xxl-order-12 {
+  order: 12;
+}
+.xxl-order-last {
+  order: 99999999;
+}
+.line .margin > .s-1,
+.line .margin > .s-2,
+.line .margin > .s-five,
+.line .margin > .s-3,
+.line .margin > .s-4,
+.line .margin > .s-5,
+.line .margin > .s-6,
+.line .margin > .s-7,
+.line .margin > .s-8,
+.line .margin > .s-9,
+.line .margin > .s-10,
+.line .margin > .s-11,
+.line .margin > .s-12,
+.line .margin > .m-1,
+.line .margin > .m-2,
+.line .margin > .m-five,
+.line .margin > .m-3,
+.line .margin > .m-4,
+.line .margin > .m-5,
+.line .margin > .m-6,
+.line .margin > .m-7,
+.line .margin > .m-8,
+.line .margin > .m-9,
+.line .margin > .m-10,
+.line .margin > .m-11,
+.line .margin > .m-12,
+.line .margin > .l-1,
+.line .margin > .l-2,
+.line .margin > .l-five,
+.line .margin > .l-3,
+.line .margin > .l-4,
+.line .margin > .l-5,
+.line .margin > .l-6,
+.line .margin > .l-7,
+.line .margin > .l-8,
+.line .margin > .l-9,
+.line .margin > .l-10,
+.line .margin > .l-11,
+.line .margin > .l-12,
+.line .margin > .xl-1,
+.line .margin > .xl-2,
+.line .margin > .xl-five,
+.line .margin > .xl-3,
+.line .margin > .xl-4,
+.line .margin > .xl-5,
+.line .margin > .xl-6,
+.line .margin > .xl-7,
+.line .margin > .xl-8,
+.line .margin > .xl-9,
+.line .margin > .xl-10,
+.line .margin > .xl-11,
+.line .margin > .xl-12,
+.line .margin > .xxl-1,
+.line .margin > .xxl-2,
+.line .margin > .xxl-five,
+.line .margin > .xxl-3,
+.line .margin > .xxl-4,
+.line .margin > .xxl-5,
+.line .margin > .xxl-6,
+.line .margin > .xxl-7,
+.line .margin > .xxl-8,
+.line .margin > .xxl-9,
+.line .margin > .xxl-10,
+.line .margin > .xxl-11,
+.line .margin > .xxl-12 {
+  padding: 0 0.625rem;
+}
+.line .margin2x > .s-1,
+.line .margin2x > .s-2,
+.line .margin2x > .s-five,
+.line .margin2x > .s-3,
+.line .margin2x > .s-4,
+.line .margin2x > .s-5,
+.line .margin2x > .s-6,
+.line .margin2x > .s-7,
+.line .margin2x > .s-8,
+.line .margin2x > .s-9,
+.line .margin2x > .s-10,
+.line .margin2x > .s-11,
+.line .margin2x > .s-12,
+.line .margin2x > .m-1,
+.line .margin2x > .m-2,
+.line .margin2x > .m-five,
+.line .margin2x > .m-3,
+.line .margin2x > .m-4,
+.line .margin2x > .m-5,
+.line .margin2x > .m-6,
+.line .margin2x > .m-7,
+.line .margin2x > .m-8,
+.line .margin2x > .m-9,
+.line .margin2x > .m-10,
+.line .margin2x > .m-11,
+.line .margin2x > .m-12,
+.line .margin2x > .l-1,
+.line .margin2x > .l-2,
+.line .margin2x > .l-five,
+.line .margin2x > .l-3,
+.line .margin2x > .l-4,
+.line .margin2x > .l-5,
+.line .margin2x > .l-6,
+.line .margin2x > .l-7,
+.line .margin2x > .l-8,
+.line .margin2x > .l-9,
+.line .margin2x > .l-10,
+.line .margin2x > .l-11,
+.line .margin2x > .l-12,
+.line .margin2x > .xl-1,
+.line .margin2x > .xl-2,
+.line .margin2x > .xl-five,
+.line .margin2x > .xl-3,
+.line .margin2x > .xl-4,
+.line .margin2x > .xl-5,
+.line .margin2x > .xl-6,
+.line .margin2x > .xl-7,
+.line .margin2x > .xl-8,
+.line .margin2x > .xl-9,
+.line .margin2x > .xl-10,
+.line .margin2x > .xl-11,
+.line .margin2x > .xl-12,
+.line .margin2x > .xxl-1,
+.line .margin2x > .xxl-2,
+.line .margin2x > .xxl-five,
+.line .margin2x > .xxl-3,
+.line .margin2x > .xxl-4,
+.line .margin2x > .xxl-5,
+.line .margin2x > .xxl-6,
+.line .margin2x > .xxl-7,
+.line .margin2x > .xxl-8,
+.line .margin2x > .xxl-9,
+.line .margin2x > .xxl-10,
+.line .margin2x > .xxl-11,
+.line .margin2x > .xxl-12 {
+  padding: 0 1.25rem;
+}
+.line-full-width .margin > .s-1,
+.line-full-width .margin > .s-2,
+.line-full-width .margin > .s-five,
+.line-full-width .margin > .s-3,
+.line-full-width .margin > .s-4,
+.line-full-width .margin > .s-5,
+.line-full-width .margin > .s-6,
+.line-full-width .margin > .s-7,
+.line-full-width .margin > .s-8,
+.line-full-width .margin > .s-9,
+.line-full-width .margin > .s-10,
+.line-full-width .margin > .s-11,
+.line-full-width .margin > .s-12,
+.line-full-width .margin > .m-1,
+.line-full-width .margin > .m-2,
+.line-full-width .margin > .m-five,
+.line-full-width .margin > .m-3,
+.line-full-width .margin > .m-4,
+.line-full-width .margin > .m-5,
+.line-full-width .margin > .m-6,
+.line-full-width .margin > .m-7,
+.line-full-width .margin > .m-8,
+.line-full-width .margin > .m-9,
+.line-full-width .margin > .m-10,
+.line-full-width .margin > .m-11,
+.line-full-width .margin > .m-12,
+.line-full-width .margin > .l-1,
+.line-full-width .margin > .l-2,
+.line-full-width .margin > .l-five,
+.line-full-width .margin > .l-3,
+.line-full-width .margin > .l-4,
+.line-full-width .margin > .l-5,
+.line-full-width .margin > .l-6,
+.line-full-width .margin > .l-7,
+.line-full-width .margin > .l-8,
+.line-full-width .margin > .l-9,
+.line-full-width .margin > .l-10,
+.line-full-width .margin > .l-11,
+.line-full-width .margin > .l-12,
+.line-full-width .margin > .xl-1,
+.line-full-width .margin > .xl-2,
+.line-full-width .margin > .xl-five,
+.line-full-width .margin > .xl-3,
+.line-full-width .margin > .xl-4,
+.line-full-width .margin > .xl-5,
+.line-full-width .margin > .xl-6,
+.line-full-width .margin > .xl-7,
+.line-full-width .margin > .xl-8,
+.line-full-width .margin > .xl-9,
+.line-full-width .margin > .xl-10,
+.line-full-width .margin > .xl-11,
+.line-full-width .margin > .xl-12,
+.line-full-width .margin > .xxl-1,
+.line-full-width .margin > .xxl-2,
+.line-full-width .margin > .xxl-five,
+.line-full-width .margin > .xxl-3,
+.line-full-width .margin > .xxl-4,
+.line-full-width .margin > .xxl-5,
+.line-full-width .margin > .xxl-6,
+.line-full-width .margin > .xxl-7,
+.line-full-width .margin > .xxl-8,
+.line-full-width .margin > .xxl-9,
+.line-full-width .margin > .xxl-10,
+.line-full-width .margin > .xxl-11,
+.line-full-width .margin > .xxl-12 {
+  padding: 0 0.625rem;
+}
+.line-full-width .margin2x > .s-1,
+.line-full-width .margin2x > .s-2,
+.line-full-width .margin2x > .s-five,
+.line-full-width .margin2x > .s-3,
+.line-full-width .margin2x > .s-4,
+.line-full-width .margin2x > .s-5,
+.line-full-width .margin2x > .s-6,
+.line-full-width .margin2x > .s-7,
+.line-full-width .margin2x > .s-8,
+.line-full-width .margin2x > .s-9,
+.line-full-width .margin2x > .s-10,
+.line-full-width .margin2x > .s-11,
+.line-full-width .margin2x > .s-12,
+.line-full-width .margin2x > .m-1,
+.line-full-width .margin2x > .m-2,
+.line-full-width .margin2x > .m-five,
+.line-full-width .margin2x > .m-3,
+.line-full-width .margin2x > .m-4,
+.line-full-width .margin2x > .m-5,
+.line-full-width .margin2x > .m-6,
+.line-full-width .margin2x > .m-7,
+.line-full-width .margin2x > .m-8,
+.line-full-width .margin2x > .m-9,
+.line-full-width .margin2x > .m-10,
+.line-full-width .margin2x > .m-11,
+.line-full-width .margin2x > .m-12,
+.line-full-width .margin2x > .l-1,
+.line-full-width .margin2x > .l-2,
+.line-full-width .margin2x > .l-five,
+.line-full-width .margin2x > .l-3,
+.line-full-width .margin2x > .l-4,
+.line-full-width .margin2x > .l-5,
+.line-full-width .margin2x > .l-6,
+.line-full-width .margin2x > .l-7,
+.line-full-width .margin2x > .l-8,
+.line-full-width .margin2x > .l-9,
+.line-full-width .margin2x > .l-10,
+.line-full-width .margin2x > .l-11,
+.line-full-width .margin2x > .l-12,
+.line-full-width .margin2x > .xl-1,
+.line-full-width .margin2x > .xl-2,
+.line-full-width .margin2x > .xl-five,
+.line-full-width .margin2x > .xl-3,
+.line-full-width .margin2x > .xl-4,
+.line-full-width .margin2x > .xl-5,
+.line-full-width .margin2x > .xl-6,
+.line-full-width .margin2x > .xl-7,
+.line-full-width .margin2x > .xl-8,
+.line-full-width .margin2x > .xl-9,
+.line-full-width .margin2x > .xl-10,
+.line-full-width .margin2x > .xl-11,
+.line-full-width .margin2x > .xl-12,
+.line-full-width .margin2x > .xxl-1,
+.line-full-width .margin2x > .xxl-2,
+.line-full-width .margin2x > .xxl-five,
+.line-full-width .margin2x > .xxl-3,
+.line-full-width .margin2x > .xxl-4,
+.line-full-width .margin2x > .xxl-5,
+.line-full-width .margin2x > .xxl-6,
+.line-full-width .margin2x > .xxl-7,
+.line-full-width .margin2x > .xxl-8,
+.line-full-width .margin2x > .xxl-9,
+.line-full-width .margin2x > .xxl-10,
+.line-full-width .margin2x > .xxl-11,
+.line-full-width .margin2x > .xxl-12 {
+  padding: 0 1.25rem;
+}
+.s-1,
+.grid .s-1.center {
+  width: 8.3333%;
+}
+.s-2,
+.grid .s-2.center {
+  width: 16.6666%;
+}
+.s-five {
+  width: 20%;
+}
+.s-3,
+.grid .s-3.center {
+  width: 25%;
+}
+.s-4,
+.grid .s-4.center {
+  width: 33.3333%;
+}
+.s-5,
+.grid .s-5.center {
+  width: 41.6666%;
+}
+.s-6,
+.grid .s-6.center {
+  width: 50%;
+}
+.s-7,
+.grid .s-7.center {
+  width: 58.3333%;
+}
+.s-8,
+.grid .s-8.center {
+  width: 66.6666%;
+}
+.s-9,
+.grid .s-9.center {
+  width: 75%;
+}
+.s-10,
+.grid .s-10.center {
+  width: 83.3333%;
+}
+.s-11,
+.grid .s-11.center {
+  width: 91.6666%;
+}
+.s-12,
+.grid .s-12.center {
+  width: 100%;
+}
+.grid .s-1 {
+  grid-column: span 1;
+}
+.grid .s-2 {
+  grid-column: span 2;
+}
+.grid .s-3 {
+  grid-column: span 3;
+}
+.grid .s-4 {
+  grid-column: span 4;
+}
+.grid .s-5 {
+  grid-column: span 5;
+}
+.grid .s-6 {
+  grid-column: span 6;
+}
+.grid .s-7 {
+  grid-column: span 7;
+}
+.grid .s-8 {
+  grid-column: span 8;
+}
+.grid .s-9 {
+  grid-column: span 9;
+}
+.grid .s-10 {
+  grid-column: span 10;
+}
+.grid .s-11 {
+  grid-column: span 11;
+}
+.grid .s-12 {
+  grid-column: span 12;
+}
+.grid .s-row-1 {
+  grid-row: span 1;
+}
+.grid .s-row-2 {
+  grid-row: span 2;
+}
+.grid .s-row-3 {
+  grid-row: span 3;
+}
+.grid .s-row-4 {
+  grid-row: span 4;
+}
+.grid .s-row-5 {
+  grid-row: span 5;
+}
+.grid .s-row-6 {
+  grid-row: span 6;
+}
+.grid .s-row-7 {
+  grid-row: span 7;
+}
+.grid .s-row-8 {
+  grid-row: span 8;
+}
+.grid .s-row-9 {
+  grid-row: span 9;
+}
+.grid .s-row-10 {
+  grid-row: span 10;
+}
+.grid .s-row-11 {
+  grid-row: span 11;
+}
+.grid .s-row-12 {
+  grid-row: span 12;
+}
+.m-1,
+.grid .m-1.center {
+  width: 8.3333%;
+}
+.m-2,
+.grid .m-2.center {
+  width: 16.6666%;
+}
+.m-five {
+  width: 20%;
+}
+.m-3,
+.grid .m-3.center {
+  width: 25%;
+}
+.m-4,
+.grid .m-4.center {
+  width: 33.3333%;
+}
+.m-5,
+.grid .m-5.center {
+  width: 41.6666%;
+}
+.m-6,
+.grid .m-6.center {
+  width: 50%;
+}
+.m-7,
+.grid .m-7.center {
+  width: 58.3333%;
+}
+.m-8,
+.grid .m-8.center {
+  width: 66.6666%;
+}
+.m-9,
+.grid .m-9.center {
+  width: 75%;
+}
+.m-10,
+.grid .m-10.center {
+  width: 83.3333%;
+}
+.m-11,
+.grid .m-11.center {
+  width: 91.6666%;
+}
+.m-12,
+.grid .m-12.center {
+  width: 100%;
+}
+.grid .m-1 {
+  grid-column: span 1;
+}
+.grid .m-2 {
+  grid-column: span 2;
+}
+.grid .m-3 {
+  grid-column: span 3;
+}
+.grid .m-4 {
+  grid-column: span 4;
+}
+.grid .m-5 {
+  grid-column: span 5;
+}
+.grid .m-6 {
+  grid-column: span 6;
+}
+.grid .m-7 {
+  grid-column: span 7;
+}
+.grid .m-8 {
+  grid-column: span 8;
+}
+.grid .m-9 {
+  grid-column: span 9;
+}
+.grid .m-10 {
+  grid-column: span 10;
+}
+.grid .m-11 {
+  grid-column: span 11;
+}
+.grid .m-12 {
+  grid-column: span 12;
+}
+.grid .m-row-1 {
+  grid-row: span 1;
+}
+.grid .m-row-2 {
+  grid-row: span 2;
+}
+.grid .m-row-3 {
+  grid-row: span 3;
+}
+.grid .m-row-4 {
+  grid-row: span 4;
+}
+.grid .m-row-5 {
+  grid-row: span 5;
+}
+.grid .m-row-6 {
+  grid-row: span 6;
+}
+.grid .m-row-7 {
+  grid-row: span 7;
+}
+.grid .m-row-8 {
+  grid-row: span 8;
+}
+.grid .m-row-9 {
+  grid-row: span 9;
+}
+.grid .m-row-10 {
+  grid-row: span 10;
+}
+.grid .m-row-11 {
+  grid-row: span 11;
+}
+.grid .m-row-12 {
+  grid-row: span 12;
+}
+.l-1,
+.grid .l-1.center {
+  width: 8.3333%;
+}
+.l-2,
+.grid .l-2.center {
+  width: 16.6666%;
+}
+.l-five {
+  width: 20%;
+}
+.l-3,
+.grid .l-3.center {
+  width: 25%;
+}
+.l-4,
+.grid .l-4.center {
+  width: 33.3333%;
+}
+.l-5,
+.grid .l-5.center {
+  width: 41.6666%;
+}
+.l-6,
+.grid .l-6.center {
+  width: 50%;
+}
+.l-7,
+.grid .l-7.center {
+  width: 58.3333%;
+}
+.l-8,
+.grid .l-8.center {
+  width: 66.6666%;
+}
+.l-9,
+.grid .l-9.center {
+  width: 75%;
+}
+.l-10,
+.grid .l-10.center {
+  width: 83.3333%;
+}
+.l-11,
+.grid .l-11.center {
+  width: 91.6666%;
+}
+.l-12,
+.grid .l-12.center {
+  width: 100%;
+}
+.grid .l-1 {
+  grid-column: span 1;
+}
+.grid .l-2 {
+  grid-column: span 2;
+}
+.grid .l-3 {
+  grid-column: span 3;
+}
+.grid .l-4 {
+  grid-column: span 4;
+}
+.grid .l-5 {
+  grid-column: span 5;
+}
+.grid .l-6 {
+  grid-column: span 6;
+}
+.grid .l-7 {
+  grid-column: span 7;
+}
+.grid .l-8 {
+  grid-column: span 8;
+}
+.grid .l-9 {
+  grid-column: span 9;
+}
+.grid .l-10 {
+  grid-column: span 10;
+}
+.grid .l-11 {
+  grid-column: span 11;
+}
+.grid .l-12 {
+  grid-column: span 12;
+}
+.grid .l-row-1 {
+  grid-row: span 1;
+}
+.grid .l-row-2 {
+  grid-row: span 2;
+}
+.grid .l-row-3 {
+  grid-row: span 3;
+}
+.grid .l-row-4 {
+  grid-row: span 4;
+}
+.grid .l-row-5 {
+  grid-row: span 5;
+}
+.grid .l-row-6 {
+  grid-row: span 6;
+}
+.grid .l-row-7 {
+  grid-row: span 7;
+}
+.grid .l-row-8 {
+  grid-row: span 8;
+}
+.grid .l-row-9 {
+  grid-row: span 9;
+}
+.grid .l-row-10 {
+  grid-row: span 10;
+}
+.grid .l-row-11 {
+  grid-row: span 11;
+}
+.grid .l-row-12 {
+  grid-row: span 12;
+}
+.xl-1,
+.grid .xl-1.center {
+  width: 8.3333%;
+}
+.xl-2,
+.grid .xl-2.center {
+  width: 16.6666%;
+}
+.xl-five {
+  width: 20%;
+}
+.xl-3,
+.grid .xl-3.center {
+  width: 25%;
+}
+.xl-4,
+.grid .xl-4.center {
+  width: 33.3333%;
+}
+.xl-5,
+.grid .xl-5.center {
+  width: 41.6666%;
+}
+.xl-6,
+.grid .xl-6.center {
+  width: 50%;
+}
+.xl-7,
+.grid .xl-7.center {
+  width: 58.3333%;
+}
+.xl-8,
+.grid .xl-8.center {
+  width: 66.6666%;
+}
+.xl-9,
+.grid .xl-9.center {
+  width: 75%;
+}
+.xl-10,
+.grid .xl-10.center {
+  width: 83.3333%;
+}
+.xl-11,
+.grid .xl-11.center {
+  width: 91.6666%;
+}
+.xl-12,
+.grid .xl-12.center {
+  width: 100%;
+}
+.grid .xl-1 {
+  grid-column: span 1;
+}
+.grid .xl-2 {
+  grid-column: span 2;
+}
+.grid .xl-3 {
+  grid-column: span 3;
+}
+.grid .xl-4 {
+  grid-column: span 4;
+}
+.grid .xl-5 {
+  grid-column: span 5;
+}
+.grid .xl-6 {
+  grid-column: span 6;
+}
+.grid .xl-7 {
+  grid-column: span 7;
+}
+.grid .xl-8 {
+  grid-column: span 8;
+}
+.grid .xl-9 {
+  grid-column: span 9;
+}
+.grid .xl-10 {
+  grid-column: span 10;
+}
+.grid .xl-11 {
+  grid-column: span 11;
+}
+.grid .xl-12 {
+  grid-column: span 12;
+}
+.grid .xl-row-1 {
+  grid-row: span 1;
+}
+.grid .xl-row-2 {
+  grid-row: span 2;
+}
+.grid .xl-row-3 {
+  grid-row: span 3;
+}
+.grid .xl-row-4 {
+  grid-row: span 4;
+}
+.grid .xl-row-5 {
+  grid-row: span 5;
+}
+.grid .xl-row-6 {
+  grid-row: span 6;
+}
+.grid .xl-row-7 {
+  grid-row: span 7;
+}
+.grid .xl-row-8 {
+  grid-row: span 8;
+}
+.grid .xl-row-9 {
+  grid-row: span 9;
+}
+.grid .xl-row-10 {
+  grid-row: span 10;
+}
+.grid .xl-row-11 {
+  grid-row: span 11;
+}
+.grid .xl-row-12 {
+  grid-row: span 12;
+}
+.xxl-1,
+.grid .xxl-1.center {
+  width: 8.3333%;
+}
+.xxl-2,
+.grid .xxl-2.center {
+  width: 16.6666%;
+}
+.xxl-five {
+  width: 20%;
+}
+.xxl-3,
+.grid .xxl-3.center {
+  width: 25%;
+}
+.xxl-4,
+.grid .xxl-4.center {
+  width: 33.3333%;
+}
+.xxl-5,
+.grid .xxl-5.center {
+  width: 41.6666%;
+}
+.xxl-6,
+.grid .xxl-6.center {
+  width: 50%;
+}
+.xxl-7,
+.grid .xxl-7.center {
+  width: 58.3333%;
+}
+.xxl-8,
+.grid .xxl-8.center {
+  width: 66.6666%;
+}
+.xxl-9,
+.grid .xxl-9.center {
+  width: 75%;
+}
+.xxl-10,
+.grid .xxl-10.center {
+  width: 83.3333%;
+}
+.xxl-11,
+.grid .xxl-11.center {
+  width: 91.6666%;
+}
+.xxl-12,
+.grid .xxl-12.center {
+  width: 100%;
+}
+.grid .xxl-1 {
+  grid-column: span 1;
+}
+.grid .xxl-2 {
+  grid-column: span 2;
+}
+.grid .xxl-3 {
+  grid-column: span 3;
+}
+.grid .xxl-4 {
+  grid-column: span 4;
+}
+.grid .xxl-5 {
+  grid-column: span 5;
+}
+.grid .xxl-6 {
+  grid-column: span 6;
+}
+.grid .xxl-7 {
+  grid-column: span 7;
+}
+.grid .xxl-8 {
+  grid-column: span 8;
+}
+.grid .xxl-9 {
+  grid-column: span 9;
+}
+.grid .xxl-10 {
+  grid-column: span 10;
+}
+.grid .xxl-11 {
+  grid-column: span 11;
+}
+.grid .xxl-12 {
+  grid-column: span 12;
+}
+.grid .xxl-row-1 {
+  grid-row: span 1;
+}
+.grid .xxl-row-2 {
+  grid-row: span 2;
+}
+.grid .xxl-row-3 {
+  grid-row: span 3;
+}
+.grid .xxl-row-4 {
+  grid-row: span 4;
+}
+.grid .xxl-row-5 {
+  grid-row: span 5;
+}
+.grid .xxl-row-6 {
+  grid-row: span 6;
+}
+.grid .xxl-row-7 {
+  grid-row: span 7;
+}
+.grid .xxl-row-8 {
+  grid-row: span 8;
+}
+.grid .xxl-row-9 {
+  grid-row: span 9;
+}
+.grid .xxl-row-10 {
+  grid-row: span 10;
+}
+.grid .xxl-row-11 {
+  grid-row: span 11;
+}
+.grid .xxl-row-12 {
+  grid-row: span 12;
+}
+.right {
+  float: right;
+}
+.left {
+  float: left;
 }
 
-@media screen and (max-width:1140px) {
-  .hide-xxl,.hide-xl,.hide-m,.hide-s {display:initial!important;}
-  .hide-l {display:none!important;}
-  .size-960,.size-1140,.size-1280,.size-1520 {max-width:1140px;}
-  .xl-offset-1,.xl-offset-2,.xl-offset-five,.xl-offset-3,.xl-offset-4,.xl-offset-5,.xl-offset-6,.xl-offset-7,.xl-offset-8,.xl-offset-9,.xl-offset-10,.xl-offset-11,.xl-offset-12 {margin-left:0;}
-  .l-offset-1 {margin-left:8.3333%;}
-  .l-offset-2 {margin-left:16.6666%;}
-  .l-offset-five {margin-left:20%;}
-  .l-offset-3 {margin-left:25%;}
-  .l-offset-4 {margin-left:33.3333%;}
-  .l-offset-5 {margin-left:41.6666%;}
-  .l-offset-6 {margin-left:50%;}
-  .l-offset-7 {margin-left:58.3333%;}
-  .l-offset-8 {margin-left:66.6666%;}
-  .l-offset-9 {margin-left:75%;}
-  .l-offset-10 {margin-left:83.3333%;}
-  .l-offset-11 {margin-left:91.6666%;}
-  .l-offset-12 {margin-left:100%;}
-  .xl-order-1,.xl-order-2,.xl-order-3,.xl-order-4,.xl-order-5,.xl-order-6,.xl-order-7,.xl-order-8,.xl-order-9,.xl-order-10,.xl-order-11,.xl-order-12,.xl-order-last {order:initial;} 
-  .l-order-1 {order:-1;}
-  .l-order-2 {order:2;}
-  .l-order-3 {order:3;}
-  .l-order-4 {order:4;}
-  .l-order-5 {order:5;}
-  .l-order-6 {order:6;}
-  .l-order-7 {order:7;}
-  .l-order-8 {order:8;}
-  .l-order-9 {order:9;}
-  .l-order-10 {order:10;}
-  .l-order-11 {order:11;}
-  .l-order-12 {order:12;} 
-  .l-order-last {order:99999999;} 
-  .l-1, .grid .l-1.center {width:8.3333%;}
-  .l-2, .grid .l-2.center {width:16.6666%;}
-  .l-five {width:20%;}
-  .l-3, .grid .l-3.center {width:25%;}
-  .l-4, .grid .l-4.center {width:33.3333%;}
-  .l-5, .grid .l-5.center {width:41.6666%;}
-  .l-6, .grid .l-6.center {width:50%;}
-  .l-7, .grid .l-7.center {width:58.3333%;}
-  .l-8, .grid .l-8.center {width:66.6666%;}
-  .l-9, .grid .l-9.center {width:75%;}
-  .l-10, .grid .l-10.center {width:83.3333%;}
-  .l-11, .grid .l-11.center {width:91.6666%;}
-  .l-12, .grid .l-12.center {width:100%}
-  .grid .l-1 {grid-column:span 1;}
-  .grid .l-2 {grid-column:span 2;}
-  .grid .l-3 {grid-column:span 3;}
-  .grid .l-4 {grid-column:span 4;}
-  .grid .l-5 {grid-column:span 5;}
-  .grid .l-6 {grid-column:span 6;}
-  .grid .l-7 {grid-column:span 7;}
-  .grid .l-8 {grid-column:span 8;}
-  .grid .l-9 {grid-column:span 9;}
-  .grid .l-10 {grid-column:span 10;}
-  .grid .l-11 {grid-column:span 11;}
-  .grid .l-12 {grid-column:span 12;}
-  .grid .l-row-1 {grid-row:span 1;}
-  .grid .l-row-2 {grid-row:span 2;}
-  .grid .l-row-3 {grid-row:span 3;}
-  .grid .l-row-4 {grid-row:span 4;}
-  .grid .l-row-5 {grid-row:span 5;}
-  .grid .l-row-6 {grid-row:span 6;}
-  .grid .l-row-7 {grid-row:span 7;}
-  .grid .l-row-8 {grid-row:span 8;}
-  .grid .l-row-9 {grid-row:span 9;}
-  .grid .l-row-10 {grid-row:span 10;}
-  .grid .l-row-11 {grid-row:span 11;}
-  .grid .l-row-12 {grid-row:span 12;}  
-}
- 
-@media screen and (max-width:768px) {
-  .size-960,.size-1140,.size-1280,.size-1520 {max-width:768px;}
-  .hide-xxl,.hide-xl,.hide-l,.hide-s {display:initial!important;}
-  .hide-m {display:none!important;}
-  nav {
-    display:block;
-    cursor:pointer;
-    line-height:3;
+@media screen and (max-width: 1366px) {
+  .hide-xxl,
+  .hide-l,
+  .hide-m,
+  .hide-s {
+    display: initial !important;
   }
-  .top-nav li a {background:none repeat scroll 0 0 #1c3849;}
-  .top-nav > ul {
-    height:0;
-    max-width:100%;
-    overflow:hidden;
-    position:relative;
-    z-index:999;
+  .hide-xl {
+    display: none !important;
   }
-  .top-nav > ul.show-menu,.aside-nav.minimize-on-small > ul.show-menu {height:auto;}
-  .top-nav ul ul {
-    left:0;
-    margin-top:0;
-    position:relative;
-    right:0;
-  } 
-  .top-nav li ul li a {min-width:100%;}
-  .top-nav li {
-    float:none;
-    list-style:none outside none;
-    padding:0;
+  .size-960,
+  .size-1140,
+  .size-1280,
+  .size-1520 {
+    max-width: 1366px;
   }
-  .top-nav li a {
-    color:#fff;
-    display:block;
-    padding:1.25rem 0.625rem;
-    text-align:center;
-    text-decoration:none;
+  .xxl-offset-1,
+  .xxl-offset-2,
+  .xxl-offset-five,
+  .xxl-offset-3,
+  .xxl-offset-4,
+  .xxl-offset-5,
+  .xxl-offset-6,
+  .xxl-offset-7,
+  .xxl-offset-8,
+  .xxl-offset-9,
+  .xxl-offset-10,
+  .xxl-offset-11,
+  .xxl-offset-12 {
+    margin-left: 0;
   }
-  .top-nav li a:hover {
-    background:none repeat scroll 0 0 #152732;
-    color:#fff;
-  }
-  .top-nav li ul,.top-nav li ul li ul {
-    display:block;  
-    overflow:hidden; 
-    height:0;   
-  } 
-  .top-nav > ul ul.show-ul {
-    display:block;
-    height:auto;  
+  .xl-offset-1 {
+    margin-left: 8.3333%;
   }
-  .top-nav li ul li a {
-    background:none repeat scroll 0 0 #2b4c61;
-    padding:0.625rem;
+  .xl-offset-2 {
+    margin-left: 16.6666%;
   }
-  .top-nav li ul li ul li a { background:none repeat scroll 0 0 #456274;}
-  .top-nav {
-    position:fixed;
-    top:0;
-    z-index:10;
-    left:-100%;
-    width:100%!important;
-    bottom:0;
-    background:none repeat scroll 0 0 #1c3849;
-    overflow-y:auto;
-    transition:left 0.20s linear 0s;
-    -o-transition:left 0.20s linear 0s;
-    -ms-transition:left 0.20s linear 0s;
-    -moz-transition:left 0.20s linear 0s;
-    -webkit-transition:left 0.20s linear 0s;
-  }
-  body.show-menu {overflow: hidden;}
-  .show-menu .top-nav {
-    left:0;
-    right:60px
+  .xl-offset-five {
+    margin-left: 20%;
+  }
+  .xl-offset-3 {
+    margin-left: 25%;
+  }
+  .xl-offset-4 {
+    margin-left: 33.3333%;
+  }
+  .xl-offset-5 {
+    margin-left: 41.6666%;
+  }
+  .xl-offset-6 {
+    margin-left: 50%;
+  }
+  .xl-offset-7 {
+    margin-left: 58.3333%;
+  }
+  .xl-offset-8 {
+    margin-left: 66.6666%;
+  }
+  .xl-offset-9 {
+    margin-left: 75%;
+  }
+  .xl-offset-10 {
+    margin-left: 83.3333%;
+  }
+  .xl-offset-11 {
+    margin-left: 91.6666%;
+  }
+  .xl-offset-12 {
+    margin-left: 100%;
+  }
+  .xxl-order-1,
+  .xxl-order-2,
+  .xxl-order-3,
+  .xxl-order-4,
+  .xxl-order-5,
+  .xxl-order-6,
+  .xxl-order-7,
+  .xxl-order-8,
+  .xxl-order-9,
+  .xxl-order-10,
+  .xxl-order-11,
+  .xxl-order-12,
+  .xxl-order-last {
+    order: initial;
+  }
+  .xl-order-1 {
+    order: -1;
+  }
+  .xl-order-2 {
+    order: 2;
+  }
+  .xl-order-3 {
+    order: 3;
+  }
+  .xl-order-4 {
+    order: 4;
+  }
+  .xl-order-5 {
+    order: 5;
+  }
+  .xl-order-6 {
+    order: 6;
+  }
+  .xl-order-7 {
+    order: 7;
+  }
+  .xl-order-8 {
+    order: 8;
+  }
+  .xl-order-9 {
+    order: 9;
+  }
+  .xl-order-10 {
+    order: 10;
+  }
+  .xl-order-11 {
+    order: 11;
+  }
+  .xl-order-12 {
+    order: 12;
+  }
+  .xl-order-last {
+    order: 99999999;
+  }
+  .xl-1,
+  .grid .xl-1.center {
+    width: 8.3333%;
+  }
+  .xl-2,
+  .grid .xl-2.center {
+    width: 16.6666%;
+  }
+  .xl-five {
+    width: 20%;
+  }
+  .xl-3,
+  .grid .xl-3.center {
+    width: 25%;
+  }
+  .xl-4,
+  .grid .xl-4.center {
+    width: 33.3333%;
+  }
+  .xl-5,
+  .grid .xl-5.center {
+    width: 41.6666%;
+  }
+  .xl-6,
+  .grid .xl-6.center {
+    width: 50%;
+  }
+  .xl-7,
+  .grid .xl-7.center {
+    width: 58.3333%;
+  }
+  .xl-8,
+  .grid .xl-8.center {
+    width: 66.6666%;
+  }
+  .xl-9,
+  .grid .xl-9.center {
+    width: 75%;
+  }
+  .xl-10,
+  .grid .xl-10.center {
+    width: 83.3333%;
+  }
+  .xl-11,
+  .grid .xl-11.center {
+    width: 91.6666%;
+  }
+  .xl-12,
+  .grid .xl-12.center {
+    width: 100%;
+  }
+  .grid .xl-1 {
+    grid-column: span 1;
+  }
+  .grid .xl-2 {
+    grid-column: span 2;
+  }
+  .grid .xl-3 {
+    grid-column: span 3;
+  }
+  .grid .xl-4 {
+    grid-column: span 4;
+  }
+  .grid .xl-5 {
+    grid-column: span 5;
+  }
+  .grid .xl-6 {
+    grid-column: span 6;
+  }
+  .grid .xl-7 {
+    grid-column: span 7;
+  }
+  .grid .xl-8 {
+    grid-column: span 8;
+  }
+  .grid .xl-9 {
+    grid-column: span 9;
+  }
+  .grid .xl-10 {
+    grid-column: span 10;
+  }
+  .grid .xl-11 {
+    grid-column: span 11;
+  }
+  .grid .xl-12 {
+    grid-column: span 12;
+  }
+  .grid .xl-row-1 {
+    grid-row: span 1;
+  }
+  .grid .xl-row-2 {
+    grid-row: span 2;
+  }
+  .grid .xl-row-3 {
+    grid-row: span 3;
+  }
+  .grid .xl-row-4 {
+    grid-row: span 4;
+  }
+  .grid .xl-row-5 {
+    grid-row: span 5;
+  }
+  .grid .xl-row-6 {
+    grid-row: span 6;
+  }
+  .grid .xl-row-7 {
+    grid-row: span 7;
+  }
+  .grid .xl-row-8 {
+    grid-row: span 8;
+  }
+  .grid .xl-row-9 {
+    grid-row: span 9;
+  }
+  .grid .xl-row-10 {
+    grid-row: span 10;
+  }
+  .grid .xl-row-11 {
+    grid-row: span 11;
+  }
+  .grid .xl-row-12 {
+    grid-row: span 12;
+  }
+}
+
+@media screen and (max-width: 1140px) {
+  .hide-xxl,
+  .hide-xl,
+  .hide-m,
+  .hide-s {
+    display: initial !important;
+  }
+  .hide-l {
+    display: none !important;
+  }
+  .size-960,
+  .size-1140,
+  .size-1280,
+  .size-1520 {
+    max-width: 1140px;
+  }
+  .xl-offset-1,
+  .xl-offset-2,
+  .xl-offset-five,
+  .xl-offset-3,
+  .xl-offset-4,
+  .xl-offset-5,
+  .xl-offset-6,
+  .xl-offset-7,
+  .xl-offset-8,
+  .xl-offset-9,
+  .xl-offset-10,
+  .xl-offset-11,
+  .xl-offset-12 {
+    margin-left: 0;
+  }
+  .l-offset-1 {
+    margin-left: 8.3333%;
+  }
+  .l-offset-2 {
+    margin-left: 16.6666%;
+  }
+  .l-offset-five {
+    margin-left: 20%;
+  }
+  .l-offset-3 {
+    margin-left: 25%;
+  }
+  .l-offset-4 {
+    margin-left: 33.3333%;
+  }
+  .l-offset-5 {
+    margin-left: 41.6666%;
+  }
+  .l-offset-6 {
+    margin-left: 50%;
+  }
+  .l-offset-7 {
+    margin-left: 58.3333%;
+  }
+  .l-offset-8 {
+    margin-left: 66.6666%;
+  }
+  .l-offset-9 {
+    margin-left: 75%;
+  }
+  .l-offset-10 {
+    margin-left: 83.3333%;
+  }
+  .l-offset-11 {
+    margin-left: 91.6666%;
+  }
+  .l-offset-12 {
+    margin-left: 100%;
+  }
+  .xl-order-1,
+  .xl-order-2,
+  .xl-order-3,
+  .xl-order-4,
+  .xl-order-5,
+  .xl-order-6,
+  .xl-order-7,
+  .xl-order-8,
+  .xl-order-9,
+  .xl-order-10,
+  .xl-order-11,
+  .xl-order-12,
+  .xl-order-last {
+    order: initial;
+  }
+  .l-order-1 {
+    order: -1;
+  }
+  .l-order-2 {
+    order: 2;
+  }
+  .l-order-3 {
+    order: 3;
+  }
+  .l-order-4 {
+    order: 4;
+  }
+  .l-order-5 {
+    order: 5;
+  }
+  .l-order-6 {
+    order: 6;
+  }
+  .l-order-7 {
+    order: 7;
+  }
+  .l-order-8 {
+    order: 8;
+  }
+  .l-order-9 {
+    order: 9;
+  }
+  .l-order-10 {
+    order: 10;
+  }
+  .l-order-11 {
+    order: 11;
+  }
+  .l-order-12 {
+    order: 12;
+  }
+  .l-order-last {
+    order: 99999999;
+  }
+  .l-1,
+  .grid .l-1.center {
+    width: 8.3333%;
+  }
+  .l-2,
+  .grid .l-2.center {
+    width: 16.6666%;
+  }
+  .l-five {
+    width: 20%;
+  }
+  .l-3,
+  .grid .l-3.center {
+    width: 25%;
+  }
+  .l-4,
+  .grid .l-4.center {
+    width: 33.3333%;
+  }
+  .l-5,
+  .grid .l-5.center {
+    width: 41.6666%;
+  }
+  .l-6,
+  .grid .l-6.center {
+    width: 50%;
+  }
+  .l-7,
+  .grid .l-7.center {
+    width: 58.3333%;
+  }
+  .l-8,
+  .grid .l-8.center {
+    width: 66.6666%;
+  }
+  .l-9,
+  .grid .l-9.center {
+    width: 75%;
+  }
+  .l-10,
+  .grid .l-10.center {
+    width: 83.3333%;
+  }
+  .l-11,
+  .grid .l-11.center {
+    width: 91.6666%;
+  }
+  .l-12,
+  .grid .l-12.center {
+    width: 100%;
+  }
+  .grid .l-1 {
+    grid-column: span 1;
+  }
+  .grid .l-2 {
+    grid-column: span 2;
+  }
+  .grid .l-3 {
+    grid-column: span 3;
+  }
+  .grid .l-4 {
+    grid-column: span 4;
+  }
+  .grid .l-5 {
+    grid-column: span 5;
+  }
+  .grid .l-6 {
+    grid-column: span 6;
+  }
+  .grid .l-7 {
+    grid-column: span 7;
+  }
+  .grid .l-8 {
+    grid-column: span 8;
+  }
+  .grid .l-9 {
+    grid-column: span 9;
+  }
+  .grid .l-10 {
+    grid-column: span 10;
+  }
+  .grid .l-11 {
+    grid-column: span 11;
+  }
+  .grid .l-12 {
+    grid-column: span 12;
+  }
+  .grid .l-row-1 {
+    grid-row: span 1;
+  }
+  .grid .l-row-2 {
+    grid-row: span 2;
+  }
+  .grid .l-row-3 {
+    grid-row: span 3;
+  }
+  .grid .l-row-4 {
+    grid-row: span 4;
+  }
+  .grid .l-row-5 {
+    grid-row: span 5;
+  }
+  .grid .l-row-6 {
+    grid-row: span 6;
+  }
+  .grid .l-row-7 {
+    grid-row: span 7;
+  }
+  .grid .l-row-8 {
+    grid-row: span 8;
+  }
+  .grid .l-row-9 {
+    grid-row: span 9;
+  }
+  .grid .l-row-10 {
+    grid-row: span 10;
+  }
+  .grid .l-row-11 {
+    grid-row: span 11;
+  }
+  .grid .l-row-12 {
+    grid-row: span 12;
+  }
+}
+
+@media screen and (max-width: 768px) {
+  .size-960,
+  .size-1140,
+  .size-1280,
+  .size-1520 {
+    max-width: 768px;
+  }
+  .hide-xxl,
+  .hide-xl,
+  .hide-l,
+  .hide-s {
+    display: initial !important;
+  }
+  .hide-m {
+    display: none !important;
+  }
+  nav {
+    display: block;
+    cursor: pointer;
+    line-height: 3;
+  }
+  .top-nav li a {
+    background: none repeat scroll 0 0 #1c3849;
+  }
+  .top-nav > ul {
+    height: 0;
+    max-width: 100%;
+    overflow: hidden;
+    position: relative;
+    z-index: 999;
+  }
+  .top-nav > ul.show-menu,
+  .aside-nav.minimize-on-small > ul.show-menu {
+    height: auto;
+  }
+  .top-nav ul ul {
+    left: 0;
+    margin-top: 0;
+    position: relative;
+    right: 0;
+  }
+  .top-nav li ul li a {
+    min-width: 100%;
+  }
+  .top-nav li {
+    float: none;
+    list-style: none outside none;
+    padding: 0;
+  }
+  .top-nav li a {
+    color: #fff;
+    display: block;
+    padding: 1.25rem 0.625rem;
+    text-align: center;
+    text-decoration: none;
+  }
+  .top-nav li a:hover {
+    background: none repeat scroll 0 0 #152732;
+    color: #fff;
+  }
+  .top-nav li ul,
+  .top-nav li ul li ul {
+    display: block;
+    overflow: hidden;
+    height: 0;
+  }
+  .top-nav > ul ul.show-ul {
+    display: block;
+    height: auto;
+  }
+  .top-nav li ul li a {
+    background: none repeat scroll 0 0 #2b4c61;
+    padding: 0.625rem;
+  }
+  .top-nav li ul li ul li a {
+    background: none repeat scroll 0 0 #456274;
+  }
+  .top-nav {
+    position: fixed;
+    top: 0;
+    z-index: 10;
+    left: -100%;
+    width: 100% !important;
+    bottom: 0;
+    background: none repeat scroll 0 0 #1c3849;
+    overflow-y: auto;
+    transition: left 0.2s linear 0s;
+    -o-transition: left 0.2s linear 0s;
+    -ms-transition: left 0.2s linear 0s;
+    -moz-transition: left 0.2s linear 0s;
+    -webkit-transition: left 0.2s linear 0s;
+  }
+  body.show-menu {
+    overflow: hidden;
+  }
+  .show-menu .top-nav {
+    left: 0;
+    right: 60px;
   }
   .top-nav > ul {
-    height:auto;
-    overflow:auto;
-    position:relative;
-  	top:60px;
+    height: auto;
+    overflow: auto;
+    position: relative;
+    top: 60px;
   }
   .nav-text {
-    color:#fff;
-    display:inline-block;
-    margin-right:0;
-    width:auto;
-    position:fixed;
-    top:0;
-  	left:0;
-  	background:none repeat scroll 0 0 #1c3849;
-  	height:60px;
-  	width:60px;
-  	text-align:center;
-  	line-height:60px;
-  	z-index:50;
-  	padding-top:15px;
-  }
-  .grid.margin2x {grid-column-gap: 20px;}
-  .l-offset-1,.l-offset-2,.l-offset-five,.l-offset-3,.l-offset-4,.l-offset-5,.l-offset-6,.l-offset-7,.l-offset-8,.l-offset-9,.l-offset-10,.l-offset-11,.l-offset-12,
-  .xl-offset-1,.xl-offset-2,.xl-offset-five,.xl-offset-3,.xl-offset-4,.xl-offset-5,.xl-offset-6,.xl-offset-7,.xl-offset-8,.xl-offset-9,.xl-offset-10,.xl-offset-11,.xl-offset-12,
-  .xxl-offset-1,.xxl-offset-2,.xxl-offset-five,.xxl-offset-3,.xxl-offset-4,.xxl-offset-5,.xxl-offset-6,.xxl-offset-7,.xxl-offset-8,.xxl-offset-9,.xxl-offset-10,.xxl-offset-11,.xxl-offset-12 {margin-left:0;}
-  .m-offset-1 {margin-left:8.3333%;}
-  .m-offset-2 {margin-left:16.6666%;}
-  .m-offset-five {margin-left:20%;}
-  .m-offset-3 {margin-left:25%;}
-  .m-offset-4 {margin-left:33.3333%;}
-  .m-offset-5 {margin-left:41.6666%;}
-  .m-offset-6 {margin-left:50%;}
-  .m-offset-7 {margin-left:58.3333%;}
-  .m-offset-8 {margin-left:66.6666%;}
-  .m-offset-9 {margin-left:75%;}
-  .m-offset-10 {margin-left:83.3333%;}
-  .m-offset-11 {margin-left:91.6666%;}
-  .m-offset-12 {margin-left:100%;}
-  .l-order-1,.l-order-2,.l-order-3,.l-order-4,.l-order-5,.l-order-6,.l-order-7,.l-order-8,.l-order-9,.l-order-10,.l-order-11,.l-order-12,.l-order-last {order:initial;}   
-  .m-order-1 {order:-1;}
-  .m-order-2 {order:2;}
-  .m-order-3 {order:3;}
-  .m-order-4 {order:4;}
-  .m-order-5 {order:5;}
-  .m-order-6 {order:6;}
-  .m-order-7 {order:7;}
-  .m-order-8 {order:8;}
-  .m-order-9 {order:9;}
-  .m-order-10 {order:10;}
-  .m-order-11 {order:11;}
-  .m-order-12 {order:12;} 
-  .m-order-last {order:99999999;} 
-  .m-1, .grid .m-1.center {width:8.3333%;}
-  .m-2, .grid .m-2.center {width:16.6666%;}
-  .m-five {width:20%;}
-  .m-3, .grid .m-3.center {width:25%;}
-  .m-4, .grid .m-4.center {width:33.3333%;}
-  .m-5, .grid .m-5.center {width:41.6666%;}
-  .m-6, .grid .m-6.center {width:50%;}
-  .m-7, .grid .m-7.center {width:58.3333%;}
-  .m-8, .grid .m-8.center {width:66.6666%;}
-  .m-9, .grid .m-9.center {width:75%;}
-  .m-10, .grid .m-10.center {width:83.3333%;}
-  .m-11, .grid .m-11.center {width:91.6666%;}
-  .m-12, .grid .m-12.center {width:100%}
-  .grid .m-1 {grid-column:span 1;}
-  .grid .m-2 {grid-column:span 2;}
-  .grid .m-3 {grid-column:span 3;}
-  .grid .m-4 {grid-column:span 4;}
-  .grid .m-5 {grid-column:span 5;}
-  .grid .m-6 {grid-column:span 6;}
-  .grid .m-7 {grid-column:span 7;}
-  .grid .m-8 {grid-column:span 8;}
-  .grid .m-9 {grid-column:span 9;}
-  .grid .m-10 {grid-column:span 10;}
-  .grid .m-11 {grid-column:span 11;}
-  .grid .m-12 {grid-column:span 12;}
-  .grid .m-row-1 {grid-row:span 1;}
-  .grid .m-row-2 {grid-row:span 2;}
-  .grid .m-row-3 {grid-row:span 3;}
-  .grid .m-row-4 {grid-row:span 4;}
-  .grid .m-row-5 {grid-row:span 5;}
-  .grid .m-row-6 {grid-row:span 6;}
-  .grid .m-row-7 {grid-row:span 7;}
-  .grid .m-row-8 {grid-row:span 8;}
-  .grid .m-row-9 {grid-row:span 9;}
-  .grid .m-row-10 {grid-row:span 10;}
-  .grid .m-row-11 {grid-row:span 11;}
-  .grid .m-row-12 {grid-row:span 12;}  
+    color: #fff;
+    display: inline-block;
+    margin-right: 0;
+    width: auto;
+    position: fixed;
+    top: 0;
+    left: 0;
+    background: none repeat scroll 0 0 #1c3849;
+    height: 60px;
+    width: 60px;
+    text-align: center;
+    line-height: 60px;
+    z-index: 50;
+    padding-top: 15px;
+  }
+  .grid.margin2x {
+    grid-column-gap: 20px;
+  }
+  .l-offset-1,
+  .l-offset-2,
+  .l-offset-five,
+  .l-offset-3,
+  .l-offset-4,
+  .l-offset-5,
+  .l-offset-6,
+  .l-offset-7,
+  .l-offset-8,
+  .l-offset-9,
+  .l-offset-10,
+  .l-offset-11,
+  .l-offset-12,
+  .xl-offset-1,
+  .xl-offset-2,
+  .xl-offset-five,
+  .xl-offset-3,
+  .xl-offset-4,
+  .xl-offset-5,
+  .xl-offset-6,
+  .xl-offset-7,
+  .xl-offset-8,
+  .xl-offset-9,
+  .xl-offset-10,
+  .xl-offset-11,
+  .xl-offset-12,
+  .xxl-offset-1,
+  .xxl-offset-2,
+  .xxl-offset-five,
+  .xxl-offset-3,
+  .xxl-offset-4,
+  .xxl-offset-5,
+  .xxl-offset-6,
+  .xxl-offset-7,
+  .xxl-offset-8,
+  .xxl-offset-9,
+  .xxl-offset-10,
+  .xxl-offset-11,
+  .xxl-offset-12 {
+    margin-left: 0;
+  }
+  .m-offset-1 {
+    margin-left: 8.3333%;
+  }
+  .m-offset-2 {
+    margin-left: 16.6666%;
+  }
+  .m-offset-five {
+    margin-left: 20%;
+  }
+  .m-offset-3 {
+    margin-left: 25%;
+  }
+  .m-offset-4 {
+    margin-left: 33.3333%;
+  }
+  .m-offset-5 {
+    margin-left: 41.6666%;
+  }
+  .m-offset-6 {
+    margin-left: 50%;
+  }
+  .m-offset-7 {
+    margin-left: 58.3333%;
+  }
+  .m-offset-8 {
+    margin-left: 66.6666%;
+  }
+  .m-offset-9 {
+    margin-left: 75%;
+  }
+  .m-offset-10 {
+    margin-left: 83.3333%;
+  }
+  .m-offset-11 {
+    margin-left: 91.6666%;
+  }
+  .m-offset-12 {
+    margin-left: 100%;
+  }
+  .l-order-1,
+  .l-order-2,
+  .l-order-3,
+  .l-order-4,
+  .l-order-5,
+  .l-order-6,
+  .l-order-7,
+  .l-order-8,
+  .l-order-9,
+  .l-order-10,
+  .l-order-11,
+  .l-order-12,
+  .l-order-last {
+    order: initial;
+  }
+  .m-order-1 {
+    order: -1;
+  }
+  .m-order-2 {
+    order: 2;
+  }
+  .m-order-3 {
+    order: 3;
+  }
+  .m-order-4 {
+    order: 4;
+  }
+  .m-order-5 {
+    order: 5;
+  }
+  .m-order-6 {
+    order: 6;
+  }
+  .m-order-7 {
+    order: 7;
+  }
+  .m-order-8 {
+    order: 8;
+  }
+  .m-order-9 {
+    order: 9;
+  }
+  .m-order-10 {
+    order: 10;
+  }
+  .m-order-11 {
+    order: 11;
+  }
+  .m-order-12 {
+    order: 12;
+  }
+  .m-order-last {
+    order: 99999999;
+  }
+  .m-1,
+  .grid .m-1.center {
+    width: 8.3333%;
+  }
+  .m-2,
+  .grid .m-2.center {
+    width: 16.6666%;
+  }
+  .m-five {
+    width: 20%;
+  }
+  .m-3,
+  .grid .m-3.center {
+    width: 25%;
+  }
+  .m-4,
+  .grid .m-4.center {
+    width: 33.3333%;
+  }
+  .m-5,
+  .grid .m-5.center {
+    width: 41.6666%;
+  }
+  .m-6,
+  .grid .m-6.center {
+    width: 50%;
+  }
+  .m-7,
+  .grid .m-7.center {
+    width: 58.3333%;
+  }
+  .m-8,
+  .grid .m-8.center {
+    width: 66.6666%;
+  }
+  .m-9,
+  .grid .m-9.center {
+    width: 75%;
+  }
+  .m-10,
+  .grid .m-10.center {
+    width: 83.3333%;
+  }
+  .m-11,
+  .grid .m-11.center {
+    width: 91.6666%;
+  }
+  .m-12,
+  .grid .m-12.center {
+    width: 100%;
+  }
+  .grid .m-1 {
+    grid-column: span 1;
+  }
+  .grid .m-2 {
+    grid-column: span 2;
+  }
+  .grid .m-3 {
+    grid-column: span 3;
+  }
+  .grid .m-4 {
+    grid-column: span 4;
+  }
+  .grid .m-5 {
+    grid-column: span 5;
+  }
+  .grid .m-6 {
+    grid-column: span 6;
+  }
+  .grid .m-7 {
+    grid-column: span 7;
+  }
+  .grid .m-8 {
+    grid-column: span 8;
+  }
+  .grid .m-9 {
+    grid-column: span 9;
+  }
+  .grid .m-10 {
+    grid-column: span 10;
+  }
+  .grid .m-11 {
+    grid-column: span 11;
+  }
+  .grid .m-12 {
+    grid-column: span 12;
+  }
+  .grid .m-row-1 {
+    grid-row: span 1;
+  }
+  .grid .m-row-2 {
+    grid-row: span 2;
+  }
+  .grid .m-row-3 {
+    grid-row: span 3;
+  }
+  .grid .m-row-4 {
+    grid-row: span 4;
+  }
+  .grid .m-row-5 {
+    grid-row: span 5;
+  }
+  .grid .m-row-6 {
+    grid-row: span 6;
+  }
+  .grid .m-row-7 {
+    grid-row: span 7;
+  }
+  .grid .m-row-8 {
+    grid-row: span 8;
+  }
+  .grid .m-row-9 {
+    grid-row: span 9;
+  }
+  .grid .m-row-10 {
+    grid-row: span 10;
+  }
+  .grid .m-row-11 {
+    grid-row: span 11;
+  }
+  .grid .m-row-12 {
+    grid-row: span 12;
+  }
 }
 
-@media screen and (max-width:480px) {
-  .size-960,.size-1140,.size-1280,.size-1520 {max-width:480px;}
-  .aside-nav li a {text-align: center;}
+@media screen and (max-width: 480px) {
+  .size-960,
+  .size-1140,
+  .size-1280,
+  .size-1520 {
+    max-width: 480px;
+  }
+  .aside-nav li a {
+    text-align: center;
+  }
   .minimize-on-small .aside-nav-text {
-    background:#152732 none repeat scroll 0 0;
-    color:#fff;
-    cursor:pointer;
-    display:block;
-    font-size:1.2rem;
-    line-height:3;
-    max-width:100%;
-    padding-right:0.625rem;
-    text-align:center;
-    vertical-align:middle;
+    background: #152732 none repeat scroll 0 0;
+    color: #fff;
+    cursor: pointer;
+    display: block;
+    font-size: 1.2rem;
+    line-height: 3;
+    max-width: 100%;
+    padding-right: 0.625rem;
+    text-align: center;
+    vertical-align: middle;
   }
   .aside-nav-text:after {
-    content:"\f008";
-    font-family:"mfg";
-    font-size:1.1rem;
-    margin-left:0.5rem;
-    text-align:right;
+    content: "\f008";
+    font-family: "mfg";
+    font-size: 1.1rem;
+    margin-left: 0.5rem;
+    text-align: right;
   }
   .aside-nav.minimize-on-small > ul {
-    height:0;
-    overflow:hidden;
-  }
-  .hide-xxl,.hide-xl,.hide-l,.hide-m {display:initial!important;}
-  .hide-s {display:none!important;}
-  .count-number {margin-right:-1.25rem;} 
-  .m-offset-1,.m-offset-2,.m-offset-five,.m-offset-3,.m-offset-4,.m-offset-5,.m-offset-6,.m-offset-7,.m-offset-8,.m-offset-9,.m-offset-10,.m-offset-11,.m-offset-12,
-  .l-offset-1,.l-offset-2,.l-offset-five,.l-offset-3,.l-offset-4,.l-offset-5,.l-offset-6,.l-offset-7,.l-offset-8,.l-offset-9,.l-offset-10,.l-offset-11,.l-offset-12,
-  .xl-offset-1,.xl-offset-2,.xl-offset-five,.xl-offset-3,.xl-offset-4,.xl-offset-5,.xl-offset-6,.xl-offset-7,.xl-offset-8,.xl-offset-9,.xl-offset-10,.xl-offset-11,.xl-offset-12,
-  .xxl-offset-1,.xxl-offset-2,.xxl-offset-five,.xxl-offset-3,.xxl-offset-4,.xxl-offset-5,.xxl-offset-6,.xxl-offset-7,.xxl-offset-8,.xxl-offset-9,.xxl-offset-10,.xxl-offset-11,.xxl-offset-12 {margin-left:0;}
-  .s-offset-1 {margin-left:8.3333%;}
-  .s-offset-2 {margin-left:16.6666%;}
-  .s-offset-five {margin-left:20%;}
-  .s-offset-3 {margin-left:25%;}
-  .s-offset-4 {margin-left:33.3333%;}
-  .s-offset-5 {margin-left:41.6666%;}
-  .s-offset-6 {margin-left:50%;}
-  .s-offset-7 {margin-left:58.3333%;}
-  .s-offset-8 {margin-left:66.6666%;}
-  .s-offset-9 {margin-left:75%;}
-  .s-offset-10 {margin-left:83.3333%;}
-  .s-offset-11 {margin-left:91.6666%;}
-  .s-offset-12 {margin-left:100%;}
-  .m-order-1,.m-order-2,.m-order-3,.m-order-4,.m-order-5,.m-order-6,.m-order-7,.m-order-8,.m-order-9,.m-order-10,.m-order-11,.m-order-12,.m-order-last {order:initial;}  
-  .s-order-1 {order:-1;}
-  .s-order-2 {order:2;}
-  .s-order-3 {order:3;}
-  .s-order-4 {order:4;}
-  .s-order-5 {order:5;}
-  .s-order-6 {order:6;}
-  .s-order-7 {order:7;}
-  .s-order-8 {order:8;}
-  .s-order-9 {order:9;}
-  .s-order-10 {order:10;}
-  .s-order-11 {order:11;}
-  .s-order-12 {order:12;} 
-  .s-order-last {order:99999999;} 
-  .s-1, .grid .s-1.center {width:8.3333%;}
-  .s-2, .grid .s-2.center {width:16.6666%;}
-  .s-five {width:20%;}
-  .s-3, .grid .s-3.center {width:25%;}
-  .s-4, .grid .s-4.center {width:33.3333%;}
-  .s-5, .grid .s-5.center {width:41.6666%;}
-  .s-6, .grid .s-6.center {width:50%;}
-  .s-7, .grid .s-7.center {width:58.3333%;}
-  .s-8, .grid .s-8.center {width:66.6666%;}
-  .s-9, .grid .s-9.center {width:75%;}
-  .s-10, .grid .s-10.center {width:83.3333%;}
-  .s-11, .grid .s-11.center {width:91.6666%;}
-  .s-12, .grid .s-12.center {width:100%}
-  .grid .s-1 {grid-column:span 1;}
-  .grid .s-2 {grid-column:span 2;}
-  .grid .s-3 {grid-column:span 3;}
-  .grid .s-4 {grid-column:span 4;}
-  .grid .s-5 {grid-column:span 5;}
-  .grid .s-6 {grid-column:span 6;}
-  .grid .s-7 {grid-column:span 7;}
-  .grid .s-8 {grid-column:span 8;}
-  .grid .s-9 {grid-column:span 9;}
-  .grid .s-10 {grid-column:span 10;}
-  .grid .s-11 {grid-column:span 11;}
-  .grid .s-12 {grid-column:span 12;}
-  .grid .s-row-1 {grid-row:span 1;}
-  .grid .s-row-2 {grid-row:span 2;}
-  .grid .s-row-3 {grid-row:span 3;}
-  .grid .s-row-4 {grid-row:span 4;}
-  .grid .s-row-5 {grid-row:span 5;}
-  .grid .s-row-6 {grid-row:span 6;}
-  .grid .s-row-7 {grid-row:span 7;}
-  .grid .s-row-8 {grid-row:span 8;}
-  .grid .s-row-9 {grid-row:span 9;}
-  .grid .s-row-10 {grid-row:span 10;}
-  .grid .s-row-11 {grid-row:span 11;}
-  .grid .s-row-12 {grid-row:span 12;}  
-}
-.grid .s-1,.grid .s-2,.grid .s-five,.grid .s-3,.grid .s-4,.grid .s-5,.grid .s-6,.grid .s-7,.grid .s-8,.grid .s-9,.grid .s-10,.grid .s-11,.grid .s-12,.grid .m-1,.grid .m-2,.grid .m-five,.grid .m-3,.grid .m-4,.grid .m-5,.grid .m-6,.grid .m-7,.grid .m-8,.grid .m-9,.grid .m-10,.grid .m-11,.grid .m-12,.grid .l-1,.grid .l-2,.grid .l-five,.grid .l-3,.grid .l-4,.grid .l-5,.grid .l-6,.grid .l-7,.grid .l-8,.grid .l-9,.grid .l-10,.grid .l-11,.grid .l-12,.grid .xl-1,.grid .xl-2,.grid .xl-five,.grid .xl-3,.grid .xl-4,.grid .xl-5,.grid .xl-6,.grid .xl-7,.grid .xl-8,.grid .xl-9,.grid .xl-10,.grid .xl-11,.grid .xl-12,.grid .xxl-1,.grid .xxl-2,.grid .xxl-five,.grid .xxl-3,.grid .xxl-4,.grid .xxl-5,.grid .xxl-6,.grid .xxl-7,.grid .xxl-8,.grid .xxl-9,.grid .xxl-10,.grid .xxl-11,.grid .xxl-12 {float:none; width:auto;}  
+    height: 0;
+    overflow: hidden;
+  }
+  .hide-xxl,
+  .hide-xl,
+  .hide-l,
+  .hide-m {
+    display: initial !important;
+  }
+  .hide-s {
+    display: none !important;
+  }
+  .count-number {
+    margin-right: -1.25rem;
+  }
+  .m-offset-1,
+  .m-offset-2,
+  .m-offset-five,
+  .m-offset-3,
+  .m-offset-4,
+  .m-offset-5,
+  .m-offset-6,
+  .m-offset-7,
+  .m-offset-8,
+  .m-offset-9,
+  .m-offset-10,
+  .m-offset-11,
+  .m-offset-12,
+  .l-offset-1,
+  .l-offset-2,
+  .l-offset-five,
+  .l-offset-3,
+  .l-offset-4,
+  .l-offset-5,
+  .l-offset-6,
+  .l-offset-7,
+  .l-offset-8,
+  .l-offset-9,
+  .l-offset-10,
+  .l-offset-11,
+  .l-offset-12,
+  .xl-offset-1,
+  .xl-offset-2,
+  .xl-offset-five,
+  .xl-offset-3,
+  .xl-offset-4,
+  .xl-offset-5,
+  .xl-offset-6,
+  .xl-offset-7,
+  .xl-offset-8,
+  .xl-offset-9,
+  .xl-offset-10,
+  .xl-offset-11,
+  .xl-offset-12,
+  .xxl-offset-1,
+  .xxl-offset-2,
+  .xxl-offset-five,
+  .xxl-offset-3,
+  .xxl-offset-4,
+  .xxl-offset-5,
+  .xxl-offset-6,
+  .xxl-offset-7,
+  .xxl-offset-8,
+  .xxl-offset-9,
+  .xxl-offset-10,
+  .xxl-offset-11,
+  .xxl-offset-12 {
+    margin-left: 0;
+  }
+  .s-offset-1 {
+    margin-left: 8.3333%;
+  }
+  .s-offset-2 {
+    margin-left: 16.6666%;
+  }
+  .s-offset-five {
+    margin-left: 20%;
+  }
+  .s-offset-3 {
+    margin-left: 25%;
+  }
+  .s-offset-4 {
+    margin-left: 33.3333%;
+  }
+  .s-offset-5 {
+    margin-left: 41.6666%;
+  }
+  .s-offset-6 {
+    margin-left: 50%;
+  }
+  .s-offset-7 {
+    margin-left: 58.3333%;
+  }
+  .s-offset-8 {
+    margin-left: 66.6666%;
+  }
+  .s-offset-9 {
+    margin-left: 75%;
+  }
+  .s-offset-10 {
+    margin-left: 83.3333%;
+  }
+  .s-offset-11 {
+    margin-left: 91.6666%;
+  }
+  .s-offset-12 {
+    margin-left: 100%;
+  }
+  .m-order-1,
+  .m-order-2,
+  .m-order-3,
+  .m-order-4,
+  .m-order-5,
+  .m-order-6,
+  .m-order-7,
+  .m-order-8,
+  .m-order-9,
+  .m-order-10,
+  .m-order-11,
+  .m-order-12,
+  .m-order-last {
+    order: initial;
+  }
+  .s-order-1 {
+    order: -1;
+  }
+  .s-order-2 {
+    order: 2;
+  }
+  .s-order-3 {
+    order: 3;
+  }
+  .s-order-4 {
+    order: 4;
+  }
+  .s-order-5 {
+    order: 5;
+  }
+  .s-order-6 {
+    order: 6;
+  }
+  .s-order-7 {
+    order: 7;
+  }
+  .s-order-8 {
+    order: 8;
+  }
+  .s-order-9 {
+    order: 9;
+  }
+  .s-order-10 {
+    order: 10;
+  }
+  .s-order-11 {
+    order: 11;
+  }
+  .s-order-12 {
+    order: 12;
+  }
+  .s-order-last {
+    order: 99999999;
+  }
+  .s-1,
+  .grid .s-1.center {
+    width: 8.3333%;
+  }
+  .s-2,
+  .grid .s-2.center {
+    width: 16.6666%;
+  }
+  .s-five {
+    width: 20%;
+  }
+  .s-3,
+  .grid .s-3.center {
+    width: 25%;
+  }
+  .s-4,
+  .grid .s-4.center {
+    width: 33.3333%;
+  }
+  .s-5,
+  .grid .s-5.center {
+    width: 41.6666%;
+  }
+  .s-6,
+  .grid .s-6.center {
+    width: 50%;
+  }
+  .s-7,
+  .grid .s-7.center {
+    width: 58.3333%;
+  }
+  .s-8,
+  .grid .s-8.center {
+    width: 66.6666%;
+  }
+  .s-9,
+  .grid .s-9.center {
+    width: 75%;
+  }
+  .s-10,
+  .grid .s-10.center {
+    width: 83.3333%;
+  }
+  .s-11,
+  .grid .s-11.center {
+    width: 91.6666%;
+  }
+  .s-12,
+  .grid .s-12.center {
+    width: 100%;
+  }
+  .grid .s-1 {
+    grid-column: span 1;
+  }
+  .grid .s-2 {
+    grid-column: span 2;
+  }
+  .grid .s-3 {
+    grid-column: span 3;
+  }
+  .grid .s-4 {
+    grid-column: span 4;
+  }
+  .grid .s-5 {
+    grid-column: span 5;
+  }
+  .grid .s-6 {
+    grid-column: span 6;
+  }
+  .grid .s-7 {
+    grid-column: span 7;
+  }
+  .grid .s-8 {
+    grid-column: span 8;
+  }
+  .grid .s-9 {
+    grid-column: span 9;
+  }
+  .grid .s-10 {
+    grid-column: span 10;
+  }
+  .grid .s-11 {
+    grid-column: span 11;
+  }
+  .grid .s-12 {
+    grid-column: span 12;
+  }
+  .grid .s-row-1 {
+    grid-row: span 1;
+  }
+  .grid .s-row-2 {
+    grid-row: span 2;
+  }
+  .grid .s-row-3 {
+    grid-row: span 3;
+  }
+  .grid .s-row-4 {
+    grid-row: span 4;
+  }
+  .grid .s-row-5 {
+    grid-row: span 5;
+  }
+  .grid .s-row-6 {
+    grid-row: span 6;
+  }
+  .grid .s-row-7 {
+    grid-row: span 7;
+  }
+  .grid .s-row-8 {
+    grid-row: span 8;
+  }
+  .grid .s-row-9 {
+    grid-row: span 9;
+  }
+  .grid .s-row-10 {
+    grid-row: span 10;
+  }
+  .grid .s-row-11 {
+    grid-row: span 11;
+  }
+  .grid .s-row-12 {
+    grid-row: span 12;
+  }
+}
+.grid .s-1,
+.grid .s-2,
+.grid .s-five,
+.grid .s-3,
+.grid .s-4,
+.grid .s-5,
+.grid .s-6,
+.grid .s-7,
+.grid .s-8,
+.grid .s-9,
+.grid .s-10,
+.grid .s-11,
+.grid .s-12,
+.grid .m-1,
+.grid .m-2,
+.grid .m-five,
+.grid .m-3,
+.grid .m-4,
+.grid .m-5,
+.grid .m-6,
+.grid .m-7,
+.grid .m-8,
+.grid .m-9,
+.grid .m-10,
+.grid .m-11,
+.grid .m-12,
+.grid .l-1,
+.grid .l-2,
+.grid .l-five,
+.grid .l-3,
+.grid .l-4,
+.grid .l-5,
+.grid .l-6,
+.grid .l-7,
+.grid .l-8,
+.grid .l-9,
+.grid .l-10,
+.grid .l-11,
+.grid .l-12,
+.grid .xl-1,
+.grid .xl-2,
+.grid .xl-five,
+.grid .xl-3,
+.grid .xl-4,
+.grid .xl-5,
+.grid .xl-6,
+.grid .xl-7,
+.grid .xl-8,
+.grid .xl-9,
+.grid .xl-10,
+.grid .xl-11,
+.grid .xl-12,
+.grid .xxl-1,
+.grid .xxl-2,
+.grid .xxl-five,
+.grid .xxl-3,
+.grid .xxl-4,
+.grid .xxl-5,
+.grid .xxl-6,
+.grid .xxl-7,
+.grid .xxl-8,
+.grid .xxl-9,
+.grid .xxl-10,
+.grid .xxl-11,
+.grid .xxl-12 {
+  float: none;
+  width: auto;
+}
 .center {
-  float:none;
-  margin:0 auto;
-  display:block;
+  float: none;
+  margin: 0 auto;
+  display: block;
 }
 .grid .center {
-  justify-self:center;
-  margin:auto;
-  grid-column:1 / -1;
+  justify-self: center;
+  margin: auto;
+  grid-column: 1 / -1;
 }
 .grid .grid {
-  padding:0;
-  width:100%;
-}
\ No newline at end of file
+  padding: 0;
+  width: 100%;
+}
diff --git a/css/template-style.css b/css/template-style.css
index 5a5684f..c9a76bc 100644
--- a/css/template-style.css
+++ b/css/template-style.css
@@ -9,92 +9,128 @@ p {
   font-size: 0.85rem;
   line-height: 1.6rem;
 }
-a, a:link, a:visited, a:hover, a:active { 
-color: #000000;
-}
-h1, h2, h3, h4, h5, h6, .h1, .h2, .h3, .h4, .h5, .h6 {
-  color: #000;                                         
+a,
+a:link,
+a:visited,
+a:hover,
+a:active {
+  color: #000000;
+}
+h1,
+h2,
+h3,
+h4,
+h5,
+h6,
+.h1,
+.h2,
+.h3,
+.h4,
+.h5,
+.h6 {
+  color: #000;
   margin-bottom: 15px;
   margin-top: 0;
 }
-h1, .h1 {
+h1,
+.h1 {
   font-size: 1.8rem;
 }
-h2, .h2 {
+h2,
+.h2 {
   font-size: 1.4rem;
 }
-h3, .h3 {
+h3,
+.h3 {
   font-size: 1.2rem;
 }
-h4, .h4 {
+h4,
+.h4 {
   font-size: 1.1rem;
 }
-h5, .h5 {
+h5,
+.h5 {
   font-size: 1rem;
 }
-h6, .h6 {
+h6,
+.h6 {
   font-size: 0.9rem;
 }
-h1.headline, .h1.headline {
-  font-size: 3.8rem; 
+h1.headline,
+.h1.headline {
+  font-size: 3.8rem;
   letter-spacing: -2.5px;
 }
-h2.headline, .h2.headline {
-  font-size: 3rem; 
-  letter-spacing: -2px; 
+h2.headline,
+.h2.headline {
+  font-size: 3rem;
+  letter-spacing: -2px;
 }
-h3.headline, .h3.headline {
+h3.headline,
+.h3.headline {
   font-size: 2.6rem;
   letter-spacing: -2px;
 }
-h4.headline, .h4.headline {
+h4.headline,
+.h4.headline {
   font-size: 2.4rem;
-  letter-spacing: -1.5px; 
+  letter-spacing: -1.5px;
 }
-h5.headline, .h5.headline {
+h5.headline,
+.h5.headline {
   font-size: 2.2rem;
-  letter-spacing: -1.4px; 
+  letter-spacing: -1.4px;
 }
-h6.headline, .h6.headline {
+h6.headline,
+.h6.headline {
   font-size: 2rem;
   letter-spacing: -1.3px;
 }
-.text-size-12, .text-l-size-12 {
+.text-size-12,
+.text-l-size-12 {
   font-size: 12px !important;
   line-height: 1.4;
 }
-.text-size-16, .text-l-size-16 {
+.text-size-16,
+.text-l-size-16 {
   font-size: 16px !important;
   line-height: 1.4;
 }
-.text-size-20, .text-l-size-20 {
+.text-size-20,
+.text-l-size-20 {
   font-size: 20px !important;
   line-height: 1.4;
 }
-.text-size-25, .text-l-size-25 {
+.text-size-25,
+.text-l-size-25 {
   font-size: 25px !important;
   line-height: 1.4;
 }
-.text-size-30, .text-l-size-30 {
+.text-size-30,
+.text-l-size-30 {
   font-size: 30px !important;
   line-height: 1.4;
 }
-.text-size-40, .text-l-size-40 {
+.text-size-40,
+.text-l-size-40 {
   font-size: 40px !important;
   line-height: 1.4;
 }
-.text-size-50, .text-l-size-50 {
+.text-size-50,
+.text-l-size-50 {
   font-size: 50px !important;
   line-height: 1.4;
 }
-.text-size-60, .text-l-size-60 {
+.text-size-60,
+.text-l-size-60 {
   font-size: 60px !important;
   line-height: 1.4;
 }
-.text-size-70, .text-l-size-70 {
+.text-size-70,
+.text-l-size-70 {
   font-size: 70px !important;
   line-height: 1.4;
-} 
+}
 .text-center {
   text-align: center;
 }
@@ -104,7 +140,9 @@ h6.headline, .h6.headline {
 .text-thin {
   font-weight: 300;
 }
-b, strong, .text-strong {
+b,
+strong,
+.text-strong {
   font-weight: 700;
 }
 .text-extra-strong {
@@ -140,19 +178,21 @@ a.text-tag:link:hover {
   background: #002633 none repeat scroll 0 0;
   border: 1px solid #002633;
   color: #fff;
-  transition: all 0.20s linear 0s;
-  -o-transition: all 0.20s linear 0s;
-  -ms-transition: all 0.20s linear 0s;
-  -moz-transition: all 0.20s linear 0s;
-  -webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
 }
 
-ul.text-list, ol.text-list {
+ul.text-list,
+ol.text-list {
   font-size: 0.85rem;
   line-height: 1.8rem;
   padding: 0 16px;
 }
-ul.text-list ul, ol.text-list ol {
+ul.text-list ul,
+ol.text-list ol {
   padding: 0 14px;
 }
 iframe {
@@ -171,68 +211,123 @@ iframe {
 
 /* Tables */
 table {
-	background:none repeat scroll 0 0 #fff;
-	border:0;
-	font-size: 0.85rem;
+  background: none repeat scroll 0 0 #fff;
+  border: 0;
+  font-size: 0.85rem;
   line-height: 1.6rem;
-	}
-table tr td, table tr th {padding:10px;}
-table tfoot, table thead {
-  background:none repeat scroll 0 0 #f5f5f5;
-  border-top:1px solid #f0f0f0;
-  border-bottom:1px solid #f0f0f0;
+}
+table tr td,
+table tr th {
+  padding: 10px;
+}
+table tfoot,
+table thead {
+  background: none repeat scroll 0 0 #f5f5f5;
+  border-top: 1px solid #f0f0f0;
+  border-bottom: 1px solid #f0f0f0;
 }
 table tr:nth-of-type(2n) {
-  background:none repeat scroll 0 0 #f5f5f5;
-  border-top:1px solid #f0f0f0;
-  border-bottom:1px solid #f0f0f0;
+  background: none repeat scroll 0 0 #f5f5f5;
+  border-top: 1px solid #f0f0f0;
+  border-bottom: 1px solid #f0f0f0;
+}
+th {
+  border-right: 1px solid #fff;
+}
+td {
+  border-right: 1px solid #fff;
 }
-th {border-right:1px solid #fff;}
-td {border-right:1px solid #fff;}
-
 
 /* Backgrounds */
-.background-white-hightlight .top-nav .active-item > a, .background-white-hightlight .top-nav li a:hover, .background-white-hightlight .aside-nav li a:hover, 
-.background-white-hightlight .aside-nav > ul > li.active-item > a:link, .background-white-hightlight .aside-nav > ul > li.active-item > a:visited,
-.primary-color-white .background-primary-hightlight .top-nav .active-item > a, .primary-color-white .background-primary-hightlight .top-nav li a:hover, .primary-color-white .background-primary-hightlight .aside-nav li a:hover, 
-.primary-color-white .background-primary-hightlight .aside-nav > ul > li.active-item > a:link, .primary-color-white .background-primary-hightlight .aside-nav > ul > li.active-item > a:visited {
+.background-white-hightlight .top-nav .active-item > a,
+.background-white-hightlight .top-nav li a:hover,
+.background-white-hightlight .aside-nav li a:hover,
+.background-white-hightlight .aside-nav > ul > li.active-item > a:link,
+.background-white-hightlight .aside-nav > ul > li.active-item > a:visited,
+.primary-color-white .background-primary-hightlight .top-nav .active-item > a,
+.primary-color-white .background-primary-hightlight .top-nav li a:hover,
+.primary-color-white .background-primary-hightlight .aside-nav li a:hover,
+.primary-color-white
+  .background-primary-hightlight
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:link,
+.primary-color-white
+  .background-primary-hightlight
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:visited {
   background: #fff none repeat scroll 0 0;
   color: #002633;
 }
 
-.background-primary-hightlight .top-nav .active-item > a, .background-primary-hightlight .top-nav li a:hover, .background-primary-hightlight .aside-nav li a:hover, 
-.background-primary-hightlight .aside-nav > ul > li.active-item > a:link, .background-primary-hightlight .aside-nav > ul > li.active-item > a:visited,
-.primary-color-primary .background-primary-hightlight .top-nav .active-item > a, .primary-color-primary .background-primary-hightlight .top-nav li a:hover, .primary-color-primary .background-primary-hightlight .aside-nav li a:hover, 
-.primary-color-primary .background-primary-hightlight .aside-nav > ul > li.active-item > a:link, .primary-color-primary .background-primary-hightlight .aside-nav > ul > li.active-item > a:visited {
-  background: #C81010 none repeat scroll 0 0;
+.background-primary-hightlight .top-nav .active-item > a,
+.background-primary-hightlight .top-nav li a:hover,
+.background-primary-hightlight .aside-nav li a:hover,
+.background-primary-hightlight .aside-nav > ul > li.active-item > a:link,
+.background-primary-hightlight .aside-nav > ul > li.active-item > a:visited,
+.primary-color-primary .background-primary-hightlight .top-nav .active-item > a,
+.primary-color-primary .background-primary-hightlight .top-nav li a:hover,
+.primary-color-primary .background-primary-hightlight .aside-nav li a:hover,
+.primary-color-primary
+  .background-primary-hightlight
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:link,
+.primary-color-primary
+  .background-primary-hightlight
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:visited {
+  background: #c81010 none repeat scroll 0 0;
   color: #fff;
 }
-.background-dark-hightlight .top-nav .active-item > a, .background-dark-hightlight .top-nav li a:hover, .background-dark-hightlight .aside-nav li a:hover, 
-.background-dark-hightlight .aside-nav > ul > li.active-item > a:link, .background-dark-hightlight .aside-nav > ul > li.active-item > a:visited,
-.primary-color-dark .background-primary-hightlight .top-nav .active-item > a, .primary-color-dark .background-primary-hightlight .top-nav li a:hover, .primary-color-dark .background-primary-hightlight .aside-nav li a:hover, 
-.primary-color-dark .background-primary-hightlight .aside-nav > ul > li.active-item > a:link, .primary-color-dark .background-primary-hightlight .aside-nav > ul > li.active-item > a:visited {
+.background-dark-hightlight .top-nav .active-item > a,
+.background-dark-hightlight .top-nav li a:hover,
+.background-dark-hightlight .aside-nav li a:hover,
+.background-dark-hightlight .aside-nav > ul > li.active-item > a:link,
+.background-dark-hightlight .aside-nav > ul > li.active-item > a:visited,
+.primary-color-dark .background-primary-hightlight .top-nav .active-item > a,
+.primary-color-dark .background-primary-hightlight .top-nav li a:hover,
+.primary-color-dark .background-primary-hightlight .aside-nav li a:hover,
+.primary-color-dark
+  .background-primary-hightlight
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:link,
+.primary-color-dark
+  .background-primary-hightlight
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:visited {
   background: #002633 none repeat scroll 0 0;
   color: #fff;
 }
 .background-none {
-  background: rgba(0, 0, 0, 0) none repeat scroll 0 0!important;
+  background: rgba(0, 0, 0, 0) none repeat scroll 0 0 !important;
   border: 0;
 }
 
 /* Breaks */
 hr.break {
   border: 0;
-  border-top: 1px solid #e5e5e5; 
+  border-top: 1px solid #e5e5e5;
   display: block;
   margin: 40px 0;
 }
 hr.break:after {
-clear:both;
-content:".";
-display:block;
-height:0;
-line-height:0;
-visibility:hidden;
+  clear: both;
+  content: ".";
+  display: block;
+  height: 0;
+  line-height: 0;
+  visibility: hidden;
 }
 hr.break.break-dashed {
   border-top: 1px dashed #e5e5e5;
@@ -269,7 +364,7 @@ hr.break-small.break-center {
   margin: 20px auto 35px;
 }
 hr.break-small.break-double {
-  height: 0; 
+  height: 0;
   margin-bottom: 39px;
 }
 hr.break-small.break-double:before {
@@ -296,22 +391,26 @@ hr.break-small.break-center.break-double:before {
 hr.break.break-small.break-center.break-double:after {
   margin: 4px auto 35px;
 }
-hr.break-small.break-double.background-white:before, hr.break-small.break-double.background-white:after, 
-.primary-color-white hr.break-small.break-double.background-primary:before, .primary-color-white hr.break-small.break-double.background-primary:after {
+hr.break-small.break-double.background-white:before,
+hr.break-small.break-double.background-white:after,
+.primary-color-white hr.break-small.break-double.background-primary:before,
+.primary-color-white hr.break-small.break-double.background-primary:after {
   background: #fff;
 }
-hr.break-small.break-double.background-primary:before, hr.break-small.break-double.background-primary:after,
-.primary-color-primary hr.break-small.break-double.background-primary:before, .primary-color-primary hr.break-small.break-double.background-primary:after {
-  background: #C81010;
+hr.break-small.break-double.background-primary:before,
+hr.break-small.break-double.background-primary:after,
+.primary-color-primary hr.break-small.break-double.background-primary:before,
+.primary-color-primary hr.break-small.break-double.background-primary:after {
+  background: #c81010;
 }
 
-
 video {
   display: block;
-} 
+}
 
 /* Top Nav */
-.top-nav li a, .background-white .top-nav li a {
+.top-nav li a,
+.background-white .top-nav li a {
   color: #002633;
   font-size: 0.85rem;
   padding: 0.7em 1.25em;
@@ -322,7 +421,7 @@ nav {
   padding: 1.7rem 0;
   position: relative;
   z-index: 2;
-}  
+}
 .top-nav ul ul {
   background: #002633 none repeat scroll 0 0;
 }
@@ -332,22 +431,27 @@ nav {
 .top-nav li ul li:last-child {
   border-bottom: 0;
 }
-.top-nav li ul li a, .background-white .top-nav li ul li a, .top-nav .active-item li a {
+.top-nav li ul li a,
+.background-white .top-nav li ul li a,
+.top-nav .active-item li a {
   background: #002633 none repeat scroll 0 0;
-  color: rgba(255,255,255, 0.75);
+  color: rgba(255, 255, 255, 0.75);
 }
-ul.chevron .submenu > a::after, ul.chevron .sub-submenu > a::after, ul.chevron .aside-submenu > a::after, ul.chevron .aside-sub-submenu > a::after {
+ul.chevron .submenu > a::after,
+ul.chevron .sub-submenu > a::after,
+ul.chevron .aside-submenu > a::after,
+ul.chevron .aside-sub-submenu > a::after {
   margin: 0 0 0 0.625rem;
 }
 .top-nav ul ul a {
   color: #eee;
 }
 .sticky {
-  transition: all 0.20s linear 0s;
-  -o-transition: all 0.20s linear 0s;
-  -ms-transition: all 0.20s linear 0s;
-  -moz-transition: all 0.20s linear 0s;
-  -webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
 }
 .fixed {
   left: 0;
@@ -357,7 +461,8 @@ ul.chevron .submenu > a::after, ul.chevron .sub-submenu > a::after, ul.chevron .
   width: 100%;
   z-index: 10;
 }
-nav.fixed, .fixed nav {
+nav.fixed,
+.fixed nav {
   padding: 1rem 0;
 }
 .logo img {
@@ -379,13 +484,17 @@ aside {
 .aside-nav ul ul {
   margin: 0;
 }
-.aside-nav li a, .aside-nav li a:link, .aside-nav li a:visited {
+.aside-nav li a,
+.aside-nav li a:link,
+.aside-nav li a:visited {
   border-bottom: medium none;
   font-size: 0.85rem;
   padding: 15px;
-  border-left: 5px solid rgba(0,0,0,0);
+  border-left: 5px solid rgba(0, 0, 0, 0);
 }
-.aside-nav > ul > li > a:hover, .aside-nav > ul > li.active-item > a:link, .aside-nav > ul > li.active-item > a:visited {
+.aside-nav > ul > li > a:hover,
+.aside-nav > ul > li.active-item > a:link,
+.aside-nav > ul > li.active-item > a:visited {
   border-style: solid;
   border-width: 0 0 0 5px;
   border-color: #e5e5e5;
@@ -405,109 +514,282 @@ aside.aside-left {
 }
 .aside-left .aside-nav li a {
   border-left: 0;
-  border-right: 5px solid rgba(0,0,0,0);
+  border-right: 5px solid rgba(0, 0, 0, 0);
 }
-.aside-left .aside-nav > ul > li > a:hover, .aside-left .aside-nav > ul > li.active-item > a:link, .aside-left .aside-nav > ul > li.active-item > a:visited {
+.aside-left .aside-nav > ul > li > a:hover,
+.aside-left .aside-nav > ul > li.active-item > a:link,
+.aside-left .aside-nav > ul > li.active-item > a:visited {
   border-style: solid;
   border-width: 0 5px 0 0;
   border-color: #e5e5e5;
 }
 
-.aside-nav.background-white-hightlight > ul > li > a:hover, .aside-nav.background-white-hightlight > ul > li.active-item > a:link, .aside-nav.background-white-hightlight > ul > li.active-item > a:visited,
-.primary-color-white .aside-nav.background-primary-hightlight > ul > li > a:hover, .primary-color-white .aside-nav.background-primary-hightlight > ul > li.active-item > a:link, .primary-color-white .aside-nav.background-primary-hightlight > ul > li.active-item > a:visited {
+.aside-nav.background-white-hightlight > ul > li > a:hover,
+.aside-nav.background-white-hightlight > ul > li.active-item > a:link,
+.aside-nav.background-white-hightlight > ul > li.active-item > a:visited,
+.primary-color-white
+  .aside-nav.background-primary-hightlight
+  > ul
+  > li
+  > a:hover,
+.primary-color-white
+  .aside-nav.background-primary-hightlight
+  > ul
+  > li.active-item
+  > a:link,
+.primary-color-white
+  .aside-nav.background-primary-hightlight
+  > ul
+  > li.active-item
+  > a:visited {
   border-color: #fff;
-} 
+}
 
-.aside-nav.background-primary-hightlight > ul > li > a:hover, .aside-nav.background-primary-hightlight > ul > li.active-item > a:link, .aside-nav.background-primary-hightlight > ul > li.active-item > a:visited,
-.primary-color-primary .aside-nav.background-primary-hightlight > ul > li > a:hover, .primary-color-primary .aside-nav.background-primary-hightlight > ul > li.active-item > a:link, .primary-color-primary .aside-nav.background-primary-hightlight > ul > li.active-item > a:visited {
-  border-color: #C81010;
-}  
-.aside-nav.background-dark-hightlight > ul > li > a:hover, .aside-nav.background-dark-hightlight > ul > li.active-item > a:link, .aside-nav.background-dark-hightlight > ul > li.active-item > a:visited,
-.primary-color-dark .aside-nav.background-primary-hightlight > ul > li > a:hover, .primary-color-dark .aside-nav.background-primary-hightlight > ul > li.active-item > a:link, .primary-color-dark .aside-nav.background-primary-hightlight > ul > li.active-item > a:visited {
+.aside-nav.background-primary-hightlight > ul > li > a:hover,
+.aside-nav.background-primary-hightlight > ul > li.active-item > a:link,
+.aside-nav.background-primary-hightlight > ul > li.active-item > a:visited,
+.primary-color-primary
+  .aside-nav.background-primary-hightlight
+  > ul
+  > li
+  > a:hover,
+.primary-color-primary
+  .aside-nav.background-primary-hightlight
+  > ul
+  > li.active-item
+  > a:link,
+.primary-color-primary
+  .aside-nav.background-primary-hightlight
+  > ul
+  > li.active-item
+  > a:visited {
+  border-color: #c81010;
+}
+.aside-nav.background-dark-hightlight > ul > li > a:hover,
+.aside-nav.background-dark-hightlight > ul > li.active-item > a:link,
+.aside-nav.background-dark-hightlight > ul > li.active-item > a:visited,
+.primary-color-dark
+  .aside-nav.background-primary-hightlight
+  > ul
+  > li
+  > a:hover,
+.primary-color-dark
+  .aside-nav.background-primary-hightlight
+  > ul
+  > li.active-item
+  > a:link,
+.primary-color-dark
+  .aside-nav.background-primary-hightlight
+  > ul
+  > li.active-item
+  > a:visited {
   border-color: #002633;
 }
 
 /* Font colors */
-.background-white, .background-white p, a.background-white, .background-white a, .background-white a:link, .background-white a:visited, .background-white a:hover, .background-white a:active {
+.background-white,
+.background-white p,
+a.background-white,
+.background-white a,
+.background-white a:link,
+.background-white a:visited,
+.background-white a:hover,
+.background-white a:active {
   color: rgb(95, 115, 230);
-} 
-.background-dark, .background-dark p, a.background-dark, a.background-dark:visited, a.background-dark:link, .background-dark a, .background-dark a:link, .background-dark a:visited, .background-dark a:hover, .background-dark a:active,
-.primary-color-dark .background-primary, .primary-color-dark .background-primary p, .primary-color-dark a.background-primary, .primary-color-dark a.background-primary:visited, .primary-color-dark a.background-primary:link, .primary-color-dark a.background-primary:visited, .primary-color-dark .background-primary a, .primary-color-dark .background-primary a:link, .primary-color-dark .background-primary a:visited, .primary-color-dark .background-primary a:hover, .primary-color-dark .background-primary a:active {
+}
+.background-dark,
+.background-dark p,
+a.background-dark,
+a.background-dark:visited,
+a.background-dark:link,
+.background-dark a,
+.background-dark a:link,
+.background-dark a:visited,
+.background-dark a:hover,
+.background-dark a:active,
+.primary-color-dark .background-primary,
+.primary-color-dark .background-primary p,
+.primary-color-dark a.background-primary,
+.primary-color-dark a.background-primary:visited,
+.primary-color-dark a.background-primary:link,
+.primary-color-dark a.background-primary:visited,
+.primary-color-dark .background-primary a,
+.primary-color-dark .background-primary a:link,
+.primary-color-dark .background-primary a:visited,
+.primary-color-dark .background-primary a:hover,
+.primary-color-dark .background-primary a:active {
   color: #ffffff;
 }
-.background-white h1, .background-white h2, .background-white h3, .background-white h4, .background-white h5, .background-white h6,
-.background-white .h1, .background-white .h2, .background-white .h3, .background-white .h4, .background-white .h5, .background-white .h6, 
-.primary-color-white .background-primary h1, .primary-color-white .background-primary h2, .primary-color-white .background-primary h3, .primary-color-white .background-primary h4, .primary-color-white .background-primary h5, .primary-color-white .background-primary h6,
-.primary-color-white .background-primary .h1, .primary-color-white .background-primary .h2, .primary-color-white .background-primary .h3, .primary-color-white .background-primary .h4, .primary-color-white .background-primary .h5, .primary-color-white .background-primary .h6 {
+.background-white h1,
+.background-white h2,
+.background-white h3,
+.background-white h4,
+.background-white h5,
+.background-white h6,
+.background-white .h1,
+.background-white .h2,
+.background-white .h3,
+.background-white .h4,
+.background-white .h5,
+.background-white .h6,
+.primary-color-white .background-primary h1,
+.primary-color-white .background-primary h2,
+.primary-color-white .background-primary h3,
+.primary-color-white .background-primary h4,
+.primary-color-white .background-primary h5,
+.primary-color-white .background-primary h6,
+.primary-color-white .background-primary .h1,
+.primary-color-white .background-primary .h2,
+.primary-color-white .background-primary .h3,
+.primary-color-white .background-primary .h4,
+.primary-color-white .background-primary .h5,
+.primary-color-white .background-primary .h6 {
   color: #002633;
-} 
+}
 .image-hover-overlay-content *,
-.background-primary, .background-primary p, a.background-primary, a.background-primary:visited, a.background-primary:link, .background-primary a, .background-primary a:link, .background-primary a:visited, .background-primary a:hover, .background-primary a:active,
-.primary-color-primary .background-primary, .primary-color-primary .background-primary p, .primary-color-primary a.background-primary, .primary-color-primary a.background-primary:visited, .primary-color-primary a.background-primary:link, .primary-color-primary .background-primary a, .primary-color-primary .background-primary a:link, .primary-color-primary .background-primary a:visited, .primary-color-primary .background-primary a:hover, .primary-color-primary .background-primary a:active {
-  color: rgba(255,255,255, 0.75);
-}
-.background-dark h1, .background-dark h2, .background-dark h3, .background-dark h4, .background-dark h5, .background-dark h6,
-.background-dark .h1, .background-dark .h2, .background-dark .h3, .background-dark .h4, .background-dark .h5, .background-dark .h6, 
-.primary-color-dark .background-primary h1, .primary-color-dark .background-primary h2, .primary-color-dark .background-primary h3, .primary-color-dark .background-primary h4, .primary-color-dark .background-primary h5, .primary-color-dark .background-primary h6,
-.primary-color-dark .background-primary .h1, .primary-color-dark .background-primary .h2, .primary-color-dark .background-primary .h3, .primary-color-dark .background-primary .h4, .primary-color-dark .background-primary .h5, .primary-color-dark .background-primary .h6, 
-.background-primary h1, .background-primary h2, .background-primary h3, .background-primary h4, .background-primary h5, .background-primary h6,
-.background-primary .h1, .background-primary .h2, .background-primary .h3, .background-primary .h4, .background-primary .h5, .background-primary .h6,
-.primary-color-primary .background-primary h1, .primary-color-primary .background-primary h2, .primary-color-primary .background-primary h3, .primary-color-primary .background-primary h4, .primary-color-primary .background-primary h5, .primary-color-primary .background-primary h6,
-.primary-color-primary .background-primary .h1, .primary-color-primary .background-primary .h2, .primary-color-primary .background-primary .h3, .primary-color-primary .background-primary .h4, .primary-color-primary .background-primary .h5, .primary-color-primary .background-primary .h6 {
+.background-primary,
+.background-primary p,
+a.background-primary,
+a.background-primary:visited,
+a.background-primary:link,
+.background-primary a,
+.background-primary a:link,
+.background-primary a:visited,
+.background-primary a:hover,
+.background-primary a:active,
+.primary-color-primary .background-primary,
+.primary-color-primary .background-primary p,
+.primary-color-primary a.background-primary,
+.primary-color-primary a.background-primary:visited,
+.primary-color-primary a.background-primary:link,
+.primary-color-primary .background-primary a,
+.primary-color-primary .background-primary a:link,
+.primary-color-primary .background-primary a:visited,
+.primary-color-primary .background-primary a:hover,
+.primary-color-primary .background-primary a:active {
+  color: rgba(255, 255, 255, 0.75);
+}
+.background-dark h1,
+.background-dark h2,
+.background-dark h3,
+.background-dark h4,
+.background-dark h5,
+.background-dark h6,
+.background-dark .h1,
+.background-dark .h2,
+.background-dark .h3,
+.background-dark .h4,
+.background-dark .h5,
+.background-dark .h6,
+.primary-color-dark .background-primary h1,
+.primary-color-dark .background-primary h2,
+.primary-color-dark .background-primary h3,
+.primary-color-dark .background-primary h4,
+.primary-color-dark .background-primary h5,
+.primary-color-dark .background-primary h6,
+.primary-color-dark .background-primary .h1,
+.primary-color-dark .background-primary .h2,
+.primary-color-dark .background-primary .h3,
+.primary-color-dark .background-primary .h4,
+.primary-color-dark .background-primary .h5,
+.primary-color-dark .background-primary .h6,
+.background-primary h1,
+.background-primary h2,
+.background-primary h3,
+.background-primary h4,
+.background-primary h5,
+.background-primary h6,
+.background-primary .h1,
+.background-primary .h2,
+.background-primary .h3,
+.background-primary .h4,
+.background-primary .h5,
+.background-primary .h6,
+.primary-color-primary .background-primary h1,
+.primary-color-primary .background-primary h2,
+.primary-color-primary .background-primary h3,
+.primary-color-primary .background-primary h4,
+.primary-color-primary .background-primary h5,
+.primary-color-primary .background-primary h6,
+.primary-color-primary .background-primary .h1,
+.primary-color-primary .background-primary .h2,
+.primary-color-primary .background-primary .h3,
+.primary-color-primary .background-primary .h4,
+.primary-color-primary .background-primary .h5,
+.primary-color-primary .background-primary .h6 {
   color: #fff;
 }
-.text-white, .text-white *, .primary-color-white .text-primary, .primary-color-white .text-primary * {
+.text-white,
+.text-white *,
+.primary-color-white .text-primary,
+.primary-color-white .text-primary * {
   color: #fff !important;
 }
-.text-primary, .text-primary *, .primary-color-primary .text-primary, .primary-color-primary .text-primary * {
-  color: #C81010 !important;
+.text-primary,
+.text-primary *,
+.primary-color-primary .text-primary,
+.primary-color-primary .text-primary * {
+  color: #c81010 !important;
 }
-.text-dark, .text-dark *, .primary-color-dark .text-primary, .primary-color-dark .text-primary * {
+.text-dark,
+.text-dark *,
+.primary-color-dark .text-primary,
+.primary-color-dark .text-primary * {
   color: #002633 !important;
-} 
-.text-white-hover, .text-primary-hover, .text-dark-hover {
-  transition: color 0.20s linear 0s;
-  -o-transition: color 0.20s linear 0s;
-  -ms-transition: color 0.20s linear 0s;
-  -moz-transition: color 0.20s linear 0s;
-  -webkit-transition: color 0.20s linear 0s;
-}
-.text-white-hover:hover, .primary-color-white .text-primary-hover:hover {
+}
+.text-white-hover,
+.text-primary-hover,
+.text-dark-hover {
+  transition: color 0.2s linear 0s;
+  -o-transition: color 0.2s linear 0s;
+  -ms-transition: color 0.2s linear 0s;
+  -moz-transition: color 0.2s linear 0s;
+  -webkit-transition: color 0.2s linear 0s;
+}
+.text-white-hover:hover,
+.primary-color-white .text-primary-hover:hover {
   color: #fff !important;
 }
-.text-primary-hover:hover, .primary-color-primary .text-primary-hover:hover {
-  color: #C81010 !important;
+.text-primary-hover:hover,
+.primary-color-primary .text-primary-hover:hover {
+  color: #c81010 !important;
 }
-.text-dark-hover:hover, .primary-color-dark .text-primary-hover:hover {
+.text-dark-hover:hover,
+.primary-color-dark .text-primary-hover:hover {
   color: #002633 !important;
-} 
+}
 
 /* Background Colors */
-.background-white, .primary-color-white .background-primary {
+.background-white,
+.primary-color-white .background-primary {
   background-color: #f7efef !important;
 }
-.background-primary, .primary-color-primary .background-primary {
-  background-color: #C81010 !important;
+.background-primary,
+.primary-color-primary .background-primary {
+  background-color: #c81010 !important;
 }
-.background-dark, .primary-color-dark .background-primary {
-  background-color: #002633 !important; 
+.background-dark,
+.primary-color-dark .background-primary {
+  background-color: #002633 !important;
 }
 /* Background Opacity */
-.background-white.background-transparent, .primary-color-white .background-primary.background-transparent {
+.background-white.background-transparent,
+.primary-color-white .background-primary.background-transparent {
   background-color: rgba(255, 255, 255, 0.85) !important;
 }
-.background-primary.background-transparent, .primary-color-primary .background-primary.background-transparent {
+.background-primary.background-transparent,
+.primary-color-primary .background-primary.background-transparent {
   background-color: rgba(200, 16, 16, 0.85) !important;
 }
-.background-dark.background-transparent, .primary-color-dark .background-primary.background-transparent {
+.background-dark.background-transparent,
+.primary-color-dark .background-primary.background-transparent {
   background-color: rgba(0, 38, 51, 0.85) !important;
 }
 
-
 /* Hover Overlay */
 .image-hover-overlay {
   bottom: 0;
-  color: rgba(255,255,255, 0.75)!important;
+  color: rgba(255, 255, 255, 0.75) !important;
   left: 0;
   opacity: 0;
   padding: 1.25rem;
@@ -515,11 +797,11 @@ aside.aside-left {
   right: 0;
   top: 0;
   z-index: 1;
-  transition: all 0.20s linear 0s;
-  -o-transition: all 0.20s linear 0s;
-  -ms-transition: all 0.20s linear 0s;
-  -moz-transition: all 0.20s linear 0s;
-  -webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
   transform-style: preserve-3d;
   -o-transform-style: preserve-3d;
   -ms-transform-style: preserve-3d;
@@ -537,11 +819,11 @@ aside.aside-left {
   left: 0;
   right: 0;
   top: 60%;
-  transition: all 0.20s linear 0s;
-  -o-transition: all 0.20s linear 0s;
-  -ms-transition: all 0.20s linear 0s;
-  -moz-transition: all 0.20s linear 0s;
-  -webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
   transform: translateY(-50%);
   -o-transform: translateY(-50%);
   -ms-transform: translateY(-50%);
@@ -565,11 +847,11 @@ aside.aside-left {
   overflow: hidden;
 }
 .image-hover-zoom img {
-  transition: all 0.20s linear 0s;
-  -o-transition: all 0.20s linear 0s;
-  -ms-transition: all 0.20s linear 0s;
-  -moz-transition: all 0.20s linear 0s;
-  -webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
 }
 .image-with-hover-overlay img {
   width: 100%;
@@ -578,75 +860,105 @@ aside.aside-left {
   transform: scale(1.1);
 }
 
-
 /* Buttons */
-.button, a.button, a.button:link, a.button:visited {
-  border-color: rgba(255, 255, 255, 0.4) rgba(255, 255, 255, 0) rgba(0, 0, 0, 0.3);
+.button,
+a.button,
+a.button:link,
+a.button:visited {
+  border-color: rgba(255, 255, 255, 0.4) rgba(255, 255, 255, 0)
+    rgba(0, 0, 0, 0.3);
   border-style: solid;
   border-width: 1px;
   color: white;
   display: inline-block;
   padding: 0.625rem 1.25rem;
   text-align: center;
-  transition: all 0.20s linear 0s !important;
-  -o-transition: all 0.20s linear 0s !important;
-  -ms-transition: all 0.20s linear 0s !important;
-  -moz-transition: all 0.20s linear 0s !important;
-  -webkit-transition: all 0.20s linear 0s !important;
+  transition: all 0.2s linear 0s !important;
+  -o-transition: all 0.2s linear 0s !important;
+  -ms-transition: all 0.2s linear 0s !important;
+  -moz-transition: all 0.2s linear 0s !important;
+  -webkit-transition: all 0.2s linear 0s !important;
 }
 
-.button:hover, a.button:hover, a.button:link:hover, a.button:visited:hover {
+.button:hover,
+a.button:hover,
+a.button:link:hover,
+a.button:visited:hover {
   box-shadow: 0 0 100px 100px rgba(255, 255, 255, 0.25) inset;
 }
-/* Stroke Buttons */ 
-.button.button-white-stroke, a.button.button-white-stroke, a.button.button-white-stroke:link, a.button.button-white-stroke:visited,
-.primary-color-white .button.button-primary-stroke, .primary-color-white a.button.button-primary-stroke, .primary-color-white a.button.button-primary-stroke:link, .primary-color-white a.button.button-primary-stroke:visited {
+/* Stroke Buttons */
+.button.button-white-stroke,
+a.button.button-white-stroke,
+a.button.button-white-stroke:link,
+a.button.button-white-stroke:visited,
+.primary-color-white .button.button-primary-stroke,
+.primary-color-white a.button.button-primary-stroke,
+.primary-color-white a.button.button-primary-stroke:link,
+.primary-color-white a.button.button-primary-stroke:visited {
   background: none;
   border: 1px solid #fff;
   box-shadow: none;
 }
-.button.button-white-stroke:hover, a.button.button-white-stroke:hover,
-.primary-color-white .button.button-primary-stroke:hover, .primary-color-white a.button.button-primary-stroke:hover {
+.button.button-white-stroke:hover,
+a.button.button-white-stroke:hover,
+.primary-color-white .button.button-primary-stroke:hover,
+.primary-color-white a.button.button-primary-stroke:hover {
   background: #fff none repeat scroll 0 0;
   color: #002633;
 }
-.button.button-primary-stroke, a.button.button-primary-stroke, a.button.button-primary-stroke:link, a.button.button-primary-stroke:visited,
-.primary-color-primary .button.button-primary-stroke, .primary-color-primary a.button.button-primary-stroke, .primary-color-primary a.button.button-primary-stroke:link, .primary-color-primary a.button.button-primary-stroke:visited {
+.button.button-primary-stroke,
+a.button.button-primary-stroke,
+a.button.button-primary-stroke:link,
+a.button.button-primary-stroke:visited,
+.primary-color-primary .button.button-primary-stroke,
+.primary-color-primary a.button.button-primary-stroke,
+.primary-color-primary a.button.button-primary-stroke:link,
+.primary-color-primary a.button.button-primary-stroke:visited {
   background: none;
-  border: 1px solid #C81010;
+  border: 1px solid #c81010;
   box-shadow: none;
-  color: #C81010;
+  color: #c81010;
 }
-.button.button-primary-stroke:hover, a.button.button-primary-stroke:hover,
-.primary-color-primary .button.button-primary-stroke:hover, .primary-color-primary a.button.button-primary-stroke:hover {
-  background: #C81010 none repeat scroll 0 0;
+.button.button-primary-stroke:hover,
+a.button.button-primary-stroke:hover,
+.primary-color-primary .button.button-primary-stroke:hover,
+.primary-color-primary a.button.button-primary-stroke:hover {
+  background: #c81010 none repeat scroll 0 0;
   color: #fff;
 }
 
-.button.button-dark-stroke, a.button.button-dark-stroke, a.button.button-dark-stroke:link, a.button.button-dark-stroke:visited,
-.primary-color-dark .button.button-primary-stroke, .primary-color-dark a.button.button-primary-stroke, .primary-color-dark a.button.button-primary-stroke:link, .primary-color-dark a.button.button-primary-stroke:visited {
+.button.button-dark-stroke,
+a.button.button-dark-stroke,
+a.button.button-dark-stroke:link,
+a.button.button-dark-stroke:visited,
+.primary-color-dark .button.button-primary-stroke,
+.primary-color-dark a.button.button-primary-stroke,
+.primary-color-dark a.button.button-primary-stroke:link,
+.primary-color-dark a.button.button-primary-stroke:visited {
   background: none;
   border: 1px solid #002633;
   box-shadow: none;
   color: #002633;
 }
-.button.button-dark-stroke:hover, a.button.button-dark-stroke:hover,
-.primary-color-dark .button.button-primary-stroke:hover, .primary-color-dark a.button.button-primary-stroke:hover {
+.button.button-dark-stroke:hover,
+a.button.button-dark-stroke:hover,
+.primary-color-dark .button.button-primary-stroke:hover,
+.primary-color-dark a.button.button-primary-stroke:hover {
   background: #002633 none repeat scroll 0 0;
   color: #fff;
 }
 
 /* Containers */
-.section  { 
+.section {
   padding: 4rem 1.25rem;
 }
-.section-small-padding  { 
+.section-small-padding {
   padding: 2.5rem 1.25rem;
 }
-.section-top-padding  { 
+.section-top-padding {
   padding-top: 6rem;
 }
-.section-top-small-padding  { 
+.section-top-small-padding {
   padding-top: 2.5rem;
 }
 .float-left {
@@ -656,43 +968,43 @@ aside.aside-left {
   border: 1px solid rgba(0, 0, 0, 0.1);
 }
 .padding {
-  padding: 1.25rem!important;
+  padding: 1.25rem !important;
 }
 .padding-2x {
-  padding: 2.5rem!important;
+  padding: 2.5rem !important;
 }
 .full-width:after {
-  clear:both;
-  content:".";
-  display:block;
-  height:0;
-  line-height:0;
-  visibility:hidden;
+  clear: both;
+  content: ".";
+  display: block;
+  height: 0;
+  line-height: 0;
+  visibility: hidden;
 }
 .full-width > .line {
-    padding: 0 1.875rem;
+  padding: 0 1.875rem;
 }
-.position-fixed  { 
+.position-fixed {
   position: fixed;
   top: 0;
   width: 100%;
 }
 .center {
-  display: block!important;
+  display: block !important;
 }
-.border-radius  { 
+.border-radius {
   border-radius: 3px;
 }
 .content-center-vertical {
   position: absolute;
   left: 0;
   right: 0;
-  top: 50%; 
+  top: 50%;
   transform: translateY(-50%);
   -o-transform: translateY(-50%);
   -ms-transform: translateY(-50%);
   -moz-transform: translateY(-50%);
-  -webkit-transform:translateY(-50%);
+  -webkit-transform: translateY(-50%);
 }
 .content-bottom {
   bottom: 0;
@@ -701,25 +1013,24 @@ aside.aside-left {
 .grayscale {
   filter: url('data:image/svg+xml;utf8,<svg xmlns="http://www.w3.org/2000/svg"><filter id="g"><feColorMatrix type="matrix" values="0.3 0.3 0.3 0 0 0.3 0.3 0.3 0 0 0.3 0.3 0.3 0 0 0 0 0 1 0"/></filter></svg>#g');
   -webkit-filter: grayscale(100%);
-  filter: grayscale(100%);    
+  filter: grayscale(100%);
   filter: progid:DXImageTransform.Microsoft.BasicImage(grayScale=1);
 }
 
 .image-grayscale {
   filter: url('data:image/svg+xml;utf8,<svg xmlns="http://www.w3.org/2000/svg"><filter id="g"><feColorMatrix type="matrix" values="0.3 0.3 0.3 0 0 0.3 0.3 0.3 0 0 0.3 0.3 0.3 0 0 0 0 0 1 0"/></filter></svg>#g');
   -webkit-filter: grayscale(100%);
-  filter: grayscale(100%);    
+  filter: grayscale(100%);
   filter: progid:DXImageTransform.Microsoft.BasicImage(grayScale=1);
   position: relative;
 }
 *:hover > .image-grayscale {
   filter: none;
   -webkit-filter: grayscale(0%);
-  filter: grayscale(0%);    
+  filter: grayscale(0%);
   filter: progid:DXImageTransform.Microsoft.BasicImage(grayScale=0);
 }
 
-
 /* Margins */
 .margin-top {
   margin-top: 1.25rem !important;
@@ -749,15 +1060,15 @@ aside.aside-left {
 .margin-top-15 {
   margin-top: 15px !important;
   display: block;
-} 
+}
 .margin-top-20 {
   margin-top: 20px !important;
   display: block;
-} 
+}
 .margin-top-30 {
   margin-top: 30px !important;
   display: block;
-} 
+}
 .margin-top-40 {
   margin-top: 40px !important;
   display: block;
@@ -789,7 +1100,7 @@ aside.aside-left {
 .margin-bottom-15 {
   margin-bottom: 15px !important;
   display: block;
-} 
+}
 .margin-bottom-18 {
   margin-bottom: 18px !important;
   display: block;
@@ -797,11 +1108,11 @@ aside.aside-left {
 .margin-bottom-20 {
   margin-bottom: 20px !important;
   display: block;
-} 
+}
 .margin-bottom-30 {
   margin-bottom: 30px !important;
   display: block;
-} 
+}
 .margin-bottom-40 {
   margin-bottom: 40px !important;
   display: block;
@@ -836,17 +1147,17 @@ aside.aside-left {
   margin-top: 15px !important;
   margin-bottom: 15px !important;
   display: block;
-} 
+}
 .margin-top-bottom-20 {
   margin-top: 20px !important;
   margin-bottom: 20px !important;
   display: block;
-} 
+}
 .margin-top-bottom-30 {
   margin-top: 30px !important;
   margin-bottom: 30px !important;
   display: block;
-} 
+}
 .margin-top-bottom-40 {
   margin-top: 40px !important;
   margin-bottom: 40px !important;
@@ -861,12 +1172,12 @@ aside.aside-left {
   margin-top: 60px !important;
   margin-bottom: 60px !important;
   display: block;
-} 
+}
 .margin-top-bottom-70 {
   margin-top: 70px !important;
   margin-bottom: 70px !important;
   display: block;
-} 
+}
 .margin-top-bottom-80 {
   margin-top: 80px !important;
   margin-bottom: 80px !important;
@@ -881,13 +1192,13 @@ aside.aside-left {
 }
 .margin-left-15 {
   margin-left: 15px !important;
-} 
+}
 .margin-left-20 {
   margin-left: 20px !important;
-} 
+}
 .margin-left-30 {
   margin-left: 30px !important;
-} 
+}
 .margin-left-40 {
   margin-left: 40px !important;
 }
@@ -911,13 +1222,13 @@ aside.aside-left {
 }
 .margin-right-15 {
   margin-right: 15px !important;
-} 
+}
 .margin-right-20 {
   margin-right: 20px !important;
-} 
+}
 .margin-right-30 {
   margin-right: 30px !important;
-} 
+}
 .margin-right-40 {
   margin-right: 40px !important;
 }
@@ -944,15 +1255,15 @@ aside.aside-left {
 .margin-left-right-15 {
   margin-left: 15px !important;
   margin-right: 15px !important;
-} 
+}
 .margin-left-right-20 {
   margin-left: 20px !important;
   margin-right: 20px !important;
-} 
+}
 .margin-left-right-30 {
   margin-left: 30px !important;
   margin-right: 30px !important;
-} 
+}
 .margin-left-right-40 {
   margin-left: 40px !important;
   margin-right: 40px !important;
@@ -964,15 +1275,15 @@ aside.aside-left {
 .margin-left-right-60 {
   margin-left: 60px !important;
   margin-right: 60px !important;
-} 
+}
 .margin-left-right-70 {
   margin-left: 70px !important;
   margin-right: 70px !important;
-} 
+}
 .margin-left-right-80 {
   margin-left: 80px !important;
   margin-right: 80px !important;
-}        
+}
 
 /* More info button */
 a.text-more-info {
@@ -985,11 +1296,11 @@ a.text-more-info:after {
   font-family: mfg;
   font-size: 0.8rem;
   margin-left: 0.625rem;
-  transition: all 0.20s linear 0s;
--o-transition: all 0.20s linear 0s;
--ms-transition: all 0.20s linear 0s;
--moz-transition: all 0.20s linear 0s;
--webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
 }
 a.text-more-info:hover:after {
   margin-left: 0.825rem;
@@ -1001,7 +1312,7 @@ a.text-more-info:hover:after {
   line-height: 35px;
 }
 .top-bar-social li {
-  border-left: 1px solid rgba(0,0,0, 0.05);
+  border-left: 1px solid rgba(0, 0, 0, 0.05);
   float: left;
   height: 35px;
   line-height: 35px;
@@ -1010,11 +1321,11 @@ a.text-more-info:hover:after {
   width: 35px;
 }
 .top-bar-social li:last-child {
-  border-right: 1px solid rgba(0,0,0, 0.05);
+  border-right: 1px solid rgba(0, 0, 0, 0.05);
 }
 .top-bar-social i {
-  color: rgba(170, 170, 170, 0.20);
-  font-size: 18px; 
+  color: rgba(170, 170, 170, 0.2);
+  font-size: 18px;
 }
 
 /* Icon blocks */
@@ -1045,11 +1356,11 @@ i.icon-circle-small {
 .owl-carousel .owl-nav div {
   filter: Alpha(Opacity=50);
   opacity: 0.5;
-  transition: all 0.20s linear 0s;
-  -o-transition: all 0.20s linear 0s;
-  -ms-transition: all 0.20s linear 0s;
-  -moz-transition: all 0.20s linear 0s;
-  -webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
 }
 .owl-carousel .owl-nav div:hover {
   filter: Alpha(Opacity=100);
@@ -1070,11 +1381,11 @@ i.icon-circle-small {
   width: 30px;
   filter: Alpha(Opacity=50);
   opacity: 0.5;
-  transition: all 0.20s linear 0s;
-  -o-transition: all 0.20s linear 0s;
-  -ms-transition: all 0.20s linear 0s;
-  -moz-transition: all 0.20s linear 0s;
-  -webkit-transition: all 0.20s linear 0s;
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
 }
 .owl-carousel .owl-dot.active span {
   filter: Alpha(Opacity=100);
@@ -1082,7 +1393,7 @@ i.icon-circle-small {
 }
 .owl-carousel .owl-nav div {
   background: rgba(0, 0, 0, 0) none repeat scroll 0 0;
-  color: #7697a2!important;
+  color: #7697a2 !important;
   border: 1px solid #7697a2;
   border-radius: 0;
   font-family: sli;
@@ -1092,7 +1403,7 @@ i.icon-circle-small {
   padding: 0;
   position: absolute;
   text-align: center;
-  top: 50%;    
+  top: 50%;
   width: 40px;
 }
 .carousel-bottom-arrows.owl-carousel .owl-nav div {
@@ -1100,7 +1411,7 @@ i.icon-circle-small {
   top: auto;
 }
 .owl-carousel .owl-nav .owl-prev {
-  left: 0;    
+  left: 0;
 }
 .owl-carousel .owl-nav .owl-next {
   right: 0;
@@ -1115,7 +1426,7 @@ i.icon-circle-small {
   background: #fff none repeat scroll 0 0;
 }
 .carousel-nav-white.owl-carousel .owl-nav div {
-  color: #fff!important;
+  color: #fff !important;
   border: 1px solid #fff;
 }
 .carousel-main .carousel-content {
@@ -1132,7 +1443,7 @@ i.icon-circle-small {
 }
 .owl-dots {
   margin-top: 0.625rem;
-} 
+}
 .carousel-main .owl-dots {
   bottom: 0;
   padding: 1.25rem 0;
@@ -1145,8 +1456,9 @@ i.icon-circle-small {
 .carousel-blocks .owl-item {
   padding: 0 0.625rem;
 }
-.carousel-hide-arrows .owl-nav, .carousel-hide-pagination .owl-pagination {
-display:none;
+.carousel-hide-arrows .owl-nav,
+.carousel-hide-pagination .owl-pagination {
+  display: none;
 }
 .carousel-3-blocks {
   padding: 0 3rem;
@@ -1163,45 +1475,69 @@ display:none;
 .tab-item {
   padding: 0;
 }
-a.tab-label, a.tab-label:link, a.tab-label:visited,
-.background-white a.tab-label, .background-white a.tab-label:link, .background-white a.tab-label:visited, .background-white a.tab-label:hover {
+a.tab-label,
+a.tab-label:link,
+a.tab-label:visited,
+.background-white a.tab-label,
+.background-white a.tab-label:link,
+.background-white a.tab-label:visited,
+.background-white a.tab-label:hover {
   background: #002633 none repeat scroll 0 0;
-  color: rgba(255,255,255, 0.75);
-}
-a.tab-label, a.tab-label:link, a.tab-label:visited, a.tab-label:hover,
-.background-white a.tab-label, .background-white a.tab-label:link, .background-white a.tab-label:visited, .background-white a.tab-label:hover {
+  color: rgba(255, 255, 255, 0.75);
+}
+a.tab-label,
+a.tab-label:link,
+a.tab-label:visited,
+a.tab-label:hover,
+.background-white a.tab-label,
+.background-white a.tab-label:link,
+.background-white a.tab-label:visited,
+.background-white a.tab-label:hover {
   background: rgba(0, 0, 0, 0) none repeat scroll 0 0;
   color: #002633;
 }
-.background-white-hightlight a.tab-label.active-btn, .background-white-hightlight a.tab-label:hover,
-.primary-color-white .background-primary-hightlight a.tab-label.active-btn, .primary-color-white .background-primary-hightlight a.tab-label:hover {
+.background-white-hightlight a.tab-label.active-btn,
+.background-white-hightlight a.tab-label:hover,
+.primary-color-white .background-primary-hightlight a.tab-label.active-btn,
+.primary-color-white .background-primary-hightlight a.tab-label:hover {
   background: #fff none repeat scroll 0 0;
   color: #002633;
 }
-.background-primary-hightlight a.tab-label.active-btn, .background-primary-hightlight a.tab-label:hover,
-.primary-color-primary .background-primary-hightlight a.tab-label.active-btn, .primary-color-primary .background-primary-hightlight a.tab-label:hover {
-  background: #C81010 none repeat scroll 0 0;
+.background-primary-hightlight a.tab-label.active-btn,
+.background-primary-hightlight a.tab-label:hover,
+.primary-color-primary .background-primary-hightlight a.tab-label.active-btn,
+.primary-color-primary .background-primary-hightlight a.tab-label:hover {
+  background: #c81010 none repeat scroll 0 0;
   color: #fff;
 }
-.background-dark-hightlight a.tab-label.active-btn, .background-dark-hightlight a.tab-label:hover,
-.primary-color-dark .background-primary-hightlight a.tab-label.active-btn, .primary-color-dark .background-primary-hightlight a.tab-label:hover {
+.background-dark-hightlight a.tab-label.active-btn,
+.background-dark-hightlight a.tab-label:hover,
+.primary-color-dark .background-primary-hightlight a.tab-label.active-btn,
+.primary-color-dark .background-primary-hightlight a.tab-label:hover {
   background: #002633 none repeat scroll 0 0;
   color: #fff;
 }
 
 /* Forms */
-form.customform input, form.customform textarea, form.customform select {
+form.customform input,
+form.customform textarea,
+form.customform select {
   background: rgba(0, 0, 0, 0.03) none repeat scroll 0 0;
   border: 1px solid rgba(0, 0, 0, 0.14);
   font-size: 12px;
   padding: 0.625rem;
   width: 100%;
 }
-form.customform input:hover, form.customform textarea:hover, form.customform select:hover, form.customform input:focus, form.customform textarea:focus, form.customform select:focus {
+form.customform input:hover,
+form.customform textarea:hover,
+form.customform select:hover,
+form.customform input:focus,
+form.customform textarea:focus,
+form.customform select:focus {
   background: rgba(0, 0, 0, 0) none repeat scroll 0 0;
 }
 p.form-error {
-  background-color: #DD442C;
+  background-color: #dd442c;
   color: #fff;
   display: none;
   font-size: 0.8rem;
@@ -1221,651 +1557,650 @@ p.form-success {
   border-left: 1px solid #dd442c !important;
 }
 
+/* -768px version */
+@media screen and (max-width: 768px) {
+  .top-nav .right {
+    float: none;
+  }
+  nav {
+    padding: 10px 0;
+    height: 60px;
+  }
+  .logo img {
+    max-width: 172px;
+    max-height: 40px;
+    margin: 0 auto;
+    width: auto;
+  }
 
+  .top-nav li a,
+  .background-white .top-nav li a {
+    background: #002633 none repeat scroll 0 0;
+    color: #fff;
+    font-size: 1.1em;
+    padding: 1em;
+    text-align: center;
+  }
+  aside {
+    border: none;
+    padding: 0;
+  }
+  aside.aside-left {
+    border-right: 0;
+    padding-right: 0;
+  }
+  .owl-nav {
+    display: none;
+  }
+  .carousel-main .owl-item img,
+  .carousel-main .owl-item video {
+    max-width: 250%;
+    width: auto;
+  }
+  .margin-m-top {
+    margin-top: 1.25rem !important;
+    display: block;
+  }
+  .margin-m-bottom {
+    margin-bottom: 1.25rem !important;
+    display: block;
+  }
+  .margin-m-left {
+    margin-left: 1.25rem !important;
+  }
+  .margin-m-right {
+    margin-right: 1.25rem !important;
+  }
+  .margin-m-top-bottom {
+    margin-top: 1.25rem !important;
+    margin-bottom: 1.25rem !important;
+    display: block;
+  }
+  .margin-m-left-right {
+    margin-left: 1.25rem !important;
+    margin-right: 1.25rem !important;
+  }
+  .margin-m-top-0 {
+    margin-top: 0 !important;
+    display: block;
+  }
+  .margin-m-top-10 {
+    margin-top: 10px !important;
+    display: block;
+  }
+  .margin-m-top-15 {
+    margin-top: 15px !important;
+    display: block;
+  }
+  .margin-m-top-20 {
+    margin-top: 20px !important;
+    display: block;
+  }
+  .margin-m-top-30 {
+    margin-top: 30px !important;
+    display: block;
+  }
+  .margin-m-top-40 {
+    margin-top: 40px !important;
+    display: block;
+  }
+  .margin-m-top-50 {
+    margin-top: 50px !important;
+    display: block;
+  }
+  .margin-m-top-60 {
+    margin-top: 60px !important;
+    display: block;
+  }
+  .margin-m-top-70 {
+    margin-top: 70px !important;
+    display: block;
+  }
+  .margin-m-top-80 {
+    margin-top: 80px !important;
+    display: block;
+  }
+  .margin-m-bottom-0 {
+    margin-bottom: 0 !important;
+    display: block;
+  }
+  .margin-m-bottom-10 {
+    margin-bottom: 10px !important;
+    display: block;
+  }
+  .margin-m-bottom-15 {
+    margin-bottom: 15px !important;
+    display: block;
+  }
+  .margin-m-bottom-20 {
+    margin-bottom: 20px !important;
+    display: block;
+  }
+  .margin-m-bottom-30 {
+    margin-bottom: 30px !important;
+    display: block;
+  }
+  .margin-m-bottom-40 {
+    margin-bottom: 40px !important;
+    display: block;
+  }
+  .margin-m-bottom-50 {
+    margin-bottom: 50px !important;
+    display: block;
+  }
+  .margin-m-bottom-60 {
+    margin-bottom: 60px !important;
+    display: block;
+  }
+  .margin-m-bottom-70 {
+    margin-bottom: 70px !important;
+    display: block;
+  }
+  .margin-m-bottom-80 {
+    margin-bottom: 80px !important;
+    display: block;
+  }
+  .margin-m-top-bottom-0 {
+    margin-top: 0 !important;
+    margin-bottom: 0 !important;
+    display: block;
+  }
+  .margin-m-top-bottom-10 {
+    margin-top: 10px !important;
+    margin-bottom: 10px !important;
+    display: block;
+  }
+  .margin-m-top-bottom-15 {
+    margin-top: 15px !important;
+    margin-bottom: 15px !important;
+    display: block;
+  }
+  .margin-m-top-bottom-20 {
+    margin-top: 20px !important;
+    margin-bottom: 20px !important;
+    display: block;
+  }
+  .margin-m-top-bottom-30 {
+    margin-top: 30px !important;
+    margin-bottom: 30px !important;
+    display: block;
+  }
+  .margin-m-top-bottom-40 {
+    margin-top: 40px !important;
+    margin-bottom: 40px !important;
+    display: block;
+  }
+  .margin-m-top-bottom-50 {
+    margin-top: 50px !important;
+    margin-bottom: 50px !important;
+    display: block;
+  }
+  .margin-m-top-bottom-60 {
+    margin-top: 60px !important;
+    margin-bottom: 60px !important;
+    display: block;
+  }
+  .margin-m-top-bottom-70 {
+    margin-top: 70px !important;
+    margin-bottom: 70px !important;
+    display: block;
+  }
+  .margin-m-top-bottom-80 {
+    margin-top: 80px !important;
+    margin-bottom: 80px !important;
+    display: block;
+  }
 
-
-/* -768px version */
-@media screen and (max-width:768px) {
-    .top-nav .right {
-      float: none;
-    }
-    nav {
-        padding: 10px 0;
-        height: 60px;
-    }
-    .logo img {
-      max-width: 172px;
-      max-height: 40px;
-      margin: 0 auto;
-      width: auto;
-    }
-    
-    .top-nav li a, .background-white .top-nav li a {
-      background: #002633 none repeat scroll 0 0;
-      color: #fff;
-      font-size: 1.1em;
-      padding: 1em;
-      text-align: center;
-    }
-    aside {
-        border: none;
-        padding: 0;
-    }
-    aside.aside-left {
-        border-right: 0;
-        padding-right: 0;
-    }
-    .owl-nav {
-      display: none;
-    }
-    .carousel-main .owl-item img, .carousel-main .owl-item video {
-      max-width: 250%;
-    	width:auto;
-    } 
-    .margin-m-top {
-      margin-top: 1.25rem !important;
-      display: block;
-    }
-    .margin-m-bottom {
-        margin-bottom: 1.25rem !important;
-        display: block;
-    }
-    .margin-m-left {
-        margin-left: 1.25rem !important;
-    }
-    .margin-m-right {
-        margin-right: 1.25rem !important;
-    }
-    .margin-m-top-bottom {
-        margin-top: 1.25rem !important;
-        margin-bottom: 1.25rem !important;
-    display: block;
-    }
-    .margin-m-left-right {
-        margin-left: 1.25rem !important;
-        margin-right: 1.25rem !important;
-    }
-    .margin-m-top-0 {
-        margin-top: 0 !important;
-    display: block;
-    }
-    .margin-m-top-10 {
-        margin-top: 10px !important; 
-    display: block;
-    }
-    .margin-m-top-15 {
-        margin-top: 15px !important;
-    display: block;
-    } 
-    .margin-m-top-20 {
-        margin-top: 20px !important; 
-    display: block;
-    } 
-    .margin-m-top-30 {
-        margin-top: 30px !important;
-    display: block;
-    } 
-    .margin-m-top-40 {
-        margin-top: 40px !important;
-    display: block;
-    }
-    .margin-m-top-50 {
-        margin-top: 50px !important;
-    display: block;
-    }
-    .margin-m-top-60 {
-        margin-top: 60px !important;
-    display: block;
-    }
-    .margin-m-top-70 {
-        margin-top: 70px !important; 
-    display: block;
-    }
-    .margin-m-top-80 {
-        margin-top: 80px !important;
-    display: block;
-    }
-    .margin-m-bottom-0 {
-        margin-bottom: 0 !important; 
-    display: block;
-    }
-    .margin-m-bottom-10 {
-        margin-bottom: 10px !important; 
-    display: block;
-    }
-    .margin-m-bottom-15 {
-        margin-bottom: 15px !important;
-    display: block;
-    } 
-    .margin-m-bottom-20 {
-        margin-bottom: 20px !important;
-    display: block;
-    } 
-    .margin-m-bottom-30 {
-        margin-bottom: 30px !important;
-    display: block;
-    } 
-    .margin-m-bottom-40 {
-        margin-bottom: 40px !important;
-    display: block;
-    }
-    .margin-m-bottom-50 {
-        margin-bottom: 50px !important;
-    display: block;
-    }
-    .margin-m-bottom-60 {
-        margin-bottom: 60px !important;
-    display: block;
-    }
-    .margin-m-bottom-70 {
-        margin-bottom: 70px !important;
-    display: block;
-    }
-    .margin-m-bottom-80 {
-        margin-bottom: 80px !important; 
-    display: block;
-    }
-    .margin-m-top-bottom-0 {
-        margin-top: 0 !important;
-        margin-bottom: 0 !important;
-    display: block;
-    }
-    .margin-m-top-bottom-10 {
-        margin-top: 10px !important;
-        margin-bottom: 10px !important;
-    display: block;
-    }
-    .margin-m-top-bottom-15 {
-        margin-top: 15px !important;
-        margin-bottom: 15px !important; 
-    display: block;
-    } 
-    .margin-m-top-bottom-20 {
-        margin-top: 20px !important;
-        margin-bottom: 20px !important; 
-    display: block;
-    } 
-    .margin-m-top-bottom-30 {
-        margin-top: 30px !important;
-        margin-bottom: 30px !important; 
-    display: block;
-    } 
-    .margin-m-top-bottom-40 {
-        margin-top: 40px !important;
-        margin-bottom: 40px !important; 
-    display: block;
-    }
-    .margin-m-top-bottom-50 {
-        margin-top: 50px !important;
-        margin-bottom: 50px !important;
-    display: block;
-    }
-    .margin-m-top-bottom-60 {
-        margin-top: 60px !important;
-        margin-bottom: 60px !important; 
-    display: block;
-    } 
-    .margin-m-top-bottom-70 {
-        margin-top: 70px !important;
-        margin-bottom: 70px !important;
-    display: block;
-    } 
-    .margin-m-top-bottom-80 {
-        margin-top: 80px !important;
-        margin-bottom: 80px !important;
-    display: block;
-    }
-    
-    .margin-m-left-0 {
-        margin-left: 0 !important;
-    }
-    .margin-m-left-10 {
-        margin-left: 10px !important;
-    }
-    .margin-m-left-15 {
-        margin-left: 15px !important;
-    } 
-    .margin-m-left-20 {
-        margin-left: 20px !important;
-    } 
-    .margin-m-left-30 {
-        margin-left: 30px !important;
-    } 
-    .margin-m-left-40 {
-        margin-left: 40px !important;
-    }
-    .margin-m-left-50 {
-        margin-left: 50px !important;
-    }
-    .margin-m-left-60 {
-        margin-left: 60px !important;
-    }
-    .margin-m-left-70 {
-        margin-left: 70px !important;
-    }
-    .margin-m-left-80 {
-        margin-left: 80px !important;
-    }
-    .margin-m-right-0 {
-        margin-right: 0 !important;
-    }
-    .margin-m-right-10 {
-        margin-right: 10px !important;
-    }
-    .margin-m-right-15 {
-        margin-right: 15px !important;
-    } 
-    .margin-m-right-20 {
-        margin-right: 20px !important;
-    } 
-    .margin-m-right-30 {
-        margin-right: 30px !important;
-    } 
-    .margin-m-right-40 {
-        margin-right: 40px !important;
-    }
-    .margin-m-right-50 {
-        margin-right: 50px !important;
-    }
-    .margin-m-right-60 {
-        margin-right: 60px !important;
-    }
-    .margin-m-right-70 {
-        margin-right: 70px !important;
-    }
-    .margin-m-right-80 {
-        margin-right: 80px !important;
-    }
-    .margin-m-left-right-0 {
-        margin-left: 0 !important;
-        margin-right: 0 !important;
-    }
-    .margin-m-left-right-10 {
-        margin-left: 10px !important;
-        margin-right: 10px !important;
-    }
-    .margin-m-left-right-15 {
-        margin-left: 15px !important;
-        margin-right: 15px !important;
-    } 
-    .margin-m-left-right-20 {
-        margin-left: 20px !important;
-        margin-right: 20px !important;
-    } 
-    .margin-m-left-right-30 {
-        margin-left: 30px !important;
-        margin-right: 30px !important;
-    } 
-    .margin-m-left-right-40 {
-        margin-left: 40px !important;
-        margin-right: 40px !important;
-    }
-    .margin-m-left-right-50 {
-        margin-left: 50px !important;
-        margin-right: 50px !important;
-    }
-    .margin-m-left-right-60 {
-        margin-left: 60px !important;
-        margin-right: 60px !important;
-    } 
-    .margin-m-left-right-70 {
-        margin-left: 70px !important;
-        margin-right: 70px !important;
-    } 
-    .margin-m-left-right-80 {
-        margin-left: 80px !important;
-        margin-right: 80px !important;
-    }  
-    .text-m-size-12 {
-      font-size: 12px !important;
-      line-height: 1.4;
-    }
-    .text-m-size-16 {
-        font-size: 16px !important;
-        line-height: 1.4;
-    }
-    .text-m-size-20 {
-        font-size: 20px !important;
-        line-height: 1.4;
-    }
-    .text-m-size-25 {
-        font-size: 25px !important;
-        line-height: 1.4;
-    }
-    .text-m-size-30 {
-        font-size: 30px !important;
-        line-height: 1.4;
-    }
-    .text-m-size-40 {
-        font-size: 40px !important;
-        line-height: 1.4;
-    }
-    .text-m-size-50 {
-        font-size: 50px !important;
-        line-height: 1.4;
-    }
-    .text-m-size-60 {
-        font-size: 60px !important;
-        line-height: 1.4;
-    }
-    .text-m-size-70 {
-        font-size: 70px !important;
-        line-height: 1.4;
-    } 
-    .owl-nav {
-      display: none;
-    }
-}  
+  .margin-m-left-0 {
+    margin-left: 0 !important;
+  }
+  .margin-m-left-10 {
+    margin-left: 10px !important;
+  }
+  .margin-m-left-15 {
+    margin-left: 15px !important;
+  }
+  .margin-m-left-20 {
+    margin-left: 20px !important;
+  }
+  .margin-m-left-30 {
+    margin-left: 30px !important;
+  }
+  .margin-m-left-40 {
+    margin-left: 40px !important;
+  }
+  .margin-m-left-50 {
+    margin-left: 50px !important;
+  }
+  .margin-m-left-60 {
+    margin-left: 60px !important;
+  }
+  .margin-m-left-70 {
+    margin-left: 70px !important;
+  }
+  .margin-m-left-80 {
+    margin-left: 80px !important;
+  }
+  .margin-m-right-0 {
+    margin-right: 0 !important;
+  }
+  .margin-m-right-10 {
+    margin-right: 10px !important;
+  }
+  .margin-m-right-15 {
+    margin-right: 15px !important;
+  }
+  .margin-m-right-20 {
+    margin-right: 20px !important;
+  }
+  .margin-m-right-30 {
+    margin-right: 30px !important;
+  }
+  .margin-m-right-40 {
+    margin-right: 40px !important;
+  }
+  .margin-m-right-50 {
+    margin-right: 50px !important;
+  }
+  .margin-m-right-60 {
+    margin-right: 60px !important;
+  }
+  .margin-m-right-70 {
+    margin-right: 70px !important;
+  }
+  .margin-m-right-80 {
+    margin-right: 80px !important;
+  }
+  .margin-m-left-right-0 {
+    margin-left: 0 !important;
+    margin-right: 0 !important;
+  }
+  .margin-m-left-right-10 {
+    margin-left: 10px !important;
+    margin-right: 10px !important;
+  }
+  .margin-m-left-right-15 {
+    margin-left: 15px !important;
+    margin-right: 15px !important;
+  }
+  .margin-m-left-right-20 {
+    margin-left: 20px !important;
+    margin-right: 20px !important;
+  }
+  .margin-m-left-right-30 {
+    margin-left: 30px !important;
+    margin-right: 30px !important;
+  }
+  .margin-m-left-right-40 {
+    margin-left: 40px !important;
+    margin-right: 40px !important;
+  }
+  .margin-m-left-right-50 {
+    margin-left: 50px !important;
+    margin-right: 50px !important;
+  }
+  .margin-m-left-right-60 {
+    margin-left: 60px !important;
+    margin-right: 60px !important;
+  }
+  .margin-m-left-right-70 {
+    margin-left: 70px !important;
+    margin-right: 70px !important;
+  }
+  .margin-m-left-right-80 {
+    margin-left: 80px !important;
+    margin-right: 80px !important;
+  }
+  .text-m-size-12 {
+    font-size: 12px !important;
+    line-height: 1.4;
+  }
+  .text-m-size-16 {
+    font-size: 16px !important;
+    line-height: 1.4;
+  }
+  .text-m-size-20 {
+    font-size: 20px !important;
+    line-height: 1.4;
+  }
+  .text-m-size-25 {
+    font-size: 25px !important;
+    line-height: 1.4;
+  }
+  .text-m-size-30 {
+    font-size: 30px !important;
+    line-height: 1.4;
+  }
+  .text-m-size-40 {
+    font-size: 40px !important;
+    line-height: 1.4;
+  }
+  .text-m-size-50 {
+    font-size: 50px !important;
+    line-height: 1.4;
+  }
+  .text-m-size-60 {
+    font-size: 60px !important;
+    line-height: 1.4;
+  }
+  .text-m-size-70 {
+    font-size: 70px !important;
+    line-height: 1.4;
+  }
+  .owl-nav {
+    display: none;
+  }
+}
 
 /* -480px version */
-@media screen and (max-width:480px) {
-    .top-bar .right {
-      float: none;
-    }
-    .top-bar-contact p {
-      height: auto;
-      line-height: 1.3rem;
-      padding: 10px 0;
-      text-align: center;
-    }
-    .top-bar-social.right {
-      display: table;
-      float: none;
-      margin: 0 auto;
-      padding: 0;
-      text-align: center;
-    }
-    .margin-s-top {
-        margin-top: 1.25rem !important;
-        display: block;
-    }
-    .margin-s-bottom {
-        margin-bottom: 1.25rem !important; 
-        display: block;
-    }
-    .margin-s-left {
-        margin-left: 1.25rem !important;
-    }
-    .margin-s-right {
-        margin-right: 1.25rem !important;
-    }
-    .margin-s-top-bottom {
-        margin-top: 1.25rem !important;
-        margin-bottom: 1.25rem !important;
-        display: block;
-    }
-    .margin-s-left-right {
-        margin-left: 1.25rem !important;
-        margin-right: 1.25rem !important;
-    }
-    .margin-s-top-0 {
-        margin-top: 0 !important; 
-        display: block;
-    }
-    .margin-s-top-10 {
-        margin-top: 10px !important;
-        display: block;
-    }
-    .margin-s-top-15 {
-        margin-top: 15px !important;
-        display: block;
-    } 
-    .margin-s-top-20 {
-        margin-top: 20px !important;
-        display: block;
-    } 
-    .margin-s-top-30 {
-        margin-top: 30px !important; 
-        display: block;
-    } 
-    .margin-s-top-40 {
-        margin-top: 40px !important; 
-        display: block;
-    }
-    .margin-s-top-50 {
-        margin-top: 50px !important;
-        display: block;
-    }
-    .margin-s-top-60 {
-        margin-top: 60px !important;
-        display: block;
-    }
-    .margin-s-top-70 {
-        margin-top: 70px !important;
-        display: block;
-    }
-    .margin-s-top-80 {
-        margin-top: 80px !important;
-        display: block;
-    }
-    .margin-s-bottom-0 {
-        margin-bottom: 0 !important; 
-        display: block;
-    }
-    .margin-s-bottom-10 {
-        margin-bottom: 10px !important;
-        display: block;
-    }
-    .margin-s-bottom-15 {
-        margin-bottom: 15px !important; 
-        display: block;
-    } 
-    .margin-s-bottom-20 {
-        margin-bottom: 20px !important; 
-        display: block;
-    } 
-    .margin-s-bottom-30 {
-        margin-bottom: 30px !important; 
-        display: block;
-    } 
-    .margin-s-bottom-40 {
-        margin-bottom: 40px !important;
-        display: block;
-    }
-    .margin-s-bottom-50 {
-        margin-bottom: 50px !important;
-        display: block;
-    }
-    .margin-s-bottom-60 {
-        margin-bottom: 60px !important; 
-        display: block;
-    }
-    .margin-s-bottom-70 {
-        margin-bottom: 70px !important; 
-        display: block;
-    }
-    .margin-s-bottom-80 {
-        margin-bottom: 80px !important;
-        display: block;
-    }
-    .margin-s-top-bottom-0 {
-        margin-top: 0 !important; 
-        margin-bottom: 0 !important;
-        display: block; 
-    }
-    .margin-s-top-bottom-10 {
-        margin-top: 10px !important; 
-        margin-bottom: 10px !important;
-        display: block; 
-    }
-    .margin-s-top-bottom-15 {
-        margin-top: 15px !important;
-        margin-bottom: 15px !important;
-        display: block;
-    } 
-    .margin-s-top-bottom-20 {
-        margin-top: 20px !important;  
-        margin-bottom: 20px !important; 
-        display: block;
-    } 
-    .margin-s-top-bottom-30 {
-        margin-top: 30px !important; 
-        margin-bottom: 30px !important; 
-        display: block;
-    } 
-    .margin-s-top-bottom-40 {
-        margin-top: 40px !important; 
-        margin-bottom: 40px !important;
-        display: block; 
-    }
-    .margin-s-top-bottom-50 {
-        margin-top: 50px !important; 
-        margin-bottom: 50px !important; 
-        display: block;
-    }
-    .margin-s-top-bottom-60 {
-        margin-top: 60px !important;
-        margin-bottom: 60px !important; 
-        display: block;
-    } 
-    .margin-s-top-bottom-70 {
-        margin-top: 70px !important; 
-        margin-bottom: 70px !important; 
-        display: block;
-    } 
-    .margin-s-top-bottom-80 {
-        margin-top: 80px !important;
-        margin-bottom: 80px !important; 
-        display: block;
-    }
-    
-    .margin-s-left-0 {
-        margin-left: 0 !important;
-    }
-    .margin-s-left-10 {
-        margin-left: 10px !important;
-    }
-    .margin-s-left-15 {
-        margin-left: 15px !important;
-    } 
-    .margin-s-left-20 {
-        margin-left: 20px !important;
-    } 
-    .margin-s-left-30 {
-        margin-left: 30px !important;
-    } 
-    .margin-s-left-40 {
-        margin-left: 40px !important;
-    }
-    .margin-s-left-50 {
-        margin-left: 50px !important;
-    }
-    .margin-s-left-60 {
-        margin-left: 60px !important;
-    }
-    .margin-s-left-70 {
-        margin-left: 70px !important;
-    }
-    .margin-s--80 {
-        margin-left: 80px !important;
-    }
-    .margin-s-right-0 {
-        margin-right: 0 !important;
-    }
-    .margin-s-right-10 {
-        margin-right: 10px !important;
-    }
-    .margin-s-right-15 {
-        margin-right: 15px !important;
-    } 
-    .margin-s-right-20 {
-        margin-right: 20px !important;
-    } 
-    .margin-s-right-30 {
-        margin-right: 30px !important;
-    } 
-    .margin-s-right-40 {
-        margin-right: 40px !important;
-    }
-    .margin-s-right-50 {
-        margin-right: 50px !important;
-    }
-    .margin-s-right-60 {
-        margin-right: 60px !important;
-    }
-    .margin-s-right-70 {
-        margin-right: 70px !important;
-    }
-    .margin-s-right-80 {
-        margin-right: 80px !important;
-    }
-    .margin-s-left-right-0 {
-        margin-left: 0 !important;
-        margin-right: 0 !important;
-    }
-    .margin-s-left-right-10 {
-        margin-left: 10px !important;
-        margin-right: 10px !important;
-    }
-    .margin-s-left-right-15 {
-        margin-left: 15px !important;
-        margin-right: 15px !important;
-    } 
-    .margin-s-left-right-20 {
-        margin-left: 20px !important;
-        margin-right: 20px !important;
-    } 
-    .margin-s-left-right-30 {
-        margin-left: 30px !important;
-        margin-right: 30px !important;
-    } 
-    .margin-s-left-right-40 {
-        margin-left: 40px !important;
-        margin-right: 40px !important;
-    }
-    .margin-s-left-right-50 {
-        margin-left: 50px !important;
-        margin-right: 50px !important;
-    }
-    .margin-s-left-right-60 {
-        margin-left: 60px !important;
-        margin-right: 60px !important;
-    } 
-    .margin-s-left-right-70 {
-        margin-left: 70px !important;
-        margin-right: 70px !important;
-    } 
-    .margin-s-left-right-80 {
-        margin-left: 80px !important;
-        margin-right: 80px !important;
-    }
-    .text-s-size-12 {
-      font-size: 12px !important;
-      line-height: 1.4;
-    }
-    .text-s-size-16 {
-        font-size: 16px !important;
-        line-height: 1.4;
-    }
-    .text-s-size-20 {
-        font-size: 20px !important;
-        line-height: 1.4;
-    }
-    .text-s-size-25 {
-        font-size: 25px !important;
-        line-height: 1.4;
-    }
-    .text-s-size-30 {
-        font-size: 30px !important;
-        line-height: 1.4;
-    }
-    .text-s-size-40 {
-        font-size: 40px !important;
-        line-height: 1.4;
-    }
-    .text-s-size-50 {
-        font-size: 50px !important;
-        line-height: 1.4;
-    }
-    .text-s-size-60 {
-        font-size: 60px !important;
-        line-height: 1.4;
-    }
-    .text-s-size-70 {
-        font-size: 70px !important;
-        line-height: 1.4;
-    }
-} 
+@media screen and (max-width: 480px) {
+  .top-bar .right {
+    float: none;
+  }
+  .top-bar-contact p {
+    height: auto;
+    line-height: 1.3rem;
+    padding: 10px 0;
+    text-align: center;
+  }
+  .top-bar-social.right {
+    display: table;
+    float: none;
+    margin: 0 auto;
+    padding: 0;
+    text-align: center;
+  }
+  .margin-s-top {
+    margin-top: 1.25rem !important;
+    display: block;
+  }
+  .margin-s-bottom {
+    margin-bottom: 1.25rem !important;
+    display: block;
+  }
+  .margin-s-left {
+    margin-left: 1.25rem !important;
+  }
+  .margin-s-right {
+    margin-right: 1.25rem !important;
+  }
+  .margin-s-top-bottom {
+    margin-top: 1.25rem !important;
+    margin-bottom: 1.25rem !important;
+    display: block;
+  }
+  .margin-s-left-right {
+    margin-left: 1.25rem !important;
+    margin-right: 1.25rem !important;
+  }
+  .margin-s-top-0 {
+    margin-top: 0 !important;
+    display: block;
+  }
+  .margin-s-top-10 {
+    margin-top: 10px !important;
+    display: block;
+  }
+  .margin-s-top-15 {
+    margin-top: 15px !important;
+    display: block;
+  }
+  .margin-s-top-20 {
+    margin-top: 20px !important;
+    display: block;
+  }
+  .margin-s-top-30 {
+    margin-top: 30px !important;
+    display: block;
+  }
+  .margin-s-top-40 {
+    margin-top: 40px !important;
+    display: block;
+  }
+  .margin-s-top-50 {
+    margin-top: 50px !important;
+    display: block;
+  }
+  .margin-s-top-60 {
+    margin-top: 60px !important;
+    display: block;
+  }
+  .margin-s-top-70 {
+    margin-top: 70px !important;
+    display: block;
+  }
+  .margin-s-top-80 {
+    margin-top: 80px !important;
+    display: block;
+  }
+  .margin-s-bottom-0 {
+    margin-bottom: 0 !important;
+    display: block;
+  }
+  .margin-s-bottom-10 {
+    margin-bottom: 10px !important;
+    display: block;
+  }
+  .margin-s-bottom-15 {
+    margin-bottom: 15px !important;
+    display: block;
+  }
+  .margin-s-bottom-20 {
+    margin-bottom: 20px !important;
+    display: block;
+  }
+  .margin-s-bottom-30 {
+    margin-bottom: 30px !important;
+    display: block;
+  }
+  .margin-s-bottom-40 {
+    margin-bottom: 40px !important;
+    display: block;
+  }
+  .margin-s-bottom-50 {
+    margin-bottom: 50px !important;
+    display: block;
+  }
+  .margin-s-bottom-60 {
+    margin-bottom: 60px !important;
+    display: block;
+  }
+  .margin-s-bottom-70 {
+    margin-bottom: 70px !important;
+    display: block;
+  }
+  .margin-s-bottom-80 {
+    margin-bottom: 80px !important;
+    display: block;
+  }
+  .margin-s-top-bottom-0 {
+    margin-top: 0 !important;
+    margin-bottom: 0 !important;
+    display: block;
+  }
+  .margin-s-top-bottom-10 {
+    margin-top: 10px !important;
+    margin-bottom: 10px !important;
+    display: block;
+  }
+  .margin-s-top-bottom-15 {
+    margin-top: 15px !important;
+    margin-bottom: 15px !important;
+    display: block;
+  }
+  .margin-s-top-bottom-20 {
+    margin-top: 20px !important;
+    margin-bottom: 20px !important;
+    display: block;
+  }
+  .margin-s-top-bottom-30 {
+    margin-top: 30px !important;
+    margin-bottom: 30px !important;
+    display: block;
+  }
+  .margin-s-top-bottom-40 {
+    margin-top: 40px !important;
+    margin-bottom: 40px !important;
+    display: block;
+  }
+  .margin-s-top-bottom-50 {
+    margin-top: 50px !important;
+    margin-bottom: 50px !important;
+    display: block;
+  }
+  .margin-s-top-bottom-60 {
+    margin-top: 60px !important;
+    margin-bottom: 60px !important;
+    display: block;
+  }
+  .margin-s-top-bottom-70 {
+    margin-top: 70px !important;
+    margin-bottom: 70px !important;
+    display: block;
+  }
+  .margin-s-top-bottom-80 {
+    margin-top: 80px !important;
+    margin-bottom: 80px !important;
+    display: block;
+  }
+
+  .margin-s-left-0 {
+    margin-left: 0 !important;
+  }
+  .margin-s-left-10 {
+    margin-left: 10px !important;
+  }
+  .margin-s-left-15 {
+    margin-left: 15px !important;
+  }
+  .margin-s-left-20 {
+    margin-left: 20px !important;
+  }
+  .margin-s-left-30 {
+    margin-left: 30px !important;
+  }
+  .margin-s-left-40 {
+    margin-left: 40px !important;
+  }
+  .margin-s-left-50 {
+    margin-left: 50px !important;
+  }
+  .margin-s-left-60 {
+    margin-left: 60px !important;
+  }
+  .margin-s-left-70 {
+    margin-left: 70px !important;
+  }
+  .margin-s--80 {
+    margin-left: 80px !important;
+  }
+  .margin-s-right-0 {
+    margin-right: 0 !important;
+  }
+  .margin-s-right-10 {
+    margin-right: 10px !important;
+  }
+  .margin-s-right-15 {
+    margin-right: 15px !important;
+  }
+  .margin-s-right-20 {
+    margin-right: 20px !important;
+  }
+  .margin-s-right-30 {
+    margin-right: 30px !important;
+  }
+  .margin-s-right-40 {
+    margin-right: 40px !important;
+  }
+  .margin-s-right-50 {
+    margin-right: 50px !important;
+  }
+  .margin-s-right-60 {
+    margin-right: 60px !important;
+  }
+  .margin-s-right-70 {
+    margin-right: 70px !important;
+  }
+  .margin-s-right-80 {
+    margin-right: 80px !important;
+  }
+  .margin-s-left-right-0 {
+    margin-left: 0 !important;
+    margin-right: 0 !important;
+  }
+  .margin-s-left-right-10 {
+    margin-left: 10px !important;
+    margin-right: 10px !important;
+  }
+  .margin-s-left-right-15 {
+    margin-left: 15px !important;
+    margin-right: 15px !important;
+  }
+  .margin-s-left-right-20 {
+    margin-left: 20px !important;
+    margin-right: 20px !important;
+  }
+  .margin-s-left-right-30 {
+    margin-left: 30px !important;
+    margin-right: 30px !important;
+  }
+  .margin-s-left-right-40 {
+    margin-left: 40px !important;
+    margin-right: 40px !important;
+  }
+  .margin-s-left-right-50 {
+    margin-left: 50px !important;
+    margin-right: 50px !important;
+  }
+  .margin-s-left-right-60 {
+    margin-left: 60px !important;
+    margin-right: 60px !important;
+  }
+  .margin-s-left-right-70 {
+    margin-left: 70px !important;
+    margin-right: 70px !important;
+  }
+  .margin-s-left-right-80 {
+    margin-left: 80px !important;
+    margin-right: 80px !important;
+  }
+  .text-s-size-12 {
+    font-size: 12px !important;
+    line-height: 1.4;
+  }
+  .text-s-size-16 {
+    font-size: 16px !important;
+    line-height: 1.4;
+  }
+  .text-s-size-20 {
+    font-size: 20px !important;
+    line-height: 1.4;
+  }
+  .text-s-size-25 {
+    font-size: 25px !important;
+    line-height: 1.4;
+  }
+  .text-s-size-30 {
+    font-size: 30px !important;
+    line-height: 1.4;
+  }
+  .text-s-size-40 {
+    font-size: 40px !important;
+    line-height: 1.4;
+  }
+  .text-s-size-50 {
+    font-size: 50px !important;
+    line-height: 1.4;
+  }
+  .text-s-size-60 {
+    font-size: 60px !important;
+    line-height: 1.4;
+  }
+  .text-s-size-70 {
+    font-size: 70px !important;
+    line-height: 1.4;
+  }
+}
 
 /* Typography */
 .text-uppercase {
@@ -1884,12 +2219,22 @@ p.form-success {
 .text-padding-small {
   display: inline-block !important;
   padding: 7px 10px;
-}  
-
+}
 
 /* Custom Template Styles */
 
-h1, h2, h3, h4, h5, h6, .h1, .h2, .h3, .h4, .h5, .h6 {
+h1,
+h2,
+h3,
+h4,
+h5,
+h6,
+.h1,
+.h2,
+.h3,
+.h4,
+.h5,
+.h6 {
   font-family: "Playfair Display";
 }
 
@@ -1899,7 +2244,7 @@ blockquote {
 }
 
 blockquote:before {
-  display:none;
+  display: none;
 }
 header.position-absolute {
   position: absolute;
@@ -1921,22 +2266,26 @@ nav {
   z-index: 2;
 }
 .logo-dark {
-  display:none;
+  display: none;
 }
-nav.fixed, .fixed nav {
+nav.fixed,
+.fixed nav {
   background: #fff;
   border-bottom: 1px solid rgba(0, 0, 0, 0.09);
   padding: 0 2em;
 }
-nav.fixed .top-nav li a, .fixed nav .top-nav li a {
-  color: #444;  
+nav.fixed .top-nav li a,
+.fixed nav .top-nav li a {
+  color: #444;
+}
+nav.fixed .logo-white,
+.fixed nav .logo-white {
+  display: none;
 }
-nav.fixed .logo-white, .fixed nav .logo-white {
-  display:none;
+nav.fixed .logo-dark,
+.fixed nav .logo-dark {
+  display: block;
 }
-nav.fixed .logo-dark, .fixed nav .logo-dark {
-  display:block;
-}  
 .background-transparent {
   background: none;
 }
@@ -1952,12 +2301,12 @@ nav.fixed .logo-dark, .fixed nav .logo-dark {
   color: #fff;
   padding: 1.5rem;
   opacity: 0.85;
-  transition: all 0.20s linear 0s;
--o-transition: all 0.20s linear 0s;
--ms-transition: all 0.20s linear 0s;
--moz-transition: all 0.20s linear 0s;
--webkit-transition: all 0.20s linear 0s;
-} 
+  transition: all 0.2s linear 0s;
+  -o-transition: all 0.2s linear 0s;
+  -ms-transition: all 0.2s linear 0s;
+  -moz-transition: all 0.2s linear 0s;
+  -webkit-transition: all 0.2s linear 0s;
+}
 
 .top-nav ul ul {
   background: #fff none repeat scroll 0 0;
@@ -1968,26 +2317,55 @@ nav.fixed .logo-dark, .fixed nav .logo-dark {
 .top-nav li ul li:last-child {
   border-bottom: 0;
 }
-.top-nav li ul li a, .background-white .top-nav li ul li a, .top-nav .active-item li a {
+.top-nav li ul li a,
+.background-white .top-nav li ul li a,
+.top-nav .active-item li a {
   background: #fff none repeat scroll 0 0;
-  color: rgba(0,0,0, 0.75);
+  color: rgba(0, 0, 0, 0.75);
 }
 
-.background-transparent-hightlight .top-nav .active-item > a, .background-transparent-hightlight .top-nav li a:hover, .background-transparent-hightlight .aside-nav li a:hover, .background-transparent-hightlight .aside-nav > ul > li.active-item > a:link, .background-transparent-hightlight .aside-nav > ul > li.active-item > a:visited {
+.background-transparent-hightlight .top-nav .active-item > a,
+.background-transparent-hightlight .top-nav li a:hover,
+.background-transparent-hightlight .aside-nav li a:hover,
+.background-transparent-hightlight .aside-nav > ul > li.active-item > a:link,
+.background-transparent-hightlight
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:visited {
   background: rgba(255, 255, 255, 0.08) none repeat scroll 0 0;
   color: #fff;
   opacity: 1;
 }
-nav.background-transparent-hightlight.fixed .top-nav .active-item > a, nav.background-transparent-hightlight.fixed .top-nav li a:hover, nav.background-transparent-hightlight.fixed .aside-nav li a:hover, nav.background-transparent-hightlight.fixed .aside-nav > ul > li.active-item > a:link, nav.background-transparent-hightlight.fixed .aside-nav > ul > li.active-item > a:visited {
+nav.background-transparent-hightlight.fixed .top-nav .active-item > a,
+nav.background-transparent-hightlight.fixed .top-nav li a:hover,
+nav.background-transparent-hightlight.fixed .aside-nav li a:hover,
+nav.background-transparent-hightlight.fixed
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:link,
+nav.background-transparent-hightlight.fixed
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:visited {
   background: none;
   color: #000;
   opacity: 1;
 }
-.background-transparent-hightlight .top-nav ul ul .active-item a, .background-transparent-hightlight .top-nav ul ul li a:hover, .background-transparent-hightlight .aside-nav ul ul li a:hover, .background-transparent-hightlight .aside-nav > ul > li.active-item > a:link, .background-transparent-hightlight .aside-nav > ul > li.active-item > a:visited {
+.background-transparent-hightlight .top-nav ul ul .active-item a,
+.background-transparent-hightlight .top-nav ul ul li a:hover,
+.background-transparent-hightlight .aside-nav ul ul li a:hover,
+.background-transparent-hightlight .aside-nav > ul > li.active-item > a:link,
+.background-transparent-hightlight
+  .aside-nav
+  > ul
+  > li.active-item
+  > a:visited {
   color: #000;
 }
 
-
 /* Carousel Navigation*/
 .owl-carousel .owl-dot span {
   height: 10px;
@@ -1999,7 +2377,7 @@ nav.background-transparent-hightlight.fixed .top-nav .active-item > a, nav.backg
 }
 .owl-carousel .owl-nav div {
   border: 0 none;
-  color: #C9C9C9 !important;
+  color: #c9c9c9 !important;
   font-family: sli;
   font-size: 30px;
   height: auto;
@@ -2011,28 +2389,31 @@ nav.background-transparent-hightlight.fixed .top-nav .active-item > a, nav.backg
 }
 
 /* Buttons */
-.button, a.button, a.button:link, a.button:visited {
-border: 0;
+.button,
+a.button,
+a.button:link,
+a.button:visited {
+  border: 0;
 }
 
 /* Image blocks */
 .image-hover-zoom img {
-  transition: all 0.50s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
-  -o-transition: all 0.50s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
-  -ms-transition: all 0.50s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
-  -moz-transition: all 0.50s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
-  -webkit-transition: all 0.50s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
+  transition: all 0.5s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
+  -o-transition: all 0.5s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
+  -ms-transition: all 0.5s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
+  -moz-transition: all 0.5s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
+  -webkit-transition: all 0.5s cubic-bezier(0.645, 0.045, 0.355, 1) 0s;
 }
 .owl-item .image-testimonial-small {
   margin: 0 auto 20px;
-  width: auto!important;
-} 
+  width: auto !important;
+}
 
 video {
   width: 100%;
 }
 
-@media screen and (max-width:768px) {
+@media screen and (max-width: 768px) {
   header.position-absolute {
     background: #fff none repeat scroll 0 0;
     position: relative;
@@ -2045,14 +2426,14 @@ video {
     max-width: 172px;
     max-height: 40px;
     margin: 0 auto;
-    width: auto; 
+    width: auto;
     top: 0;
-  } 
+  }
   .logo img.logo-white {
-    display:none;
+    display: none;
   }
   .logo img.logo-dark {
-    display:block;
+    display: block;
   }
   .nav-text::after {
     color: #002633;
@@ -2064,12 +2445,14 @@ video {
   .fixed .nav-text::after {
     color: #002633;
   }
-  .top-nav li a,.top-nav li ul li a {
+  .top-nav li a,
+  .top-nav li ul li a {
     border-top: 0;
-    color: #fff!important;
+    color: #fff !important;
     opacity: 1;
   }
-  .top-nav li a, .background-white .top-nav li a {
+  .top-nav li a,
+  .background-white .top-nav li a {
     background: none repeat scroll 0 0 #1c3849;
     font-size: 1.5em;
     padding: 1.2em 1em;
@@ -2082,10 +2465,19 @@ video {
   .top-nav li ul li {
     border-bottom: 0;
   }
-  nav.fixed .top-nav li a, .fixed nav .top-nav li a {
-    color: #777;  
+  nav.fixed .top-nav li a,
+  .fixed nav .top-nav li a {
+    color: #777;
   }
-  .background-transparent-hightlight .top-nav .active-item > a, .background-transparent-hightlight .top-nav li a:hover, .background-transparent-hightlight .aside-nav li a:hover, .background-transparent-hightlight .aside-nav > ul > li.active-item > a:link, .background-transparent-hightlight .aside-nav > ul > li.active-item > a:visited {
+  .background-transparent-hightlight .top-nav .active-item > a,
+  .background-transparent-hightlight .top-nav li a:hover,
+  .background-transparent-hightlight .aside-nav li a:hover,
+  .background-transparent-hightlight .aside-nav > ul > li.active-item > a:link,
+  .background-transparent-hightlight
+    .aside-nav
+    > ul
+    > li.active-item
+    > a:visited {
     color: #fff;
   }
   .carousel-3-blocks {
@@ -2096,4 +2488,4 @@ video {
   .background-image {
     background-position: center;
   }
-}    
\ No newline at end of file
+}
diff --git a/documentation.html b/documentation.html
index dfd7622..c85b777 100644
--- a/documentation.html
+++ b/documentation.html
@@ -1,66 +1,149 @@
 <!DOCTYPE html>
 <html lang="en-US">
   <head>
-    <meta charset="UTF-8">
+    <meta charset="UTF-8" />
     <meta http-equiv="X-UA-Compatible" content="chrome=1" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <meta name="description" content="PEcAn : The Predictive Ecosystem Analyzer" />
-    <meta name="google-site-verification" content="WiPnxPvenKX6-C6fNrwp9v64f23Q1qYw26Kapyswgms" />
-    <link rel="stylesheet" type="text/css" media="screen" href="stylesheets/stylesheet.css">
+    <meta
+      name="description"
+      content="PEcAn : The Predictive Ecosystem Analyzer"
+    />
+    <meta
+      name="google-site-verification"
+      content="WiPnxPvenKX6-C6fNrwp9v64f23Q1qYw26Kapyswgms"
+    />
+    <link
+      rel="stylesheet"
+      type="text/css"
+      media="screen"
+      href="stylesheets/stylesheet.css"
+    />
     <title>PEcAn</title>
-    <link rel="stylesheet" href="css/components.css">
-    <link rel="stylesheet" href="css/icons.css">
-    <link rel="stylesheet" href="css/responsee.css">
-    <link rel="stylesheet" href="owl-carousel/owl.carousel.css">
-    <link rel="stylesheet" href="owl-carousel/owl.theme.css">     
-    <link rel="stylesheet" href="css/template-style.css">
-    <link href='https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
-    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
+    <link rel="stylesheet" href="css/components.css" />
+    <link rel="stylesheet" href="css/icons.css" />
+    <link rel="stylesheet" href="css/responsee.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.carousel.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.theme.css" />
+    <link rel="stylesheet" href="css/template-style.css" />
+    <link
+      href="https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
+    <link
+      href="https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
     <script type="text/javascript" src="js/jquery-1.8.3.min.js"></script>
-    <script type="text/javascript" src="js/jquery-ui.min.js"></script>      
+    <script type="text/javascript" src="js/jquery-ui.min.js"></script>
   </head>
-  
+
   <body class="size-1140">
-  	<a target="_blank" class="hide-s" href="https://github.com/PecanProject" style="position:fixed;top:120px;right:-14px;z-index:10;"><img src="images/view-on-github.png" alt="" style="width: 200px; padding-right: 10px;"></a>
-    
+    <a
+      target="_blank"
+      class="hide-s"
+      href="https://github.com/PecanProject"
+      style="position:fixed;top:120px;right:-14px;z-index:10;"
+      ><img
+        src="images/view-on-github.png"
+        alt=""
+        style="width: 200px; padding-right: 10px;"
+    /></a>
+
     <!-- HEADER -->
-    
-        <header role="banner" class="position-absolute">    
+
+    <header role="banner" class="position-absolute">
       <!-- Top Navigation -->
       <nav class="background-dark background-transparent-hightlight full-width">
         <div class="s-12 l-2">
           <a href="index.html" class="logo">
             <!-- Logo White Version -->
-            <img class="logo-white" src="images/logo.png" alt="">
+            <img class="logo-white" src="images/logo.png" alt="" />
             <!-- Logo Dark Version -->
-            <img class="logo-dark" src="images/logo.png" alt="">
+            <img class="logo-dark" src="images/logo.png" alt="" />
           </a>
         </div>
         <div class="top-nav s-12 l-10 background-dark">
-          
           <ul class="right chevron">
             <li><a href="index.html">Home</a></li>
-            <li><a>About</a>
+            <li>
+              <a>About</a>
               <ul>
-                <li><a href="people.html" style="color: black;font-weight: 800;">People</a></li>
-                <li><a href="news.html" style="color: black;font-weight: 800;">News</a></li>
-                <li><a href="pecan_workshop.html" style="color: black;font-weight: 800;">Workshop</a></li>
-                <li><a href="contact.html" style="color: black;font-weight: 800;">Contact Us</a></li>
+                <li>
+                  <a href="people.html" style="color: black;font-weight: 800;"
+                    >People</a
+                  >
+                </li>
+                <li>
+                  <a href="news.html" style="color: black;font-weight: 800;"
+                    >News</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="pecan_workshop.html"
+                    style="color: black;font-weight: 800;"
+                    >Workshop</a
+                  >
+                </li>
+                <li>
+                  <a href="contact.html" style="color: black;font-weight: 800;"
+                    >Contact Us</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a>Documentation</a>
+            <li>
+              <a>Documentation</a>
               <ul>
-                <li><a href="documentation.html" style="color: black;font-weight: 800;">Documentation</a></li>
-                <li><a href="pkgdocs.html" style="color: black;font-weight: 800;">Package Documentation</a></li>
-                <li><a href="tutorials.html" style="color: black;font-weight: 800;">Tutorials</a></li>
-                <li><a href="http://pecan.ncsa.illinois.edu/pecan" style="color: black;font-weight: 800;">Demo</a></li>
+                <li>
+                  <a
+                    href="documentation.html"
+                    style="color: black;font-weight: 800;"
+                    >Documentation</a
+                  >
+                </li>
+                <li>
+                  <a href="pkgdocs.html" style="color: black;font-weight: 800;"
+                    >Package Documentation</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="tutorials.html"
+                    style="color: black;font-weight: 800;"
+                    >Tutorials</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="http://pecan.ncsa.illinois.edu/pecan"
+                    style="color: black;font-weight: 800;"
+                    >Demo</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN">Download</a></li>
-            <li><a>Google</a>
+            <li>
+              <a
+                href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN"
+                >Download</a
+              >
+            </li>
+            <li>
+              <a>Google</a>
               <ul>
-                <li><a href="gsoc.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
-                <li><a href="gsod.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
+                <li>
+                  <a href="gsoc.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
+                <li>
+                  <a href="gsod.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
               </ul>
             </li>
             <li><a href="Report_an_issue.html">Bug Report</a></li>
@@ -69,69 +152,136 @@
       </nav>
     </header>
 
-  
     <!--Main Content-->
 
-<section class="section background-white text-center">
-  <div id="main_content_wrap" class="outer">
+    <section class="section background-white text-center">
+      <div id="main_content_wrap" class="outer">
+        <h1
+          class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1"
+        >
+          Latest Release Documentation
+        </h1>
+        <a
+          href="https://pecanproject.github.io/pecan-documentation/master"
+          class="text-size-20 text-m-size-16"
+          style="color: blue;"
+          ><u
+            >Documentation consistent with latest release (MASTER BRANCH).</u
+          ></a
+        >
 
-    <h1 class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1">Latest Release Documentation</h1>
-    <a href="https://pecanproject.github.io/pecan-documentation/master" class="text-size-20 text-m-size-16" style="color: blue;"><u>Documentation consistent with latest release (MASTER BRANCH).</u></a>
+        <h1
+          class="text-dark margin-bottom-30 margin-top-30 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1"
+        >
+          Latest Code Documentation
+        </h1>
+        <a
+          href="https://pecanproject.github.io/pecan-documentation/develop"
+          class="text-size-20 text-m-size-16"
+          style="color: blue;"
+          ><u
+            >Documentation consistent with latest stable code (DEVELOP
+            BRANCH).</u
+          ></a
+        >
 
-    <h1 class="text-dark margin-bottom-30 margin-top-30 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1">Latest Code Documentation</h1>
-    <a href="https://pecanproject.github.io/pecan-documentation/develop" class="text-size-20 text-m-size-16" style="color: blue;"><u>Documentation consistent with latest stable code (DEVELOP BRANCH).</u></a>
+        <h1
+          class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1"
+        >
+          Release V1.5.3
+        </h1>
+        <a
+          href="https://pecanproject.github.io/pecan-documentation/v1.5.3"
+          class="text-size-20 text-m-size-16"
+          style="color: blue;"
+          ><u>Documentation consistent with release 1.5.3</u></a
+        >
 
-    <h1 class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1">Release V1.5.3</h1>
-    <a href="https://pecanproject.github.io/pecan-documentation/v1.5.3" class="text-size-20 text-m-size-16" style="color: blue;"><u>Documentation consistent with release 1.5.3</u></a>
+        <h1
+          class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1"
+        >
+          Release V1.5.1
+        </h1>
+        <a
+          href="https://pecanproject.github.io/pecan-documentation/v1.5.1"
+          class="text-size-20 text-m-size-16"
+          style="color: blue;"
+          ><u>Documentation consistent with release 1.5.1</u></a
+        >
 
-    <h1 class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1">Release V1.5.1</h1>
-    <a href="https://pecanproject.github.io/pecan-documentation/v1.5.1" class="text-size-20 text-m-size-16" style="color: blue;"><u>Documentation consistent with release 1.5.1</u></a>
+        <h1
+          class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1"
+        >
+          Release V1.5.0
+        </h1>
+        <a
+          href="https://pecanproject.github.io/pecan-documentation/1.5.0"
+          class="text-size-20 text-m-size-16"
+          style="color: blue;"
+          ><u>Documentation consistent with release 1.5.0</u></a
+        >
 
-    <h1 class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1">Release V1.5.0</h1>
-    <a href="https://pecanproject.github.io/pecan-documentation/1.5.0" class="text-size-20 text-m-size-16" style="color: blue;"><u>Documentation consistent with release 1.5.0</u></a>
+        <h1
+          class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1"
+        >
+          Release V1.4.10.1
+        </h1>
+        <a
+          href="https://pecanproject.github.io/pecan-documentation/master"
+          class="text-size-20 text-m-size-16"
+          style="color: blue;"
+          ><u>Documentation consistent with release 4.10.1</u></a
+        >
+      </div>
+    </section>
 
-    <h1 class="text-dark margin-bottom-30 margin-top-60 margin-m-top-30 text-size-20 text-m-size-16 text-line-height-1">Release V1.4.10.1</h1>
-    <a href="https://pecanproject.github.io/pecan-documentation/master" class="text-size-20 text-m-size-16" style="color: blue;"><u>Documentation consistent with release 4.10.1</u></a>
+    <!-- scripts -->
 
-  </div>
-  </section>
-  
-  <!-- scripts -->    
+    <script type="text/javascript" src="js/responsee.js"></script>
+    <script type="text/javascript" src="owl-carousel/owl.carousel.js"></script>
+    <script type="text/javascript" src="js/template-scripts.js"></script>
 
-<script type="text/javascript" src="js/responsee.js"></script>
-<script type="text/javascript" src="owl-carousel/owl.carousel.js"></script>
-<script type="text/javascript" src="js/template-scripts.js"></script>
-
-<!-- FOOTER  -->
+    <!-- FOOTER  -->
     <div id="footer_wrap" class="outer">
       <footer class="inner">
-        <p>Published with <a href="http://pages.github.com" style="color: rgb(255, 255, 255);" >GitHub Pages</a></p>
+        <p>
+          Published with
+          <a href="http://pages.github.com" style="color: rgb(255, 255, 255);"
+            >GitHub Pages</a
+          >
+        </p>
       </footer>
     </div>
 
-  <script>
-    (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-    (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
-    m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
-    })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-
-    ga('create', 'UA-28628282-1', 'pecanproject.github.io');
-    ga('require', 'displayfeatures');
-    ga('send', 'pageview');
-
-  </script>
-  <script>
-    ((window.gitter = {}).chat = {}).options = {
-  room: 'PecanProject/pecan'
-    };
-  </script>
-
+    <script>
+      (function(i, s, o, g, r, a, m) {
+        i["GoogleAnalyticsObject"] = r;
+        (i[r] =
+          i[r] ||
+          function() {
+            (i[r].q = i[r].q || []).push(arguments);
+          }),
+          (i[r].l = 1 * new Date());
+        (a = s.createElement(o)), (m = s.getElementsByTagName(o)[0]);
+        a.async = 1;
+        a.src = g;
+        m.parentNode.insertBefore(a, m);
+      })(
+        window,
+        document,
+        "script",
+        "//www.google-analytics.com/analytics.js",
+        "ga"
+      );
 
+      ga("create", "UA-28628282-1", "pecanproject.github.io");
+      ga("require", "displayfeatures");
+      ga("send", "pageview");
+    </script>
+    <script>
+      ((window.gitter = {}).chat = {}).options = {
+        room: "PecanProject/pecan"
+      };
+    </script>
   </body>
 </html>
-
-
-
-
-
-
diff --git a/gsoc.html b/gsoc.html
index eaae20f..116febe 100644
--- a/gsoc.html
+++ b/gsoc.html
@@ -1,66 +1,149 @@
 <!DOCTYPE html>
 <html lang="en-US">
   <head>
-    <meta charset="UTF-8">
+    <meta charset="UTF-8" />
     <meta http-equiv="X-UA-Compatible" content="chrome=1" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <meta name="description" content="PEcAn : The Predictive Ecosystem Analyzer" />
-    <meta name="google-site-verification" content="WiPnxPvenKX6-C6fNrwp9v64f23Q1qYw26Kapyswgms" />
-    <link rel="stylesheet" type="text/css" media="screen" href="stylesheets/stylesheet.css">
+    <meta
+      name="description"
+      content="PEcAn : The Predictive Ecosystem Analyzer"
+    />
+    <meta
+      name="google-site-verification"
+      content="WiPnxPvenKX6-C6fNrwp9v64f23Q1qYw26Kapyswgms"
+    />
+    <link
+      rel="stylesheet"
+      type="text/css"
+      media="screen"
+      href="stylesheets/stylesheet.css"
+    />
     <title>PEcAn</title>
-    <link rel="stylesheet" href="css/components.css">
-    <link rel="stylesheet" href="css/icons.css">
-    <link rel="stylesheet" href="css/responsee.css">
-    <link rel="stylesheet" href="owl-carousel/owl.carousel.css">
-    <link rel="stylesheet" href="owl-carousel/owl.theme.css">     
-    <link rel="stylesheet" href="css/template-style.css">
-    <link href='https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
-    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
+    <link rel="stylesheet" href="css/components.css" />
+    <link rel="stylesheet" href="css/icons.css" />
+    <link rel="stylesheet" href="css/responsee.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.carousel.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.theme.css" />
+    <link rel="stylesheet" href="css/template-style.css" />
+    <link
+      href="https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
+    <link
+      href="https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
     <script type="text/javascript" src="js/jquery-1.8.3.min.js"></script>
-    <script type="text/javascript" src="js/jquery-ui.min.js"></script>      
+    <script type="text/javascript" src="js/jquery-ui.min.js"></script>
   </head>
-  
+
   <body class="size-1140">
-  	<a target="_blank" class="hide-s" href="https://github.com/PecanProject" style="position:fixed;top:120px;right:-14px;z-index:10;"><img src="images/view-on-github.png" alt="" style="width: 200px; padding-right: 10px;"></a>
-    
+    <a
+      target="_blank"
+      class="hide-s"
+      href="https://github.com/PecanProject"
+      style="position:fixed;top:120px;right:-14px;z-index:10;"
+      ><img
+        src="images/view-on-github.png"
+        alt=""
+        style="width: 200px; padding-right: 10px;"
+    /></a>
+
     <!-- HEADER -->
 
-        <header role="banner" class="position-absolute">    
+    <header role="banner" class="position-absolute">
       <!-- Top Navigation -->
       <nav class="background-dark background-transparent-hightlight full-width">
         <div class="s-12 l-2">
           <a href="index.html" class="logo">
             <!-- Logo White Version -->
-            <img class="logo-white" src="images/logo.png" alt="">
+            <img class="logo-white" src="images/logo.png" alt="" />
             <!-- Logo Dark Version -->
-            <img class="logo-dark" src="images/logo.png" alt="">
+            <img class="logo-dark" src="images/logo.png" alt="" />
           </a>
         </div>
         <div class="top-nav s-12 l-10 background-dark">
-          
           <ul class="right chevron">
             <li><a href="index.html">Home</a></li>
-            <li><a>About</a>
+            <li>
+              <a>About</a>
               <ul>
-                <li><a href="people.html" style="color: black;font-weight: 800;">People</a></li>
-                <li><a href="news.html" style="color: black;font-weight: 800;">News</a></li>
-                <li><a href="pecan_workshop.html" style="color: black;font-weight: 800;">Workshop</a></li>
-                <li><a href="contact.html" style="color: black;font-weight: 800;">Contact Us</a></li>
+                <li>
+                  <a href="people.html" style="color: black;font-weight: 800;"
+                    >People</a
+                  >
+                </li>
+                <li>
+                  <a href="news.html" style="color: black;font-weight: 800;"
+                    >News</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="pecan_workshop.html"
+                    style="color: black;font-weight: 800;"
+                    >Workshop</a
+                  >
+                </li>
+                <li>
+                  <a href="contact.html" style="color: black;font-weight: 800;"
+                    >Contact Us</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a>Documentation</a>
+            <li>
+              <a>Documentation</a>
               <ul>
-                <li><a href="documentation.html" style="color: black;font-weight: 800;">Documentation</a></li>
-                <li><a href="pkgdocs.html" style="color: black;font-weight: 800;">Package Documentation</a></li>
-                <li><a href="tutorials.html" style="color: black;font-weight: 800;">Tutorials</a></li>
-                <li><a href="http://pecan.ncsa.illinois.edu/pecan" style="color: black;font-weight: 800;">Demo</a></li>
+                <li>
+                  <a
+                    href="documentation.html"
+                    style="color: black;font-weight: 800;"
+                    >Documentation</a
+                  >
+                </li>
+                <li>
+                  <a href="pkgdocs.html" style="color: black;font-weight: 800;"
+                    >Package Documentation</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="tutorials.html"
+                    style="color: black;font-weight: 800;"
+                    >Tutorials</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="http://pecan.ncsa.illinois.edu/pecan"
+                    style="color: black;font-weight: 800;"
+                    >Demo</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN">Download</a></li>
-            <li><a>Google</a>
+            <li>
+              <a
+                href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN"
+                >Download</a
+              >
+            </li>
+            <li>
+              <a>Google</a>
               <ul>
-                <li><a href="gsoc.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
-                <li><a href="gsod.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
+                <li>
+                  <a href="gsoc.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
+                <li>
+                  <a href="gsod.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
               </ul>
             </li>
             <li><a href="Report_an_issue.html">Bug Report</a></li>
@@ -68,47 +151,77 @@
         </div>
       </nav>
     </header>
-    
+
     <!-- MAIN CONTENT -->
 
     <div id="main_content_wrap" class="outer">
       <section id="main_content" class="inner" style="padding-top: 80px;">
-        
- <h1><a name="background" class="anchor" href="#background"><span class="octicon octicon-link"></span></a><a href="https://summerofcode.withgoogle.com/">Google Summer of Code (GSoC)</a></h1>
- 
-<h5>What is GSoC?</h5> 
-For over 10 years Google has sponsored a global program that pairs students with open source software development projects. For three months over the summer students receive real world experience contributing to software development and guidance from mentors. On the other hand, participating organizations are able to bring in new developers to grow their code base. Overall, GSoC helps open source communities grow and thrive. Thousands of student and organization from around the world have participated and now you can too!
+        <h1>
+          <a name="background" class="anchor" href="#background"
+            ><span class="octicon octicon-link"></span></a
+          ><a href="https://summerofcode.withgoogle.com/"
+            >Google Summer of Code (GSoC)</a
+          >
+        </h1>
 
- 
- <h4><a href="gsoc_ideas.html">Project Ideas</a></h4>
+        <h5>What is GSoC?</h5>
+        For over 10 years Google has sponsored a global program that pairs
+        students with open source software development projects. For three
+        months over the summer students receive real world experience
+        contributing to software development and guidance from mentors. On the
+        other hand, participating organizations are able to bring in new
+        developers to grow their code base. Overall, GSoC helps open source
+        communities grow and thrive. Thousands of student and organization from
+        around the world have participated and now you can too!
 
+        <h4><a href="gsoc_ideas.html">Project Ideas</a></h4>
 
-<p>Ecosystem science has many components, so does PEcAn! Some Project ideas can be found here on our <a href="gsoc_ideas.html">project ideas list.</a></p>
-  
+        <p>
+          Ecosystem science has many components, so does PEcAn! Some Project
+          ideas can be found here on our
+          <a href="gsoc_ideas.html">project ideas list.</a>
+        </p>
 
- <h4><a href="gsoc_apply.html">How to apply?</a></h4>
- 
- <h6>There are Two Parts to the application process:</h6>
- 
-First, follow the PEcAn specific application steps:
+        <h4><a href="gsoc_apply.html">How to apply?</a></h4>
 
-<p>1. Choose a project from our <a href="gsoc_ideas.html">project ideas list</a> or come up with your own.</p>
-<p>2. Fill out <a href="https://goo.gl/forms/i4RXCrJmUTD0d3373">PEcAn GSoC application form</a>. The form is self-explanatory, and it requires completing a project specific technical task which will in return help you write your GSOC proposal.</p> 
-<p>* Please fill out the form in a timely manner so that we can review it sooner and give you feedback. *</p>
-<p>3. Send an email to your project-specific mentors indicating that you have completed the form, attach your resume or CV.</p>
+        <h6>There are Two Parts to the application process:</h6>
 
+        First, follow the PEcAn specific application steps:
 
-Second, write and submit your GSoC proposal:
+        <p>
+          1. Choose a project from our
+          <a href="gsoc_ideas.html">project ideas list</a> or come up with your
+          own.
+        </p>
+        <p>
+          2. Fill out
+          <a href="https://goo.gl/forms/i4RXCrJmUTD0d3373"
+            >PEcAn GSoC application form</a
+          >. The form is self-explanatory, and it requires completing a project
+          specific technical task which will in return help you write your GSOC
+          proposal.
+        </p>
+        <p>
+          * Please fill out the form in a timely manner so that we can review it
+          sooner and give you feedback. *
+        </p>
+        <p>
+          3. Send an email to your project-specific mentors indicating that you
+          have completed the form, attach your resume or CV.
+        </p>
 
+        Second, write and submit your GSoC proposal:
 
-<p>1. With guidance from your mentors, write your proposal.</p>
-<p>2. Start coding! Go on our Slack channels and github repository and start coding! </p>
+        <p>1. With guidance from your mentors, write your proposal.</p>
+        <p>
+          2. Start coding! Go on our Slack channels and github repository and
+          start coding!
+        </p>
+      </section>
+    </div>
 
- </section>
-</div>
+    <!-- scripts -->
 
-    <!-- scripts -->    
-  
     <script type="text/javascript" src="js/responsee.js"></script>
     <script type="text/javascript" src="owl-carousel/owl.carousel.js"></script>
     <script type="text/javascript" src="js/template-scripts.js"></script>
@@ -116,27 +229,44 @@ <h6>There are Two Parts to the application process:</h6>
     <!-- FOOTER  -->
     <div id="footer_wrap" class="outer">
       <footer class="inner">
-        <p>Published with <a href="http://pages.github.com" style="color: rgb(255, 255, 255);" >GitHub Pages</a></p>
+        <p>
+          Published with
+          <a href="http://pages.github.com" style="color: rgb(255, 255, 255);"
+            >GitHub Pages</a
+          >
+        </p>
       </footer>
     </div>
 
     <script>
-      (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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-      })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
-
-      ga('create', 'UA-28628282-1', 'pecanproject.github.io');
-      ga('require', 'displayfeatures');
-      ga('send', 'pageview');
+      (function(i, s, o, g, r, a, m) {
+        i["GoogleAnalyticsObject"] = r;
+        (i[r] =
+          i[r] ||
+          function() {
+            (i[r].q = i[r].q || []).push(arguments);
+          }),
+          (i[r].l = 1 * new Date());
+        (a = s.createElement(o)), (m = s.getElementsByTagName(o)[0]);
+        a.async = 1;
+        a.src = g;
+        m.parentNode.insertBefore(a, m);
+      })(
+        window,
+        document,
+        "script",
+        "//www.google-analytics.com/analytics.js",
+        "ga"
+      );
 
+      ga("create", "UA-28628282-1", "pecanproject.github.io");
+      ga("require", "displayfeatures");
+      ga("send", "pageview");
     </script>
     <script>
       ((window.gitter = {}).chat = {}).options = {
-    room: 'PecanProject/pecan'
+        room: "PecanProject/pecan"
       };
     </script>
-
-    
   </body>
-</html>
\ No newline at end of file
+</html>
diff --git a/index.html b/index.html
index cbf832b..f532ee7 100644
--- a/index.html
+++ b/index.html
@@ -1,67 +1,149 @@
 <!DOCTYPE html>
 <html lang="en-US">
   <head>
-    <meta charset="UTF-8">
+    <meta charset="UTF-8" />
     <meta http-equiv="X-UA-Compatible" content="chrome=1" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <meta name="description" content="PEcAn : The Predictive Ecosystem Analyzer" />
-    <meta name="google-site-verification" content="WiPnxPvenKX6-C6fNrwp9v64f23Q1qYw26Kapyswgms" />
-    <link rel="stylesheet" type="text/css" media="screen" href="stylesheets/stylesheet.css">
+    <meta
+      name="description"
+      content="PEcAn : The Predictive Ecosystem Analyzer"
+    />
+    <meta
+      name="google-site-verification"
+      content="WiPnxPvenKX6-C6fNrwp9v64f23Q1qYw26Kapyswgms"
+    />
+    <link
+      rel="stylesheet"
+      type="text/css"
+      media="screen"
+      href="stylesheets/stylesheet.css"
+    />
     <title>PEcAn</title>
-    <link rel="stylesheet" href="css/components.css">
-    <link rel="stylesheet" href="css/icons.css">
-    <link rel="stylesheet" href="css/responsee.css">
-    <link rel="stylesheet" href="owl-carousel/owl.carousel.css">
-    <link rel="stylesheet" href="owl-carousel/owl.theme.css">     
-    <link rel="stylesheet" href="css/template-style.css">
-    <link href='https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
-    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
+    <link rel="stylesheet" href="css/components.css" />
+    <link rel="stylesheet" href="css/icons.css" />
+    <link rel="stylesheet" href="css/responsee.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.carousel.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.theme.css" />
+    <link rel="stylesheet" href="css/template-style.css" />
+    <link
+      href="https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
+    <link
+      href="https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
     <script type="text/javascript" src="js/jquery-1.8.3.min.js"></script>
-    <script type="text/javascript" src="js/jquery-ui.min.js"></script>      
+    <script type="text/javascript" src="js/jquery-ui.min.js"></script>
   </head>
-  
+
   <body class="size-1140">
-  	<!-- VIEW ON GITHUB -->
-  	<a target="_blank" class="hide-s" href="https://github.com/PecanProject" style="position:fixed;top:120px;right:-14px;z-index:10;"><img src="images/view-on-github.png" alt="" style="width: 200px; padding-right: 10px;"></a>
-    
-    
+    <!-- VIEW ON GITHUB -->
+    <a
+      target="_blank"
+      class="hide-s"
+      href="https://github.com/PecanProject"
+      style="position:fixed;top:120px;right:-14px;z-index:10;"
+      ><img
+        src="images/view-on-github.png"
+        alt=""
+        style="width: 200px; padding-right: 10px;"
+    /></a>
+
     <!-- HEADER -->
-    <header role="banner" class="position-absolute">    
+    <header role="banner" class="position-absolute">
       <!-- Top Navigation -->
       <nav class="background-dark background-transparent-hightlight full-width">
         <div class="s-12 l-2">
           <a href="index.html" class="logo">
             <!-- Logo White Version -->
-            <img class="logo-white" src="images/logo.png" alt="">
+            <img class="logo-white" src="images/logo.png" alt="" />
             <!-- Logo Dark Version -->
-            <img class="logo-dark" src="images/logo.png" alt="">
+            <img class="logo-dark" src="images/logo.png" alt="" />
           </a>
         </div>
         <div class="top-nav s-12 l-10 background-dark">
-          
           <ul class="right chevron">
             <li><a href="index.html">Home</a></li>
-            <li><a>About</a>
+            <li>
+              <a>About</a>
               <ul>
-                <li><a href="people.html" style="color: black;font-weight: 800;">People</a></li>
-                <li><a href="news.html" style="color: black;font-weight: 800;">News</a></li>
-                <li><a href="pecan_workshop.html" style="color: black;font-weight: 800;">Workshop</a></li>
-                <li><a href="contact.html" style="color: black;font-weight: 800;">Contact Us</a></li>
+                <li>
+                  <a href="people.html" style="color: black;font-weight: 800;"
+                    >People</a
+                  >
+                </li>
+                <li>
+                  <a href="news.html" style="color: black;font-weight: 800;"
+                    >News</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="pecan_workshop.html"
+                    style="color: black;font-weight: 800;"
+                    >Workshop</a
+                  >
+                </li>
+                <li>
+                  <a href="contact.html" style="color: black;font-weight: 800;"
+                    >Contact Us</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a>Documentation</a>
+            <li>
+              <a>Documentation</a>
               <ul>
-                <li><a href="documentation.html" style="color: black;font-weight: 800;">Documentation</a></li>
-                <li><a href="pkgdocs.html" style="color: black;font-weight: 800;">Package Documentation</a></li>
-                <li><a href="tutorials.html" style="color: black;font-weight: 800;">Tutorials</a></li>
-                <li><a href="http://pecan.ncsa.illinois.edu/pecan" style="color: black;font-weight: 800;">Demo</a></li>
+                <li>
+                  <a
+                    href="documentation.html"
+                    style="color: black;font-weight: 800;"
+                    >Documentation</a
+                  >
+                </li>
+                <li>
+                  <a href="pkgdocs.html" style="color: black;font-weight: 800;"
+                    >Package Documentation</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="tutorials.html"
+                    style="color: black;font-weight: 800;"
+                    >Tutorials</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="http://pecan.ncsa.illinois.edu/pecan"
+                    style="color: black;font-weight: 800;"
+                    >Demo</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN">Download</a></li>
-            <li><a>Google</a>
+            <li>
+              <a
+                href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN"
+                >Download</a
+              >
+            </li>
+            <li>
+              <a>Google</a>
               <ul>
-                <li><a href="gsoc.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
-                <li><a href="gsod.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
+                <li>
+                  <a href="gsoc.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
+                <li>
+                  <a href="gsod.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
               </ul>
             </li>
             <li><a href="Report_an_issue.html">Bug Report</a></li>
@@ -69,62 +151,128 @@
         </div>
       </nav>
     </header>
-    
+
     <!-- MAIN -->
-    <main role="main">    
+    <main role="main">
       <!-- Main Header -->
       <header>
-        <div class="carousel-default owl-carousel carousel-main carousel-nav-white background-dark text-center">
+        <div
+          class="carousel-default owl-carousel carousel-main carousel-nav-white background-dark text-center"
+        >
           <div class="item">
             <div class="s-12">
-              <img src="images/PNW.jpg" alt="">
+              <img src="images/PNW.jpg" alt="" />
               <div class="carousel-content">
                 <div class="content-center-vertical line">
                   <div class="margin-top-bottom-80">
                     <!-- Title -->
                     <div class="s-12 m-10 l-8 center">
-                      <h1 class="text-white margin-top-10 text-size-30 text-m-size-16 text-line-height-1" style="padding-top: 3ch;">Ecosystem science, policy, and management informed by the best available data and models</h1>
-                      <iframe width="560" height="315" src="https://www.youtube.com/embed/E2W_Qmc5qec" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
-                      <p class="text-white text-size-20 text-m-size-16 margin-bottom-18" style="font-weight: bold;" >Our Mission:<br>Develop and promote accessible tools for reproducible ecosystem modeling and forecasting</p></div>
+                      <h1
+                        class="text-white margin-top-10 text-size-30 text-m-size-16 text-line-height-1"
+                        style="padding-top: 3ch;"
+                      >
+                        Ecosystem science, policy, and management informed by
+                        the best available data and models
+                      </h1>
+                      <iframe
+                        width="560"
+                        height="315"
+                        src="https://www.youtube.com/embed/E2W_Qmc5qec"
+                        frameborder="0"
+                        allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture"
+                        allowfullscreen
+                      ></iframe>
+                      <p
+                        class="text-white text-size-20 text-m-size-16 margin-bottom-18"
+                        style="font-weight: bold;"
+                      >
+                        Our Mission:<br />Develop and promote accessible tools
+                        for reproducible ecosystem modeling and forecasting
+                      </p>
+                    </div>
                     <div class="line">
                       <div class="s-12 m-12 l-3 center">
-                        <a class="button button-white-stroke s-12" href="http://pecan.ncsa.illinois.edu/pecan">Get Started Now</a>
-                      </div>       
-                    </div>  
+                        <a
+                          class="button button-white-stroke s-12"
+                          href="http://pecan.ncsa.illinois.edu/pecan"
+                          >Get Started Now</a
+                        >
+                      </div>
+                    </div>
                   </div>
                 </div>
               </div>
             </div>
-          </div>              
-        </div>               
+          </div>
+        </div>
       </header>
-      
-      <!-- Main Content -->    
+
+      <!-- Main Content -->
       <section class="section background-white text-center">
         <div class="line">
           <h2 class="text-size-50  text-m-size-40 text-center">About Us</h2>
-          <hr class="break-small background-primary break-center">
-          <p class="text-dark text-size-14 margin-top-10">Climate change science has witnessed an explosion in the amount and types of data that can be brought to bear on the potential responses of the terrestrial carbon cycle and biodiversity to global change.
-             Many of the most pressing questions about global change are not necessarily limited by the need to collect new data as much as by our ability to synthesize existing data. This project specifically seeks to improve this ability. Because no one measurement provides a complete picture, multiple data sources must be integrated in a sensible manner. Process-based models represent an ideal framework for integrating these data streams because they represent multiple processes at different spatial and temporal scales in ways that capture our current understanding of the causal connections across scales and among data types. Three components are required to bridge this gap between the available data and the required level of understanding: 
-            1) a state-of-the-art ecosystem model, 2) a workflow management system to handle the numerous streams of data, and 3) a data assimilation statistical framework in order to synthesize the data with the model.
+          <hr class="break-small background-primary break-center" />
+          <p class="text-dark text-size-14 margin-top-10">
+            Climate change science has witnessed an explosion in the amount and
+            types of data that can be brought to bear on the potential responses
+            of the terrestrial carbon cycle and biodiversity to global change.
+            Many of the most pressing questions about global change are not
+            necessarily limited by the need to collect new data as much as by
+            our ability to synthesize existing data. This project specifically
+            seeks to improve this ability. Because no one measurement provides a
+            complete picture, multiple data sources must be integrated in a
+            sensible manner. Process-based models represent an ideal framework
+            for integrating these data streams because they represent multiple
+            processes at different spatial and temporal scales in ways that
+            capture our current understanding of the causal connections across
+            scales and among data types. Three components are required to bridge
+            this gap between the available data and the required level of
+            understanding: 1) a state-of-the-art ecosystem model, 2) a workflow
+            management system to handle the numerous streams of data, and 3) a
+            data assimilation statistical framework in order to synthesize the
+            data with the model.
           </p>
-          <br>
+          <br />
           <p class="text-dark text-size-14 margin-top-10">
-            <strong>Acknowledgements:</strong> The PEcAn project is supported by the National Science Foundation (ABI #1062547, ABI #1458021, DIBBS #1261582, ARC #1023477, EF #1318164, EF #1241894, EF #1241891),
-             NASA Terrestrial Ecosystems, the Department of Energy (ARPA-E awards #DE-AR0000594 and DE-AR0000598), the Energy Biosciences Institute, and an Amazon AWS in Education Grant.
+            <strong>Acknowledgements:</strong> The PEcAn project is supported by
+            the National Science Foundation (ABI #1062547, ABI #1458021, DIBBS
+            #1261582, ARC #1023477, EF #1318164, EF #1241894, EF #1241891), NASA
+            Terrestrial Ecosystems, the Department of Energy (ARPA-E awards
+            #DE-AR0000594 and DE-AR0000598), the Energy Biosciences Institute,
+            and an Amazon AWS in Education Grant.
           </p>
-          <br>
+          <br />
           <p class="text-dark text-size-14 margin-top-10">
-            PEcAn is open-source and built using open source software, and we benefit from the use of a wide range of other software, 
-            including R, JAGS, MySQL, Ruby on Rails, PHP, C, and Fortran.  In addition, we appreciate the availability of development tools including RStudio, Vim, Emacs, Navicat, and Git/GitHub
+            PEcAn is open-source and built using open source software, and we
+            benefit from the use of a wide range of other software, including R,
+            JAGS, MySQL, Ruby on Rails, PHP, C, and Fortran. In addition, we
+            appreciate the availability of development tools including RStudio,
+            Vim, Emacs, Navicat, and Git/GitHub
           </p>
-          <br>
-          <a class="twitter-timeline" href="https://twitter.com/PEcAnProject" data-widget-id="469825011251826689">Tweets by @PEcAnProject</a>
-          <script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
+          <br />
+          <a
+            class="twitter-timeline"
+            href="https://twitter.com/PEcAnProject"
+            data-widget-id="469825011251826689"
+            >Tweets by @PEcAnProject</a
+          >
+          <script>
+            !(function(d, s, id) {
+              var js,
+                fjs = d.getElementsByTagName(s)[0],
+                p = /^http:/.test(d.location) ? "http" : "https";
+              if (!d.getElementById(id)) {
+                js = d.createElement(s);
+                js.id = id;
+                js.src = p + "://platform.twitter.com/widgets.js";
+                fjs.parentNode.insertBefore(js, fjs);
+              }
+            })(document, "script", "twitter-wjs");
+          </script>
         </div>
       </section>
     </main>
-    
+
     <script type="text/javascript" src="js/responsee.js"></script>
     <script type="text/javascript" src="owl-carousel/owl.carousel.js"></script>
     <script type="text/javascript" src="js/template-scripts.js"></script>
@@ -132,27 +280,44 @@ <h2 class="text-size-50  text-m-size-40 text-center">About Us</h2>
     <!-- FOOTER  -->
     <div id="footer_wrap" class="outer">
       <footer class="inner">
-        <p>Published with <a href="http://pages.github.com" style="color: rgb(255, 255, 255);" >GitHub Pages</a></p>
+        <p>
+          Published with
+          <a href="http://pages.github.com" style="color: rgb(255, 255, 255);"
+            >GitHub Pages</a
+          >
+        </p>
       </footer>
     </div>
 
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-      ga('require', 'displayfeatures');
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+      (function(i, s, o, g, r, a, m) {
+        i["GoogleAnalyticsObject"] = r;
+        (i[r] =
+          i[r] ||
+          function() {
+            (i[r].q = i[r].q || []).push(arguments);
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+        (a = s.createElement(o)), (m = s.getElementsByTagName(o)[0]);
+        a.async = 1;
+        a.src = g;
+        m.parentNode.insertBefore(a, m);
+      })(
+        window,
+        document,
+        "script",
+        "//www.google-analytics.com/analytics.js",
+        "ga"
+      );
 
+      ga("create", "UA-28628282-1", "pecanproject.github.io");
+      ga("require", "displayfeatures");
+      ga("send", "pageview");
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     <script>
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-    room: 'PecanProject/pecan'
+        room: "PecanProject/pecan"
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-
-    
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-</html>
\ No newline at end of file
+</html>
diff --git a/javascripts/main.js b/javascripts/main.js
index d8135d3..acbcf56 100644
--- a/javascripts/main.js
+++ b/javascripts/main.js
@@ -1 +1 @@
-console.log('This would be the main JS file.');
+console.log("This would be the main JS file.");
diff --git a/js/modernizr.js b/js/modernizr.js
index 3f5166e..3914fc2 100644
--- a/js/modernizr.js
+++ b/js/modernizr.js
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+        ((m ? l : n).innerHTML += h),
+        n.appendChild(l),
+        m ||
+          ((n.style.background = ""),
+          (n.style.overflow = "hidden"),
+          (k = f.style.overflow),
+          (f.style.overflow = "hidden"),
+          f.appendChild(n)),
+        (i = c(l, a)),
+        m
+          ? l.parentNode.removeChild(l)
+          : (n.parentNode.removeChild(n), (f.style.overflow = k)),
+        !!i
+      );
+    },
+    x = function(b) {
+      var c = a.matchMedia || a.msMatchMedia;
+      if (c) return c(b).matches;
+      var d;
+      return (
+        w("@media " + b + " { #" + g + " { position: absolute; } }", function(
+          b
+        ) {
+          d =
+            (a.getComputedStyle ? getComputedStyle(b, null) : b.currentStyle)[
+              "position"
+            ] == "absolute";
+        }),
+        d
+      );
+    },
+    y = {}.hasOwnProperty,
+    z;
+  !C(y, "undefined") && !C(y.call, "undefined")
+    ? (z = function(a, b) {
+        return y.call(a, b);
+      })
+    : (z = function(a, b) {
+        return b in a && C(a.constructor.prototype[b], "undefined");
+      }),
+    Function.prototype.bind ||
+      (Function.prototype.bind = function(b) {
+        var c = this;
+        if (typeof c != "function") throw new TypeError();
+        var d = u.call(arguments, 1),
+          e = function() {
+            if (this instanceof e) {
+              var a = function() {};
+              a.prototype = c.prototype;
+              var f = new a(),
+                g = c.apply(f, d.concat(u.call(arguments)));
+              return Object(g) === g ? g : f;
+            }
+            return c.apply(b, d.concat(u.call(arguments)));
+          };
+        return e;
+      }),
+    (q.rgba = function() {
+      return (
+        A("background-color:rgba(150,255,150,.5)"), D(i.backgroundColor, "rgba")
+      );
+    }),
+    (q.borderradius = function() {
+      return G("borderRadius");
+    }),
+    (q.opacity = function() {
+      return B("opacity:.55"), /^0.55$/.test(i.opacity);
+    }),
+    (q.cssanimations = function() {
+      return G("animationName");
+    }),
+    (q.fontface = function() {
+      var a;
+      return (
+        w('@font-face {font-family:"font";src:url("https://")}', function(
+          c,
+          d
+        ) {
+          var e = b.getElementById("smodernizr"),
+            f = e.sheet || e.styleSheet,
+            g = f
+              ? f.cssRules && f.cssRules[0]
+                ? f.cssRules[0].cssText
+                : f.cssText || ""
+              : "";
+          a = /src/i.test(g) && g.indexOf(d.split(" ")[0]) === 0;
+        }),
+        a
+      );
+    }),
+    (q.generatedcontent = function() {
+      var a;
+      return (
+        w(
+          [
+            "#",
+            g,
+            "{font:0/0 a}#",
+            g,
+            ':after{content:"',
+            k,
+            '";visibility:hidden;font:3px/1 a}'
+          ].join(""),
+          function(b) {
+            a = b.offsetHeight >= 3;
+          }
+        ),
+        a
+      );
+    });
+  for (var I in q)
+    z(q, I) &&
+      ((v = I.toLowerCase()), (e[v] = q[I]()), t.push((e[v] ? "" : "no-") + v));
+  return (
+    e.input || H(),
+    (e.addTest = function(a, b) {
+      if (typeof a == "object") for (var d in a) z(a, d) && e.addTest(d, a[d]);
+      else {
+        a = a.toLowerCase();
+        if (e[a] !== c) return e;
+        (b = typeof b == "function" ? b() : b),
+          typeof enableClasses != "undefined" &&
+            enableClasses &&
+            (f.className += " " + (b ? "" : "no-") + a),
+          (e[a] = b);
+      }
+      return e;
+    }),
+    A(""),
+    (h = j = null),
+    (function(a, b) {
+      function l(a, b) {
+        var c = a.createElement("p"),
+          d = a.getElementsByTagName("head")[0] || a.documentElement;
+        return (
+          (c.innerHTML = "x<style>" + b + "</style>"),
+          d.insertBefore(c.lastChild, d.firstChild)
+        );
+      }
+      function m() {
+        var a = s.elements;
+        return typeof a == "string" ? a.split(" ") : a;
+      }
+      function n(a) {
+        var b = j[a[h]];
+        return b || ((b = {}), i++, (a[h] = i), (j[i] = b)), b;
+      }
+      function o(a, c, d) {
+        c || (c = b);
+        if (k) return c.createElement(a);
+        d || (d = n(c));
+        var g;
+        return (
+          d.cache[a]
+            ? (g = d.cache[a].cloneNode())
+            : f.test(a)
+            ? (g = (d.cache[a] = d.createElem(a)).cloneNode())
+            : (g = d.createElem(a)),
+          g.canHaveChildren && !e.test(a) && !g.tagUrn
+            ? d.frag.appendChild(g)
+            : g
+        );
+      }
+      function p(a, c) {
+        a || (a = b);
+        if (k) return a.createDocumentFragment();
+        c = c || n(a);
+        var d = c.frag.cloneNode(),
+          e = 0,
+          f = m(),
+          g = f.length;
+        for (; e < g; e++) d.createElement(f[e]);
+        return d;
+      }
+      function q(a, b) {
+        b.cache ||
+          ((b.cache = {}),
+          (b.createElem = a.createElement),
+          (b.createFrag = a.createDocumentFragment),
+          (b.frag = b.createFrag())),
+          (a.createElement = function(c) {
+            return s.shivMethods ? o(c, a, b) : b.createElem(c);
+          }),
+          (a.createDocumentFragment = Function(
+            "h,f",
+            "return function(){var n=f.cloneNode(),c=n.createElement;h.shivMethods&&(" +
+              m()
+                .join()
+                .replace(/[\w\-]+/g, function(a) {
+                  return (
+                    b.createElem(a), b.frag.createElement(a), 'c("' + a + '")'
+                  );
+                }) +
+              ");return n}"
+          )(s, b.frag));
+      }
+      function r(a) {
+        a || (a = b);
+        var c = n(a);
+        return (
+          s.shivCSS &&
+            !g &&
+            !c.hasCSS &&
+            (c.hasCSS = !!l(
+              a,
+              "article,aside,dialog,figcaption,figure,footer,header,hgroup,main,nav,section{display:block}mark{background:#FF0;color:#000}template{display:none}"
+            )),
+          k || q(a, c),
+          a
+        );
+      }
+      var c = "3.7.0",
+        d = a.html5 || {},
+        e = /^<|^(?:button|map|select|textarea|object|iframe|option|optgroup)$/i,
+        f = /^(?:a|b|code|div|fieldset|h1|h2|h3|h4|h5|h6|i|label|li|ol|p|q|span|strong|style|table|tbody|td|th|tr|ul)$/i,
+        g,
+        h = "_html5shiv",
+        i = 0,
+        j = {},
+        k;
+      (function() {
+        try {
+          var a = b.createElement("a");
+          (a.innerHTML = "<xyz></xyz>"),
+            (g = "hidden" in a),
+            (k =
+              a.childNodes.length == 1 ||
+              (function() {
+                b.createElement("a");
+                var a = b.createDocumentFragment();
+                return (
+                  typeof a.cloneNode == "undefined" ||
+                  typeof a.createDocumentFragment == "undefined" ||
+                  typeof a.createElement == "undefined"
+                );
+              })());
+        } catch (c) {
+          (g = !0), (k = !0);
+        }
+      })();
+      var s = {
+        elements:
+          d.elements ||
+          "abbr article aside audio bdi canvas data datalist details dialog figcaption figure footer header hgroup main mark meter nav output progress section summary template time video",
+        version: c,
+        shivCSS: d.shivCSS !== !1,
+        supportsUnknownElements: k,
+        shivMethods: d.shivMethods !== !1,
+        type: "default",
+        shivDocument: r,
+        createElement: o,
+        createDocumentFragment: p
+      };
+      (a.html5 = s), r(b);
+    })(this, b),
+    (e._version = d),
+    (e._prefixes = m),
+    (e._domPrefixes = p),
+    (e._cssomPrefixes = o),
+    (e.mq = x),
+    (e.testProp = function(a) {
+      return E([a]);
+    }),
+    (e.testAllProps = G),
+    (e.testStyles = w),
+    e
+  );
+})(this, this.document)),
+  (function(a, b, c) {
+    function d(a) {
+      return "[object Function]" == o.call(a);
+    }
+    function e(a) {
+      return "string" == typeof a;
+    }
+    function f() {}
+    function g(a) {
+      return !a || "loaded" == a || "complete" == a || "uninitialized" == a;
+    }
+    function h() {
+      var a = p.shift();
+      (q = 1),
+        a
+          ? a.t
+            ? m(function() {
+                ("c" == a.t
+                  ? B.injectCss
+                  : B.injectJs)(a.s, 0, a.a, a.x, a.e, 1);
+              }, 0)
+            : (a(), h())
+          : (q = 0);
+    }
+    function i(a, c, d, e, f, i, j) {
+      function k(b) {
+        if (
+          !o &&
+          g(l.readyState) &&
+          ((u.r = o = 1),
+          !q && h(),
+          (l.onload = l.onreadystatechange = null),
+          b)
+        ) {
+          "img" != a &&
+            m(function() {
+              t.removeChild(l);
+            }, 50);
+          for (var d in y[c]) y[c].hasOwnProperty(d) && y[c][d].onload();
+        }
+      }
+      var j = j || B.errorTimeout,
+        l = b.createElement(a),
+        o = 0,
+        r = 0,
+        u = { t: d, s: c, e: f, a: i, x: j };
+      1 === y[c] && ((r = 1), (y[c] = [])),
+        "object" == a ? (l.data = c) : ((l.src = c), (l.type = a)),
+        (l.width = l.height = "0"),
+        (l.onerror = l.onload = l.onreadystatechange = function() {
+          k.call(this, r);
+        }),
+        p.splice(e, 0, u),
+        "img" != a &&
+          (r || 2 === y[c]
+            ? (t.insertBefore(l, s ? null : n), m(k, j))
+            : y[c].push(l));
+    }
+    function j(a, b, c, d, f) {
+      return (
+        (q = 0),
+        (b = b || "j"),
+        e(a)
+          ? i("c" == b ? v : u, a, b, this.i++, c, d, f)
+          : (p.splice(this.i++, 0, a), 1 == p.length && h()),
+        this
+      );
+    }
+    function k() {
+      var a = B;
+      return (a.loader = { load: j, i: 0 }), a;
+    }
+    var l = b.documentElement,
+      m = a.setTimeout,
+      n = b.getElementsByTagName("script")[0],
+      o = {}.toString,
+      p = [],
+      q = 0,
+      r = "MozAppearance" in l.style,
+      s = r && !!b.createRange().compareNode,
+      t = s ? l : n.parentNode,
+      l = a.opera && "[object Opera]" == o.call(a.opera),
+      l = !!b.attachEvent && !l,
+      u = r ? "object" : l ? "script" : "img",
+      v = l ? "script" : u,
+      w =
+        Array.isArray ||
+        function(a) {
+          return "[object Array]" == o.call(a);
+        },
+      x = [],
+      y = {},
+      z = {
+        timeout: function(a, b) {
+          return b.length && (a.timeout = b[0]), a;
+        }
+      },
+      A,
+      B;
+    (B = function(a) {
+      function b(a) {
+        var a = a.split("!"),
+          b = x.length,
+          c = a.pop(),
+          d = a.length,
+          c = { url: c, origUrl: c, prefixes: a },
+          e,
+          f,
+          g;
+        for (f = 0; f < d; f++)
+          (g = a[f].split("=")), (e = z[g.shift()]) && (c = e(c, g));
+        for (f = 0; f < b; f++) c = x[f](c);
+        return c;
+      }
+      function g(a, e, f, g, h) {
+        var i = b(a),
+          j = i.autoCallback;
+        i.url
+          .split(".")
+          .pop()
+          .split("?")
+          .shift(),
+          i.bypass ||
+            (e &&
+              (e = d(e)
+                ? e
+                : e[a] ||
+                  e[g] ||
+                  e[
+                    a
+                      .split("/")
+                      .pop()
+                      .split("?")[0]
+                  ]),
+            i.instead
+              ? i.instead(a, e, f, g, h)
+              : (y[i.url] ? (i.noexec = !0) : (y[i.url] = 1),
+                f.load(
+                  i.url,
+                  i.forceCSS ||
+                    (!i.forceJS &&
+                      "css" ==
+                        i.url
+                          .split(".")
+                          .pop()
+                          .split("?")
+                          .shift())
+                    ? "c"
+                    : c,
+                  i.noexec,
+                  i.attrs,
+                  i.timeout
+                ),
+                (d(e) || d(j)) &&
+                  f.load(function() {
+                    k(),
+                      e && e(i.origUrl, h, g),
+                      j && j(i.origUrl, h, g),
+                      (y[i.url] = 2);
+                  })));
+      }
+      function h(a, b) {
+        function c(a, c) {
+          if (a) {
+            if (e(a))
+              c ||
+                (j = function() {
+                  var a = [].slice.call(arguments);
+                  k.apply(this, a), l();
+                }),
+                g(a, j, b, 0, h);
+            else if (Object(a) === a)
+              for (n in ((m = (function() {
+                var b = 0,
+                  c;
+                for (c in a) a.hasOwnProperty(c) && b++;
+                return b;
+              })()),
+              a))
+                a.hasOwnProperty(n) &&
+                  (!c &&
+                    !--m &&
+                    (d(j)
+                      ? (j = function() {
+                          var a = [].slice.call(arguments);
+                          k.apply(this, a), l();
+                        })
+                      : (j[n] = (function(a) {
+                          return function() {
+                            var b = [].slice.call(arguments);
+                            a && a.apply(this, b), l();
+                          };
+                        })(k[n]))),
+                  g(a[n], j, b, n, h));
+          } else !c && l();
+        }
+        var h = !!a.test,
+          i = a.load || a.both,
+          j = a.callback || f,
+          k = j,
+          l = a.complete || f,
+          m,
+          n;
+        c(h ? a.yep : a.nope, !!i), i && c(i);
+      }
+      var i,
+        j,
+        l = this.yepnope.loader;
+      if (e(a)) g(a, 0, l, 0);
+      else if (w(a))
+        for (i = 0; i < a.length; i++)
+          (j = a[i]),
+            e(j) ? g(j, 0, l, 0) : w(j) ? B(j) : Object(j) === j && h(j, l);
+      else Object(a) === a && h(a, l);
+    }),
+      (B.addPrefix = function(a, b) {
+        z[a] = b;
+      }),
+      (B.addFilter = function(a) {
+        x.push(a);
+      }),
+      (B.errorTimeout = 1e4),
+      null == b.readyState &&
+        b.addEventListener &&
+        ((b.readyState = "loading"),
+        b.addEventListener(
+          "DOMContentLoaded",
+          (A = function() {
+            b.removeEventListener("DOMContentLoaded", A, 0),
+              (b.readyState = "complete");
+          }),
+          0
+        )),
+      (a.yepnope = k()),
+      (a.yepnope.executeStack = h),
+      (a.yepnope.injectJs = function(a, c, d, e, i, j) {
+        var k = b.createElement("script"),
+          l,
+          o,
+          e = e || B.errorTimeout;
+        k.src = a;
+        for (o in d) k.setAttribute(o, d[o]);
+        (c = j ? h : c || f),
+          (k.onreadystatechange = k.onload = function() {
+            !l &&
+              g(k.readyState) &&
+              ((l = 1), c(), (k.onload = k.onreadystatechange = null));
+          }),
+          m(function() {
+            l || ((l = 1), c(1));
+          }, e),
+          i ? k.onload() : n.parentNode.insertBefore(k, n);
+      }),
+      (a.yepnope.injectCss = function(a, c, d, e, g, i) {
+        var e = b.createElement("link"),
+          j,
+          c = i ? h : c || f;
+        (e.href = a), (e.rel = "stylesheet"), (e.type = "text/css");
+        for (j in d) e.setAttribute(j, d[j]);
+        g || (n.parentNode.insertBefore(e, n), m(c, 0));
+      });
+  })(this, document),
+  (Modernizr.load = function() {
+    yepnope.apply(window, [].slice.call(arguments, 0));
+  });
diff --git a/js/responsee.js b/js/responsee.js
index f0246b7..967a413 100644
--- a/js/responsee.js
+++ b/js/responsee.js
@@ -3,172 +3,260 @@
  * https://www.myresponsee.com
  * Copyright 2019, Vision Design - graphic zoo
  * Free to use under the MIT license.
-*/
+ */
 jQuery(document).ready(function($) {
   //Responsee tabs
-  $('.tabs').each(function(intex, element) {
-    current_tabs = $(this);       
-    $('.tab-label').each(function(i) {
-      var tab_url = $(this).attr('data-url');                   
-      if ($(this).attr('data-url')) {        
-        $(this).closest('.tab-item').attr("id", tab_url);
-        $(this).attr("href", "#" + tab_url);          
-      }else{                  
-        $(this).closest('.tab-item').attr("id", "tab-" + (i + 1));
-        $(this).attr("href", "#tab-" + (i + 1));         
+  $(".tabs").each(function(intex, element) {
+    current_tabs = $(this);
+    $(".tab-label").each(function(i) {
+      var tab_url = $(this).attr("data-url");
+      if ($(this).attr("data-url")) {
+        $(this)
+          .closest(".tab-item")
+          .attr("id", tab_url);
+        $(this).attr("href", "#" + tab_url);
+      } else {
+        $(this)
+          .closest(".tab-item")
+          .attr("id", "tab-" + (i + 1));
+        $(this).attr("href", "#tab-" + (i + 1));
       }
-    });  
+    });
     $(this).prepend('<div class="tab-nav line"></div>');
-    var tab_buttons = $(element).find('.tab-label');
-    $(this).children('.tab-nav').prepend(tab_buttons);      
-    function loadTab() {   
-        $(this).parent().children().removeClass("active-btn");
-        $(this).addClass("active-btn");
-        var tab = $(this).attr("href");
-        $(this).parent().parent().find(".tab-item").not(tab).css("display", "none");
-        $(this).parent().parent().find(tab).fadeIn();
-        $('html,body').animate({scrollTop: $(tab).offset().top - 160},'slow'); 
-      if ($(this).attr('data-url')) { 
-      }else{
+    var tab_buttons = $(element).find(".tab-label");
+    $(this)
+      .children(".tab-nav")
+      .prepend(tab_buttons);
+    function loadTab() {
+      $(this)
+        .parent()
+        .children()
+        .removeClass("active-btn");
+      $(this).addClass("active-btn");
+      var tab = $(this).attr("href");
+      $(this)
+        .parent()
+        .parent()
+        .find(".tab-item")
+        .not(tab)
+        .css("display", "none");
+      $(this)
+        .parent()
+        .parent()
+        .find(tab)
+        .fadeIn();
+      $("html,body").animate({ scrollTop: $(tab).offset().top - 160 }, "slow");
+      if ($(this).attr("data-url")) {
+      } else {
         return false;
-      }  
-    } 
-    $(this).find(".tab-nav a").click( loadTab );
-    $(this).find('.tab-label').each(function() {
-      if ($(this).attr('data-url')) {  
-        var tab_url = window.location.hash;      
-        if( $(this).parent().find('a[href="' + tab_url + '"]').length ) {
-            loadTab.call($(this).parent().find('a[href="' + tab_url + '"]')[0]);
-        }
       }
-    }); 
+    }
+    $(this)
+      .find(".tab-nav a")
+      .click(loadTab);
+    $(this)
+      .find(".tab-label")
+      .each(function() {
+        if ($(this).attr("data-url")) {
+          var tab_url = window.location.hash;
+          if (
+            $(this)
+              .parent()
+              .find('a[href="' + tab_url + '"]').length
+          ) {
+            loadTab.call(
+              $(this)
+                .parent()
+                .find('a[href="' + tab_url + '"]')[0]
+            );
+          }
+        }
+      });
     var url = window.location.hash;
-    if( $(url).length ) {
-      $('html,body').animate({scrollTop: $(url).offset().top - 160},'slow');
+    if ($(url).length) {
+      $("html,body").animate({ scrollTop: $(url).offset().top - 160 }, "slow");
     }
   });
   //Slide nav
-  $('<div class="slide-nav-button"><div class="nav-icon"><div></div></div></div>').insertBefore(".slide-nav");
+  $(
+    '<div class="slide-nav-button"><div class="nav-icon"><div></div></div></div>'
+  ).insertBefore(".slide-nav");
   $(".slide-nav-button").click(function() {
     $("body").toggleClass("active-slide-nav");
   });
   //Responsee eside nav
-  $('.aside-nav > ul > li ul').each(function(index, element) {
-    var count = $(element).find('li').length;
-    var content = '<span class="count-number"> ' + count + '</span>';
-    $(element).closest('li').children('a').append(content);
-  });
-  $('.aside-nav > ul > li:has(ul)').addClass('aside-submenu');
-  $('.aside-nav > ul ul > li:has(ul)').addClass('aside-sub-submenu'); 
-    $('.aside-nav > ul > li.aside-submenu > a').attr('aria-haspopup', 'true').click(function() {
-    //Close other open sub menus
-    $('.aside-nav ul li.aside-submenu:not(:hover) > ul').removeClass('show-aside-ul', 'fast');
-    $('.aside-nav ul li.aside-submenu:hover > ul').toggleClass('show-aside-ul', 'fast'); 
-  }); 
-  $('.aside-nav > ul ul > li.aside-sub-submenu > a').attr('aria-haspopup', 'true').click(function() { 
-    //Close other open sub menus
-    $('.aside-nav ul ul li:not(:hover) > ul').removeClass('show-aside-ul', 'fast');
-    $('.aside-nav ul ul li:hover > ul').toggleClass('show-aside-ul', 'fast');
+  $(".aside-nav > ul > li ul").each(function(index, element) {
+    var count = $(element).find("li").length;
+    var content = '<span class="count-number"> ' + count + "</span>";
+    $(element)
+      .closest("li")
+      .children("a")
+      .append(content);
   });
+  $(".aside-nav > ul > li:has(ul)").addClass("aside-submenu");
+  $(".aside-nav > ul ul > li:has(ul)").addClass("aside-sub-submenu");
+  $(".aside-nav > ul > li.aside-submenu > a")
+    .attr("aria-haspopup", "true")
+    .click(function() {
+      //Close other open sub menus
+      $(".aside-nav ul li.aside-submenu:not(:hover) > ul").removeClass(
+        "show-aside-ul",
+        "fast"
+      );
+      $(".aside-nav ul li.aside-submenu:hover > ul").toggleClass(
+        "show-aside-ul",
+        "fast"
+      );
+    });
+  $(".aside-nav > ul ul > li.aside-sub-submenu > a")
+    .attr("aria-haspopup", "true")
+    .click(function() {
+      //Close other open sub menus
+      $(".aside-nav ul ul li:not(:hover) > ul").removeClass(
+        "show-aside-ul",
+        "fast"
+      );
+      $(".aside-nav ul ul li:hover > ul").toggleClass("show-aside-ul", "fast");
+    });
   //Mobile aside navigation
-  $('.aside-nav-text').each(function(index, element) {
-    $(element).click(function() { 
-      $('.aside-nav > ul').toggleClass('show-menu', 'fast');
+  $(".aside-nav-text").each(function(index, element) {
+    $(element).click(function() {
+      $(".aside-nav > ul").toggleClass("show-menu", "fast");
     });
-  });  
+  });
   //Responsee nav
   // Add nav-text before top-nav
-  $('.top-nav').before('<p class="nav-text"><span></span></p>');   
-  $('.top-nav > ul > li ul').each(function(index, element) {
-    var count = $(element).find('li').length;
-    var content = '<span class="count-number"> ' + count + '</span>';
-    $(element).closest('li').children('a').append(content);
-  });
-  $('.top-nav > ul li:has(ul)').addClass('submenu');
-  $('.top-nav > ul ul li:has(ul)').addClass('sub-submenu').removeClass('submenu');
-  $('.top-nav > ul li.submenu > a').attr('aria-haspopup', 'true').click(function() { 
-    //Close other open sub menus
-    $('.top-nav > ul li.submenu > ul').removeClass('show-ul', 'fast'); 
-    $('.top-nav > ul li.submenu:hover > ul').toggleClass('show-ul', 'fast');
-  }); 
-  $('.top-nav > ul ul > li.sub-submenu > a').attr('aria-haspopup', 'true').click(function() {  
-    //Close other open sub menus
-    $('.top-nav ul ul li > ul').removeClass('show-ul', 'fast');  
-    $('.top-nav ul ul li:hover > ul').toggleClass('show-ul', 'fast');   
+  $(".top-nav").before('<p class="nav-text"><span></span></p>');
+  $(".top-nav > ul > li ul").each(function(index, element) {
+    var count = $(element).find("li").length;
+    var content = '<span class="count-number"> ' + count + "</span>";
+    $(element)
+      .closest("li")
+      .children("a")
+      .append(content);
   });
+  $(".top-nav > ul li:has(ul)").addClass("submenu");
+  $(".top-nav > ul ul li:has(ul)")
+    .addClass("sub-submenu")
+    .removeClass("submenu");
+  $(".top-nav > ul li.submenu > a")
+    .attr("aria-haspopup", "true")
+    .click(function() {
+      //Close other open sub menus
+      $(".top-nav > ul li.submenu > ul").removeClass("show-ul", "fast");
+      $(".top-nav > ul li.submenu:hover > ul").toggleClass("show-ul", "fast");
+    });
+  $(".top-nav > ul ul > li.sub-submenu > a")
+    .attr("aria-haspopup", "true")
+    .click(function() {
+      //Close other open sub menus
+      $(".top-nav ul ul li > ul").removeClass("show-ul", "fast");
+      $(".top-nav ul ul li:hover > ul").toggleClass("show-ul", "fast");
+    });
   //Mobile navigation
-  $('.nav-text').click(function() { 
-    $("body").toggleClass('show-menu');
-  });  
+  $(".nav-text").click(function() {
+    $("body").toggleClass("show-menu");
+  });
   //Custom forms
   $(function() {
     var input = document.createElement("input");
-    if (('placeholder' in input) == false) {
-      $('[placeholder]').focus(function() {
-        var i = $(this);
-        if (i.val() == i.attr('placeholder')) {
-          i.val('').removeClass('placeholder');
-          if (i.hasClass('password')) {
-            i.removeClass('password');
-            this.type = 'password';
-          }
-        }
-      }).blur(function() {
-        var i = $(this);
-        if (i.val() == '' || i.val() == i.attr('placeholder')) {
-          if (this.type == 'password') {
-            i.addClass('password');
-            this.type = 'text';
+    if ("placeholder" in input == false) {
+      $("[placeholder]")
+        .focus(function() {
+          var i = $(this);
+          if (i.val() == i.attr("placeholder")) {
+            i.val("").removeClass("placeholder");
+            if (i.hasClass("password")) {
+              i.removeClass("password");
+              this.type = "password";
+            }
           }
-          i.addClass('placeholder').val(i.attr('placeholder'));
-        }
-      }).blur().parents('form').submit(function() {
-        $(this).find('[placeholder]').each(function() {
+        })
+        .blur(function() {
           var i = $(this);
-          if (i.val() == i.attr('placeholder')) i.val('');
+          if (i.val() == "" || i.val() == i.attr("placeholder")) {
+            if (this.type == "password") {
+              i.addClass("password");
+              this.type = "text";
+            }
+            i.addClass("placeholder").val(i.attr("placeholder"));
+          }
         })
-      });
+        .blur()
+        .parents("form")
+        .submit(function() {
+          $(this)
+            .find("[placeholder]")
+            .each(function() {
+              var i = $(this);
+              if (i.val() == i.attr("placeholder")) i.val("");
+            });
+        });
     }
   });
   //Tooltip
-  $(".tooltip-container").each(function () {
-    $(this).hover(function(){  
-      var pos = $(this).position();  
-      var container = $(this);
-      var pos = container.offset();
-      tip = $(this).find('.tooltip-content');
-      tip_top = $(this).find('.tooltip-content.tooltip-top');
-      tip_bottom = $(this).find('.tooltip-content.tooltip-bottom');
-      
-      var height = tip.height();
-      tip.fadeIn("fast"); //Show tooltip
-      tip_top.css({
-        top: pos.top - height,
-        left: pos.left + (container.width() /2) - (tip.outerWidth(true)/2)
-      })
-      tip_bottom.css({
-        top: pos.top,
-        left: pos.left + (container.width() /2) - (tip.outerWidth(true)/2)
-      })
-      }, function() {
-          tip.fadeOut("fast"); //Hide tooltip
-    });
+  $(".tooltip-container").each(function() {
+    $(this).hover(
+      function() {
+        var pos = $(this).position();
+        var container = $(this);
+        var pos = container.offset();
+        tip = $(this).find(".tooltip-content");
+        tip_top = $(this).find(".tooltip-content.tooltip-top");
+        tip_bottom = $(this).find(".tooltip-content.tooltip-bottom");
+
+        var height = tip.height();
+        tip.fadeIn("fast"); //Show tooltip
+        tip_top.css({
+          top: pos.top - height,
+          left: pos.left + container.width() / 2 - tip.outerWidth(true) / 2
+        });
+        tip_bottom.css({
+          top: pos.top,
+          left: pos.left + container.width() / 2 - tip.outerWidth(true) / 2
+        });
+      },
+      function() {
+        tip.fadeOut("fast"); //Hide tooltip
+      }
+    );
   });
   //Active item
   var url = window.location.href;
-  $('a').filter(function() {
-    return this.href == url;
-  }).parent('li').addClass('active-item');
+  $("a")
+    .filter(function() {
+      return this.href == url;
+    })
+    .parent("li")
+    .addClass("active-item");
   var url = window.location.href;
-  $('.aside-nav a').filter(function() {
-    return this.href == url;
-  }).parent('li').parent('ul').addClass('active-aside-item');
+  $(".aside-nav a")
+    .filter(function() {
+      return this.href == url;
+    })
+    .parent("li")
+    .parent("ul")
+    .addClass("active-aside-item");
   var url = window.location.href;
-  $('.aside-nav a').filter(function() {
-    return this.href == url;
-  }).parent('li').parent('ul').parent('li').parent('ul').addClass('active-aside-item');
+  $(".aside-nav a")
+    .filter(function() {
+      return this.href == url;
+    })
+    .parent("li")
+    .parent("ul")
+    .parent("li")
+    .parent("ul")
+    .addClass("active-aside-item");
   var url = window.location.href;
-  $('.aside-nav a').filter(function() {
-    return this.href == url;
-  }).parent('li').parent('ul').parent('li').parent('ul').parent('li').parent('ul').addClass('active-aside-item');
-});
\ No newline at end of file
+  $(".aside-nav a")
+    .filter(function() {
+      return this.href == url;
+    })
+    .parent("li")
+    .parent("ul")
+    .parent("li")
+    .parent("ul")
+    .parent("li")
+    .parent("ul")
+    .addClass("active-aside-item");
+});
diff --git a/js/template-scripts.js b/js/template-scripts.js
index a89fdc1..8de3ad7 100644
--- a/js/template-scripts.js
+++ b/js/template-scripts.js
@@ -1,18 +1,18 @@
-jQuery(document).ready(function($) {      
-  // Owl Carousel                     
-  var owl = $('.carousel-default');
+jQuery(document).ready(function($) {
+  // Owl Carousel
+  var owl = $(".carousel-default");
   owl.owlCarousel({
     nav: true,
     dots: true,
     items: 1,
     loop: true,
-    navText: ["&#xe605","&#xe606"],
+    navText: ["&#xe605", "&#xe606"],
     autoplay: true,
     autoplayTimeout: 4000
   });
 
-  // Owl Carousel - Content Blocks  
-  var owl = $('.carousel-blocks');
+  // Owl Carousel - Content Blocks
+  var owl = $(".carousel-blocks");
   owl.owlCarousel({
     nav: true,
     dots: false,
@@ -29,13 +29,13 @@ jQuery(document).ready(function($) {
       }
     },
     loop: true,
-    navText: ["&#xe605","&#xe606"],
+    navText: ["&#xe605", "&#xe606"],
     autoplay: true,
     autoplayTimeout: 5000
   });
-  
+
   // Owl Carousel - Content 3 Blocks
-  var owl = $('.carousel-3-blocks');
+  var owl = $(".carousel-3-blocks");
   owl.owlCarousel({
     nav: true,
     dots: true,
@@ -52,30 +52,29 @@ jQuery(document).ready(function($) {
       }
     },
     loop: true,
-    navText: ["&#xe605","&#xe606"],
+    navText: ["&#xe605", "&#xe606"],
     autoplay: true,
     autoplayTimeout: 5000
-  });  
-  
-  var owl = $('.carousel-fade-transition');
+  });
+
+  var owl = $(".carousel-fade-transition");
   owl.owlCarousel({
     nav: true,
     dots: true,
     items: 1,
     loop: true,
-    navText: ["&#xe605","&#xe606"],
+    navText: ["&#xe605", "&#xe606"],
     autoplay: true,
-    animateOut: 'fadeOut',
+    animateOut: "fadeOut",
     autoplayTimeout: 4000
-  }); 
-  
+  });
+
   // Sticky Nav Bar
   $(window).scroll(function() {
-    if ($(this).scrollTop() > 20){  
-        $('.sticky').addClass("fixed");
-    }
-    else{
-        $('.sticky').removeClass("fixed");
+    if ($(this).scrollTop() > 20) {
+      $(".sticky").addClass("fixed");
+    } else {
+      $(".sticky").removeClass("fixed");
     }
-  });   
-});
\ No newline at end of file
+  });
+});
diff --git a/models/biocro/docs/LICENSE-text.html b/models/biocro/docs/LICENSE-text.html
index 24cb693..8a73f3e 100644
--- a/models/biocro/docs/LICENSE-text.html
+++ b/models/biocro/docs/LICENSE-text.html
@@ -2,112 +2,147 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>License • PEcAn.BIOCRO</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="License" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>License • PEcAn.BIOCRO</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.BIOCRO</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/workflow.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="articles/workflow.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -141,27 +176,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
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 </html>
-
diff --git a/models/biocro/docs/articles/C4grass_sa_vd.html b/models/biocro/docs/articles/C4grass_sa_vd.html
index e5657e0..04b8d58 100644
--- a/models/biocro/docs/articles/C4grass_sa_vd.html
+++ b/models/biocro/docs/articles/C4grass_sa_vd.html
@@ -1,88 +1,142 @@
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <!-- pkgdown -->
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+  </head>
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-        <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
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-            
-      
-      
-      <div class="hidden name"><code>C4grass_sa_vd.Rmd</code></div>
-
-    </div>
-
-    
-    
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAn.all)
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li class="dropdown">
+                  <a
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
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+                    </li>
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+              </ul>
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+          <!--/.container -->
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+          <div class="page-header toc-ignore">
+            <h1></h1>
+
+            <div class="hidden name"><code>C4grass_sa_vd.Rmd</code></div>
+          </div>
+
+          <div class="sourceCode">
+            <pre
+              class="sourceCode r"
+            ><code class="sourceCode r"><span class="kw">library</span>(PEcAn.all)
 <span class="kw">logger.setQuitOnSevere</span>(<span class="ot">FALSE</span>)
 
 settings &lt;-<span class="st"> </span><span class="kw">read.settings</span>(<span class="st">"models/biocro/inst/extdata/c4grass.xml"</span>)
@@ -105,27 +159,24 @@ <h1></h1>
 
 <span class="kw">run.sensitivity.analysis</span>()      <span class="co"># Run sensitivity analysis and variance decomposition on model output</span>
 
-<span class="kw">run.ensemble.analysis</span>()           <span class="co"># Run ensemble analysis on model output. </span></code></pre></div>
-  </div>
+<span class="kw">run.ensemble.analysis</span>()           <span class="co"># Run ensemble analysis on model output. </span></code></pre>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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diff --git a/models/biocro/docs/articles/index.html b/models/biocro/docs/articles/index.html
index a65eb77..6bdb4d9 100644
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+++ b/models/biocro/docs/articles/index.html
@@ -2,137 +2,168 @@
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+    <!-- Bootstrap -->
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
+    <!-- sticky kit -->
+    <script
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+            <p class="section-desc"></p>
 
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/models/biocro/docs/articles/workflow.html b/models/biocro/docs/articles/workflow.html
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+          <div class="page-header toc-ignore">
+            <h1></h1>
 
-    </div>
+            <div class="hidden name"><code>workflow.Rmd</code></div>
+          </div>
 
-    
-    
-<div id="biocro-pecan-workflow" class="section level1">
-<h1 class="hasAnchor">
-<a href="#biocro-pecan-workflow" class="anchor"></a>BioCro PEcAn workflow</h1>
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-</div>
-<div id="run-meta-analysis" class="section level3">
-<h3 class="hasAnchor">
-<a href="#run-meta-analysis" class="anchor"></a>Run Meta-analysis</h3>
-</div>
-</div>
-  </div>
+          <div id="biocro-pecan-workflow" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#biocro-pecan-workflow" class="anchor"></a>BioCro PEcAn
+              workflow
+            </h1>
+            <div id="load-pecan-settings-file-" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#load-pecan-settings-file-" class="anchor"></a>Load
+                PEcAn settings file.
+              </h3>
+              <p>Open and read in settings file for PEcAn run.</p>
+            </div>
+            <div id="query-database-for-trait-data" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#query-database-for-trait-data" class="anchor"></a
+                >Query database for trait data
+              </h3>
+            </div>
+            <div id="run-meta-analysis" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#run-meta-analysis" class="anchor"></a>Run
+                Meta-analysis
+              </h3>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#biocro-pecan-workflow">BioCro PEcAn workflow</a></li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#biocro-pecan-workflow">BioCro PEcAn workflow</a>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
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+          <p>
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   </body>
 </html>
diff --git a/models/biocro/docs/authors.html b/models/biocro/docs/authors.html
index 0a7b3f8..eb6c4e7 100644
--- a/models/biocro/docs/authors.html
+++ b/models/biocro/docs/authors.html
@@ -2,145 +2,170 @@
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
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+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    <!-- pkgdown -->
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+    <meta property="og:title" content="Authors" />
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+                    href="#"
+                    class="dropdown-toggle"
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+                    role="button"
+                    aria-expanded="false"
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+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Chris Black</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Deepak Jaiswal</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Chris Black</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Deepak Jaiswal</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/biocro/docs/docsearch.css b/models/biocro/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/biocro/docs/docsearch.css
+++ b/models/biocro/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/biocro/docs/docsearch.js b/models/biocro/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/biocro/docs/docsearch.js
+++ b/models/biocro/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/biocro/docs/index.html b/models/biocro/docs/index.html
index 45ef7fd..93b2f5d 100644
--- a/models/biocro/docs/index.html
+++ b/models/biocro/docs/index.html
@@ -1,118 +1,181 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the BioCro model • PEcAn.BIOCRO</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the BioCro model">
-<meta property="og:description" content="This module provides functions to link BioCro to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn package for integration of the BioCro model • PEcAn.BIOCRO
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the BioCro model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to link BioCro to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.BIOCRO</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/workflow.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    This module provides functions to link BioCro to PEcAn.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="articles/workflow.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          This module provides functions to link BioCro to PEcAn.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/biocro/docs/pkgdown.css b/models/biocro/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/biocro/docs/pkgdown.css
+++ b/models/biocro/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
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+  width: 40%;
+}
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+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
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@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
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   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
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diff --git a/models/biocro/docs/pkgdown.js b/models/biocro/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/biocro/docs/pkgdown.js
+++ b/models/biocro/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/biocro/docs/reference/cf2biocro.html b/models/biocro/docs/reference/cf2biocro.html
index 6c43924..4b55892 100644
--- a/models/biocro/docs/reference/cf2biocro.html
+++ b/models/biocro/docs/reference/cf2biocro.html
@@ -2,202 +2,275 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Convert CF-formatted met data to BioCro met — cf2biocro • PEcAn.BIOCRO</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
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-<!-- sticky kit -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Convert CF-formatted met data to BioCro met — cf2biocro" />
-
-<meta property="og:description" content="Converts a CF data frame into a BioCro met input" />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Convert CF-formatted met data to BioCro met — cf2biocro • PEcAn.BIOCRO
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Convert CF-formatted met data to BioCro met — cf2biocro"
+    />
+
+    <meta
+      property="og:description"
+      content="Converts a CF data frame into a BioCro met input"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
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-      <a href="../articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
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-      </ul>
-      
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-      
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-  </div><!--/.container -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="../articles/workflow.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert CF-formatted met data to BioCro met</h1>
-    
-    <div class="hidden name"><code>cf2biocro.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Converts a CF data frame into a BioCro met input</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert CF-formatted met data to BioCro met</h1>
+
+            <div class="hidden name"><code>cf2biocro.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Converts a CF data frame into a BioCro met input</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>cf2biocro</span>(<span class='no'>met</span>, <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>zulu2solarnoon</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>met</th>
+              <td>
+                <p>
+                  data.table object with met for a single site; output from
+                  <code>load.cfmet</code>
+                </p>
+                <ul>
+                  <li><p>year int</p></li>
+                  <li><p>month int</p></li>
+                  <li><p>day int: day of month (1-31)</p></li>
+                  <li><p>doy int: day of year (1-366)</p></li>
+                  <li><p>hour int (0-23)</p></li>
+                  <li><p>date YYYY-MM-DD HH:MM:SS POSIXct</p></li>
+                  <li><p>wind_speed num m/s</p></li>
+                  <li><p>northward_wind</p></li>
+                  <li><p>eastward_wind</p></li>
+                  <li>
+                    <p>
+                      ppfd optional; if missing, requires
+                      surface_downwelling_shortwave_flux_in_air
+                    </p>
+                  </li>
+                  <li><p>surface_downwelling_shortwave_flux_in_air</p></li>
+                  <li>
+                    <p>
+                      air_pressure (Pa) optional; if missing, requires
+                      relative_humidity
+                    </p>
+                  </li>
+                  <li>
+                    <p>
+                      specific_humidity optional; if missing, requires
+                      relative_humidity
+                    </p>
+                  </li>
+                  <li>
+                    <p>
+                      relative_humidity optional; if missing, requires
+                      air_pressure and specific_humidity
+                    </p>
+                  </li>
+                  <li><p>precipitation_flux</p></li>
+                  <li><p>air_temperature</p></li>
+                </ul>
+              </td>
+            </tr>
+            <tr>
+              <th>longitude</th>
+              <td><p>in degrees east, used for calculating solar noon</p></td>
+            </tr>
+            <tr>
+              <th>zulu2solarnoon</th>
+              <td>
+                <p>
+                  logical; if TRUE, convert time from GMT to local solar time.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>data.table / data.frame with fields</p>
+          <ul>
+            <li><p>doy day of year</p></li>
+            <li><p>hr hour</p></li>
+            <li><p>solar solar radiation (PPFD)</p></li>
+            <li><p>temp temperature, degrees celsius</p></li>
+            <li><p>rh relative humidity, as fraction (0-1)</p></li>
+            <li><p>windspeed m/s</p></li>
+            <li><p>precip cm/h</p></li>
+          </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-    <pre class="usage"><span class='fu'>cf2biocro</span>(<span class='no'>met</span>, <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>zulu2solarnoon</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>met</th>
-      <td><p>data.table object  with met for a single site; output from <code>load.cfmet</code></p><ul>
-<li><p>year int</p></li>
-<li><p>month int</p></li>
-<li><p>day int: day of month (1-31)</p></li>
-<li><p>doy int: day of year (1-366)</p></li>
-<li><p>hour int (0-23)</p></li>
-<li><p>date YYYY-MM-DD HH:MM:SS POSIXct</p></li>
-<li><p>wind_speed num m/s</p></li>
-<li><p>northward_wind</p></li>
-<li><p>eastward_wind</p></li>
-<li><p>ppfd optional; if missing, requires surface_downwelling_shortwave_flux_in_air</p></li>
-<li><p>surface_downwelling_shortwave_flux_in_air</p></li>
-<li><p>air_pressure (Pa) optional; if missing, requires relative_humidity</p></li>
-<li><p>specific_humidity optional; if missing, requires relative_humidity</p></li>
-<li><p>relative_humidity optional; if missing, requires air_pressure and specific_humidity</p></li>
-<li><p>precipitation_flux</p></li>
-<li><p>air_temperature</p></li>
-</ul></td>
-    </tr>
-    <tr>
-      <th>longitude</th>
-      <td><p>in degrees east, used for calculating solar noon</p></td>
-    </tr>
-    <tr>
-      <th>zulu2solarnoon</th>
-      <td><p>logical; if TRUE, convert time from GMT to local solar time.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data.table / data.frame with fields</p><ul>
-<li><p>doy day of year</p></li>
-<li><p>hr hour</p></li>
-<li><p>solar solar radiation (PPFD)</p></li>
-<li><p>temp temperature, degrees celsius</p></li>
-<li><p>rh relative humidity, as fraction (0-1)</p></li>
-<li><p>windspeed m/s</p></li>
-<li><p>precip cm/h</p></li>
-</ul>
-
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/models/biocro/docs/reference/convert.samples.BIOCRO.html b/models/biocro/docs/reference/convert.samples.BIOCRO.html
index 455ce1c..b722704 100644
--- a/models/biocro/docs/reference/convert.samples.BIOCRO.html
+++ b/models/biocro/docs/reference/convert.samples.BIOCRO.html
@@ -2,179 +2,240 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Convert samples for biocro — convert.samples.BIOCRO" />
-
-<meta property="og:description" content="convert parameters from PEcAn database default units to biocro defaults" />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Convert samples for biocro — convert.samples.BIOCRO • PEcAn.BIOCRO
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Convert samples for biocro — convert.samples.BIOCRO"
+    />
+
+    <meta
+      property="og:description"
+      content="convert parameters from PEcAn database default units to biocro defaults"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
+                    </li>
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+                      <a href="../articles/workflow.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert samples for biocro</h1>
-    
-    <div class="hidden name"><code>convert.samples.BIOCRO.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>convert parameters from PEcAn database default units to biocro defaults</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>convert.samples.BIOCRO</span>(<span class='no'>trait.samples</span>, <span class='kw'>biocro_version</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>a matrix or dataframe of samples from the trait distribution</p></td>
-    </tr>
-    <tr>
-      <th>biocro_version</th>
-      <td><p>numeric, but currently only checks whether version is less than 1.0</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dataframe with values transformed</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Performs model specific unit conversions on a list of trait values,
-such as those provided to write.config</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert samples for biocro</h1>
+
+            <div class="hidden name">
+              <code>convert.samples.BIOCRO.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              convert parameters from PEcAn database default units to biocro
+              defaults
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>convert.samples.BIOCRO</span>(<span class='no'>trait.samples</span>, <span class='kw'>biocro_version</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.samples</th>
+              <td>
+                <p>
+                  a matrix or dataframe of samples from the trait distribution
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>biocro_version</th>
+              <td>
+                <p>
+                  numeric, but currently only checks whether version is less
+                  than 1.0
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>dataframe with values transformed</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Performs model specific unit conversions on a list of trait values,
+            such as those provided to write.config
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
-
diff --git a/models/biocro/docs/reference/get.model.output.BIOCRO.html b/models/biocro/docs/reference/get.model.output.BIOCRO.html
index b47f905..a09f999 100644
--- a/models/biocro/docs/reference/get.model.output.BIOCRO.html
+++ b/models/biocro/docs/reference/get.model.output.BIOCRO.html
@@ -2,162 +2,211 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Retrieve model output from local server — get.model.output.BIOCRO •
+      PEcAn.BIOCRO
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
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-    <h1>Retrieve model output from local server</h1>
-    
-    <div class="hidden name"><code>get.model.output.BIOCRO.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to retrieve model output from local server</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.model.output.BIOCRO</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>list generated from <code>read.settings</code> function applied to settings file</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze, David LeBauer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Retrieve model output from local server</h1>
+
+            <div class="hidden name">
+              <code>get.model.output.BIOCRO.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Function to retrieve model output from local server</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.model.output.BIOCRO</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  list generated from <code>read.settings</code> function
+                  applied to settings file
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze, David LeBauer
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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diff --git a/models/biocro/docs/reference/get_biocro_defaults.html b/models/biocro/docs/reference/get_biocro_defaults.html
index c11b516..fd24ff4 100644
--- a/models/biocro/docs/reference/get_biocro_defaults.html
+++ b/models/biocro/docs/reference/get_biocro_defaults.html
@@ -2,168 +2,223 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      get_biocro_defaults • PEcAn.BIOCRO
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
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+    />
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+*_initial_values, *_parameters, *_modules"
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+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Look for defaults provided as datasets in the BioCro model package</h1>
-    
-    <div class="hidden name"><code>get_biocro_defaults.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>When available, default parameters come in sets of three:
-*_initial_values, *_parameters, *_modules</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_biocro_defaults</span>(<span class='no'>genus</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>genus</th>
-      <td><p>Name of the genus (or really any string BioCro uses as a *_parameters prefix)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a list in the format expected by <code>BioCro::Gro</code>,
-  containing four lists named `type`, `initial_values`, `parameters`, and `modules`,
-  or NULL if genus not found</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Look for defaults provided as datasets in the BioCro model package
+            </h1>
+
+            <div class="hidden name"><code>get_biocro_defaults.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              When available, default parameters come in sets of three:
+              *_initial_values, *_parameters, *_modules
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_biocro_defaults</span>(<span class='no'>genus</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>genus</th>
+              <td>
+                <p>
+                  Name of the genus (or really any string BioCro uses as a
+                  *_parameters prefix)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            a list in the format expected by <code>BioCro::Gro</code>,
+            containing four lists named `type`, `initial_values`, `parameters`,
+            and `modules`, or NULL if genus not found
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/models/biocro/docs/reference/index.html b/models/biocro/docs/reference/index.html
index a8750f3..7d5b4da 100644
--- a/models/biocro/docs/reference/index.html
+++ b/models/biocro/docs/reference/index.html
@@ -2,213 +2,308 @@
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 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-<title>Function reference • PEcAn.BIOCRO</title>
+    <title>Function reference • PEcAn.BIOCRO</title>
 
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
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+    <!-- sticky kit -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                <span
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
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+            <div id="navbar" class="navbar-collapse collapse">
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+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="../articles/workflow.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
 
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="cf2biocro.html">cf2biocro()</a></code> </p>
-        </td>
-        <td><p>Convert CF-formatted met data to BioCro met</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="convert.samples.BIOCRO.html">convert.samples.BIOCRO()</a></code> </p>
-        </td>
-        <td><p>Convert samples for biocro</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.model.output.BIOCRO.html">get.model.output.BIOCRO()</a></code> </p>
-        </td>
-        <td><p>Retrieve model output from local server</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_biocro_defaults.html">get_biocro_defaults()</a></code> </p>
-        </td>
-        <td><p>Look for defaults provided as datasets in the BioCro model package</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2model.BIOCRO.html">met2model.BIOCRO()</a></code> </p>
-        </td>
-        <td><p>Write BioCro met files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.BIOCRO.html">model2netcdf.BIOCRO()</a></code> </p>
-        </td>
-        <td><p>Function to convert biocro model output to standard netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.biocro.config.html">read.biocro.config()</a></code> </p>
-        </td>
-        <td><p>Read BioCro Config</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="remove.config.BIOCRO.html">remove.config.BIOCRO()</a></code> </p>
-        </td>
-        <td><p>Clear out previous biocro config and parameter files.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="run.biocro.html">run.biocro()</a></code> </p>
-        </td>
-        <td><p>Run BioCro at a point</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.BIOCRO.html">write.config.BIOCRO()</a></code> </p>
-        </td>
-        <td><p>Write configuration files for the biocro model</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-      </footer>
-   </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="cf2biocro.html">cf2biocro()</a></code>
+                  </p>
+                </td>
+                <td><p>Convert CF-formatted met data to BioCro met</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="convert.samples.BIOCRO.html"
+                        >convert.samples.BIOCRO()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Convert samples for biocro</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.model.output.BIOCRO.html"
+                        >get.model.output.BIOCRO()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Retrieve model output from local server</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_biocro_defaults.html"
+                        >get_biocro_defaults()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Look for defaults provided as datasets in the BioCro model
+                    package
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.BIOCRO.html"
+                        >met2model.BIOCRO()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write BioCro met files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.BIOCRO.html"
+                        >model2netcdf.BIOCRO()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function to convert biocro model output to standard netCDF
+                    format
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.biocro.config.html"
+                        >read.biocro.config()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read BioCro Config</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="remove.config.BIOCRO.html"
+                        >remove.config.BIOCRO()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Clear out previous biocro config and parameter files.</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="run.biocro.html">run.biocro()</a></code>
+                  </p>
+                </td>
+                <td><p>Run BioCro at a point</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.BIOCRO.html"
+                        >write.config.BIOCRO()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write configuration files for the biocro model</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
-  
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/models/biocro/docs/reference/met2model.BIOCRO.html b/models/biocro/docs/reference/met2model.BIOCRO.html
index 86a0ef8..5d73573 100644
--- a/models/biocro/docs/reference/met2model.BIOCRO.html
+++ b/models/biocro/docs/reference/met2model.BIOCRO.html
@@ -2,195 +2,251 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
-<meta property="og:description" content="Converts a met CF file to a model specific met file. The input
-files are called &amp;lt;in.path&amp;gt;/&amp;lt;in.prefix&amp;gt;.YYYY.cf" />
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-<![endif]-->
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+
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+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Write BioCro met files — met2model.BIOCRO"
+    />
+
+    <meta
+      property="og:description"
+      content="Converts a met CF file to a model specific met file. The input
+files are called &amp;lt;in.path&amp;gt;/&amp;lt;in.prefix&amp;gt;.YYYY.cf"
+    />
+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-        <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
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-        
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-      
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-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="../articles/workflow.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write BioCro met files</h1>
-    
-    <div class="hidden name"><code>met2model.BIOCRO.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write BioCro met files</h1>
 
-    <div class="ref-description">
-    
-    <p>Converts a met CF file to a model specific met file. The input
-files are called &lt;in.path&gt;/&lt;in.prefix&gt;.YYYY.cf</p>
-    
-    </div>
+            <div class="hidden name"><code>met2model.BIOCRO.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Converts a met CF file to a model specific met file. The input
+              files are called &lt;in.path&gt;/&lt;in.prefix&gt;.YYYY.cf
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2model.BIOCRO</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>lat</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.BIOCRO</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>lat</span>,
   <span class='no'>lon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>path on disk where CF file lives</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix for each file</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location where model specific output is written</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: Write over any existing file of the same name? If FALSE, leaves the existing file untouched and skips to the next year.</p></td>
-    </tr>
-    <tr>
-      <th>lat, lon</th>
-      <td><p>Site latitude and longitude</p></td>
-    </tr>
-    <tr>
-      <th>start_date, end_date</th>
-      <td><p>Date range to convert. Each year will be written to a separate file</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>other arguments passed from PEcAn, currently ignored</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a dataframe of information about the written file</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>path on disk where CF file lives</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix for each file</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location where model specific output is written</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>
+                  logical: Write over any existing file of the same name? If
+                  FALSE, leaves the existing file untouched and skips to the
+                  next year.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lat, lon</th>
+              <td><p>Site latitude and longitude</p></td>
+            </tr>
+            <tr>
+              <th>start_date, end_date</th>
+              <td>
+                <p>
+                  Date range to convert. Each year will be written to a separate
+                  file
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>other arguments passed from PEcAn, currently ignored</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>a dataframe of information about the written file</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper, David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper, David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
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-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/models/biocro/docs/reference/model2netcdf.BIOCRO.html b/models/biocro/docs/reference/model2netcdf.BIOCRO.html
index 3228b22..1b3c358 100644
--- a/models/biocro/docs/reference/model2netcdf.BIOCRO.html
+++ b/models/biocro/docs/reference/model2netcdf.BIOCRO.html
@@ -2,188 +2,238 @@
 <!DOCTYPE html>
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-
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+      Function to convert biocro model output to standard netCDF format —
+      model2netcdf.BIOCRO • PEcAn.BIOCRO
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
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+      crossorigin="anonymous"
+    />
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+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
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+    ></script>
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+    <script src="../pkgdown.js"></script>
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+      content="Function to convert biocro model output to standard netCDF format — model2netcdf.BIOCRO"
+    />
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+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+                    <span class="caret"></span>
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+                    </li>
+                  </ul>
+                </li>
+              </ul>
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to convert biocro model output to standard netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.BIOCRO.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function to convert biocro model output to standard netCDF format
+            </h1>
 
-    <div class="ref-description">
-    
-    <p>Convert BioCro output to netCDF</p>
-    
-    </div>
+            <div class="hidden name"><code>model2netcdf.BIOCRO.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert BioCro output to netCDF</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>model2netcdf.BIOCRO</span>(<span class='no'>result</span>, <span class='kw'>genus</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>outdir</span>, <span class='kw'>lat</span> <span class='kw'>=</span> -<span class='fl'>9999</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.BIOCRO</span>(<span class='no'>result</span>, <span class='kw'>genus</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>outdir</span>, <span class='kw'>lat</span> <span class='kw'>=</span> -<span class='fl'>9999</span>,
   <span class='kw'>lon</span> <span class='kw'>=</span> -<span class='fl'>9999</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>result</th>
-      <td><p>a dataframe of model output to be converted</p></td>
-    </tr>
-    <tr>
-      <th>genus</th>
-      <td><p>character: What kind of plant was being simulated?
-Used to correct for some genus-specific differences in model output;
-Eventually that will be handled inside BioCro and this argument will be removed.</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of model output</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Converts BioCro output to netCDF.
-Modified from on model2netcdf.SIPNET and model2netcdf.ED2 by</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>result</th>
+              <td><p>a dataframe of model output to be converted</p></td>
+            </tr>
+            <tr>
+              <th>genus</th>
+              <td>
+                <p>
+                  character: What kind of plant was being simulated? Used to
+                  correct for some genus-specific differences in model output;
+                  Eventually that will be handled inside BioCro and this
+                  argument will be removed.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of model output</p></td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Converts BioCro output to netCDF. Modified from on
+            model2netcdf.SIPNET and model2netcdf.ED2 by
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Deepak Jaiswal, Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Deepak Jaiswal, Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/biocro/docs/reference/read.biocro.config.html b/models/biocro/docs/reference/read.biocro.config.html
index f2b4341..a8feb94 100644
--- a/models/biocro/docs/reference/read.biocro.config.html
+++ b/models/biocro/docs/reference/read.biocro.config.html
@@ -2,168 +2,206 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Read BioCro Config — read.biocro.config"
+    />
+
+    <meta property="og:description" content="Read BioCro config file" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-        <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
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+                <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="../articles/workflow.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read BioCro Config</h1>
-    
-    <div class="hidden name"><code>read.biocro.config.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Read BioCro config file</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read.biocro.config</span>(<span class='kw'>config.file</span> <span class='kw'>=</span> <span class='st'>"config.xml"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>config.file</th>
-      <td><p>Path to XML file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list of run configuration parameters for PEcAn</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read BioCro Config</h1>
+
+            <div class="hidden name"><code>read.biocro.config.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Read BioCro config file</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read.biocro.config</span>(<span class='kw'>config.file</span> <span class='kw'>=</span> <span class='st'>"config.xml"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>config.file</th>
+              <td><p>Path to XML file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list of run configuration parameters for PEcAn</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/biocro/docs/reference/remove.config.BIOCRO.html b/models/biocro/docs/reference/remove.config.BIOCRO.html
index 48c9931..65be00a 100644
--- a/models/biocro/docs/reference/remove.config.BIOCRO.html
+++ b/models/biocro/docs/reference/remove.config.BIOCRO.html
@@ -2,172 +2,218 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Clear out previous biocro config and parameter files. —
+      remove.config.BIOCRO • PEcAn.BIOCRO
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
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+
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="../articles/workflow.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Clear out previous biocro config and parameter files.</h1>
-    
-    <div class="hidden name"><code>remove.config.BIOCRO.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Clear out previous config and parameter files.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>remove.config.BIOCRO</span>(<span class='no'>main.outdir</span>, <span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>main.outdir</th>
-      <td><p>Primary PEcAn output directory (will be depreciated)</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing, removes config files as side effect</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Clear out previous biocro config and parameter files.</h1>
+
+            <div class="hidden name"><code>remove.config.BIOCRO.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Clear out previous config and parameter files.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>remove.config.BIOCRO</span>(<span class='no'>main.outdir</span>, <span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>main.outdir</th>
+              <td>
+                <p>Primary PEcAn output directory (will be depreciated)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing, removes config files as side effect</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/biocro/docs/reference/run.biocro.html b/models/biocro/docs/reference/run.biocro.html
index 8f43f0b..a7993d4 100644
--- a/models/biocro/docs/reference/run.biocro.html
+++ b/models/biocro/docs/reference/run.biocro.html
@@ -2,190 +2,244 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-<!-- clipboard.js -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Run BioCro at a point — run.biocro • PEcAn.BIOCRO</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+    <meta name="twitter:card" content="summary" />
+
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+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
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-    <li>
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-  </ul>
-</li>
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-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.BIOCRO</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/C4grass_sa_vd.html">UNKNOWN TITLE</a>
+                    </li>
+                    <li>
+                      <a href="../articles/workflow.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Run BioCro at a point</h1>
-    
-    <div class="hidden name"><code>run.biocro.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Run BioCro at a point</h1>
 
-    <div class="ref-description">
-    
-    <p>Run BioCro at a point</p>
-    
-    </div>
+            <div class="hidden name"><code>run.biocro.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Run BioCro at a point</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>run.biocro</span>(<span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>metpath</span>, <span class='kw'>soil.nc</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>config</span> <span class='kw'>=</span> <span class='no'>config</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>run.biocro</span>(<span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>metpath</span>, <span class='kw'>soil.nc</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>config</span> <span class='kw'>=</span> <span class='no'>config</span>,
   <span class='kw'>coppice.interval</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>lat</th>
-      <td><p>latitude in decimal degrees</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>longitude in decimal degrees</p></td>
-    </tr>
-    <tr>
-      <th>metpath</th>
-      <td><p>full path and name prefix of a csv file with hourly data in BioCro format,
-e.g. `/dir/met` if the files to be used are `/dir/met.2004.csv` and `dir/met.2005.csv'</p></td>
-    </tr>
-    <tr>
-      <th>soil.nc</th>
-      <td><p>full path and name of a netCDF file with soil data</p></td>
-    </tr>
-    <tr>
-      <th>config</th>
-      <td><p>full path and name of a config.xml file containing parameter values and configuration information for BioCro</p></td>
-    </tr>
-    <tr>
-      <th>coppice.interval</th>
-      <td><p>numeric, number of years between cuttings for coppice plant or perennial grass. Only used with BioCro 0.9; ignored when using later versions.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>output from one of the <code>BioCro::*.Gro</code> functions (determined by <code>config$genus</code>), as data.table object</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>lat</th>
+              <td><p>latitude in decimal degrees</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>longitude in decimal degrees</p></td>
+            </tr>
+            <tr>
+              <th>metpath</th>
+              <td>
+                <p>
+                  full path and name prefix of a csv file with hourly data in
+                  BioCro format, e.g. `/dir/met` if the files to be used are
+                  `/dir/met.2004.csv` and `dir/met.2005.csv'
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>soil.nc</th>
+              <td><p>full path and name of a netCDF file with soil data</p></td>
+            </tr>
+            <tr>
+              <th>config</th>
+              <td>
+                <p>
+                  full path and name of a config.xml file containing parameter
+                  values and configuration information for BioCro
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>coppice.interval</th>
+              <td>
+                <p>
+                  numeric, number of years between cuttings for coppice plant or
+                  perennial grass. Only used with BioCro 0.9; ignored when using
+                  later versions.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            output from one of the <code>BioCro::*.Gro</code> functions
+            (determined by <code>config$genus</code>), as data.table object
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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diff --git a/models/biocro/docs/reference/write.config.BIOCRO.html b/models/biocro/docs/reference/write.config.BIOCRO.html
index f40124c..7362f45 100644
--- a/models/biocro/docs/reference/write.config.BIOCRO.html
+++ b/models/biocro/docs/reference/write.config.BIOCRO.html
@@ -2,182 +2,231 @@
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+      PEcAn.BIOCRO
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write configuration files for the biocro model</h1>
-    
-    <div class="hidden name"><code>write.config.BIOCRO.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a configuration files for the biocro model</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.BIOCRO</span>(<span class='kw'>defaults</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>named list with default model parameter values</p></td>
-    </tr>
-    <tr>
-      <th>trait.values</th>
-      <td><p>named list (or dataframe of trait values)
- can either be a data.frame or named list of traits, e.g.
-<code>data.frame(vmax = 1, b0 = 2)</code> or <code>list(vmax = 1, b0 = 2)</code></p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>pecan settings file configured for BioCro</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>integer; a unique identifier for the run.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing, writes configuration file as side effect</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write configuration files for the biocro model</h1>
+
+            <div class="hidden name"><code>write.config.BIOCRO.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a configuration files for the biocro model</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.BIOCRO</span>(<span class='kw'>defaults</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>named list with default model parameter values</p></td>
+            </tr>
+            <tr>
+              <th>trait.values</th>
+              <td>
+                <p>
+                  named list (or dataframe of trait values) can either be a
+                  data.frame or named list of traits, e.g.
+                  <code>data.frame(vmax = 1, b0 = 2)</code> or
+                  <code>list(vmax = 1, b0 = 2)</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>pecan settings file configured for BioCro</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>integer; a unique identifier for the run.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing, writes configuration file as side effect</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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+        </div>
+
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index d0f5009..63db43b 100644
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@@ -2,97 +2,126 @@
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+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.CABLE</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/cable/docs/authors.html b/models/cable/docs/authors.html
index ee4d923..06b9c80 100644
--- a/models/cable/docs/authors.html
+++ b/models/cable/docs/authors.html
@@ -2,126 +2,146 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.CABLE</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.CABLE</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.CABLE</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.CABLE</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Kaitlin Ragosta</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Tony Gardella</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Kaitlin Ragosta</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Tony Gardella</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/cable/docs/docsearch.css b/models/cable/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/cable/docs/docsearch.css
+++ b/models/cable/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/cable/docs/docsearch.js b/models/cable/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/cable/docs/docsearch.js
+++ b/models/cable/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/cable/docs/index.html b/models/cable/docs/index.html
index a0bcc0c..acd29b4 100644
--- a/models/cable/docs/index.html
+++ b/models/cable/docs/index.html
@@ -1,110 +1,187 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the CABLE model • PEcAn.CABLE</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the CABLE model">
-<meta property="og:description" content="This module provides functions to link the (CABLE) to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn package for integration of the CABLE model • PEcAn.CABLE
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the CABLE model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to link the (CABLE) to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.CABLE</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    <div id="installing-cable" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#installing-cable" class="anchor"></a>Installing CABLE</h1></div>
-<p>Information on building and using CABLE can be found here: <a href="https://trac.nci.org.au/trac/cable/wiki/CableUserGuide" class="uri">https://trac.nci.org.au/trac/cable/wiki/CableUserGuide</a></p>
-<p>Follow instructions for obtaining a login and acquiring CABLE via an svn checkout found in the “Getting CABLE” section.</p>
-<p>Ensure korn shell scripts are accessible on your machine, and that there is a copy of cable.nml in the directory you are using to run CABLE.</p>
-<p>In CABLE’s offline directory, run build.ksh. This should build an executable called “cable*“, which runs the model.</p>
-</div>
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.CABLE</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div id="installing-cable" class="section level1">
+            <div class="page-header">
+              <h1 class="hasAnchor">
+                <a href="#installing-cable" class="anchor"></a>Installing CABLE
+              </h1>
+            </div>
+            <p>
+              Information on building and using CABLE can be found here:
+              <a
+                href="https://trac.nci.org.au/trac/cable/wiki/CableUserGuide"
+                class="uri"
+                >https://trac.nci.org.au/trac/cable/wiki/CableUserGuide</a
+              >
+            </p>
+            <p>
+              Follow instructions for obtaining a login and acquiring CABLE via
+              an svn checkout found in the “Getting CABLE” section.
+            </p>
+            <p>
+              Ensure korn shell scripts are accessible on your machine, and that
+              there is a copy of cable.nml in the directory you are using to run
+              CABLE.
+            </p>
+            <p>
+              In CABLE’s offline directory, run build.ksh. This should build an
+              executable called “cable*“, which runs the model.
+            </p>
+          </div>
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/cable/docs/pkgdown.css b/models/cable/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/cable/docs/pkgdown.css
+++ b/models/cable/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/cable/docs/pkgdown.js b/models/cable/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/cable/docs/pkgdown.js
+++ b/models/cable/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/cable/docs/reference/index.html b/models/cable/docs/reference/index.html
index 3cffbb2..7e54cb7 100644
--- a/models/cable/docs/reference/index.html
+++ b/models/cable/docs/reference/index.html
@@ -2,168 +2,225 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.CABLE</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.CABLE</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
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+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
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+              <span class="navbar-brand">
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+                <span
+                  class="label label-default"
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+                  title="Released package"
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-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
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-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="met2model.CABLE.html">met2model.CABLE()</a></code> </p>
-        </td>
-        <td><p>Write CABLE met files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.CABLE.html">model2netcdf.CABLE()</a></code> </p>
-        </td>
-        <td><p>Code to convert CABLE's output into netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_restart.CABLE.html">read_restart.CABLE()</a></code> </p>
-        </td>
-        <td><p>Read restart template for SDA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.CABLE.html">write.config.CABLE()</a></code> </p>
-        </td>
-        <td><p>Write CABLE configuration files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_restart.CABLE.html">write_restart.CABLE()</a></code> </p>
-        </td>
-        <td><p>Write restart template for SDA</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.CABLE.html"
+                        >met2model.CABLE()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write CABLE met files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.CABLE.html"
+                        >model2netcdf.CABLE()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Code to convert CABLE's output into netCDF format</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read_restart.CABLE.html"
+                        >read_restart.CABLE()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read restart template for SDA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.CABLE.html"
+                        >write.config.CABLE()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write CABLE configuration files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write_restart.CABLE.html"
+                        >write_restart.CABLE()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write restart template for SDA</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/models/cable/docs/reference/met2model.CABLE.html b/models/cable/docs/reference/met2model.CABLE.html
index ac6c2e7..bad9c17 100644
--- a/models/cable/docs/reference/met2model.CABLE.html
+++ b/models/cable/docs/reference/met2model.CABLE.html
@@ -2,163 +2,200 @@
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 <html>
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
-<meta property="og:description" content="Converts a met CF file to a model specific met file. The input
-files are calld &amp;lt;in.path&amp;gt;/&amp;lt;in.prefix&amp;gt;.YYYY.cf" />
-<meta name="twitter:card" content="summary" />
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      property="og:description"
+      content="Converts a met CF file to a model specific met file. The input
+files are calld &amp;lt;in.path&amp;gt;/&amp;lt;in.prefix&amp;gt;.YYYY.cf"
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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+              <button
+                type="button"
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+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.CABLE</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write CABLE met files</h1>
-    
-    <div class="hidden name"><code>met2model.CABLE.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Converts a met CF file to a model specific met file. The input
-files are calld &lt;in.path&gt;/&lt;in.prefix&gt;.YYYY.cf</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>met2model.CABLE</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>path on disk where CF file lives</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix for each file</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location where model specific output is written.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>OK if everything was succesful.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write CABLE met files</h1>
+
+            <div class="hidden name"><code>met2model.CABLE.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Converts a met CF file to a model specific met file. The input
+              files are calld &lt;in.path&gt;/&lt;in.prefix&gt;.YYYY.cf
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.CABLE</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>path on disk where CF file lives</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix for each file</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location where model specific output is written.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>OK if everything was succesful.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/cable/docs/reference/model2netcdf.CABLE.html b/models/cable/docs/reference/model2netcdf.CABLE.html
index 98bb224..1a67879 100644
--- a/models/cable/docs/reference/model2netcdf.CABLE.html
+++ b/models/cable/docs/reference/model2netcdf.CABLE.html
@@ -2,163 +2,202 @@
 <!DOCTYPE html>
 <html>
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Code to convert CABLE's output into netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.CABLE.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert CABLE output into the NACP Intercomparison format (ALMA using netCDF)</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model2netcdf.CABLE</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Code to convert CABLE's output into netCDF format</h1>
+
+            <div class="hidden name"><code>model2netcdf.CABLE.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Convert CABLE output into the NACP Intercomparison format (ALMA
+              using netCDF)
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.CABLE</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Rob Kooper
+        </div>
+      </div>
 
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diff --git a/models/cable/docs/reference/read_restart.CABLE.html b/models/cable/docs/reference/read_restart.CABLE.html
index a4b41b8..f4f26fc 100644
--- a/models/cable/docs/reference/read_restart.CABLE.html
+++ b/models/cable/docs/reference/read_restart.CABLE.html
@@ -2,173 +2,207 @@
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+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read restart template for SDA</h1>
-    
-    <div class="hidden name"><code>read_restart.CABLE.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Read restart files from model.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_restart.CABLE</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>, <span class='no'>var.names</span>, <span class='no'>params</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Output directory</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>Run ID</p></td>
-    </tr>
-    <tr>
-      <th>stop.time</th>
-      <td><p>Year that is being read</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>var.names</th>
-      <td><p>Variable names to be extracted</p></td>
-    </tr>
-    <tr>
-      <th>params</th>
-      <td><p>Any parameters required for state calculations</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Forecast numeric matrix</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read restart template for SDA</h1>
+
+            <div class="hidden name"><code>read_restart.CABLE.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Read restart files from model.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_restart.CABLE</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>, <span class='no'>var.names</span>, <span class='no'>params</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Output directory</p></td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>Run ID</p></td>
+            </tr>
+            <tr>
+              <th>stop.time</th>
+              <td><p>Year that is being read</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>var.names</th>
+              <td><p>Variable names to be extracted</p></td>
+            </tr>
+            <tr>
+              <th>params</th>
+              <td><p>Any parameters required for state calculations</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Forecast numeric matrix</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/cable/docs/reference/write.config.CABLE.html b/models/cable/docs/reference/write.config.CABLE.html
index 2ccecf1..5847315 100644
--- a/models/cable/docs/reference/write.config.CABLE.html
+++ b/models/cable/docs/reference/write.config.CABLE.html
@@ -2,172 +2,210 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Write CABLE configuration files — write.config.CABLE • PEcAn.CABLE
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write CABLE configuration files — write.config.CABLE"
+    />
+
+    <meta property="og:description" content="Writes a CABLE config file." />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.CABLE</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
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-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.CABLE</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write CABLE configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.CABLE.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a CABLE config file.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.CABLE</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file for CABLE for given run</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write CABLE configuration files</h1>
+
+            <div class="hidden name"><code>write.config.CABLE.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a CABLE config file.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.CABLE</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file for CABLE for given run</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Requires a pft xml object, a list of trait values for a single model
+            run, and the name of the file to create
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper, Kaitlin Ragosta
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper, Kaitlin Ragosta
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/cable/docs/reference/write_restart.CABLE.html b/models/cable/docs/reference/write_restart.CABLE.html
index c5c9e8d..24a57ff 100644
--- a/models/cable/docs/reference/write_restart.CABLE.html
+++ b/models/cable/docs/reference/write_restart.CABLE.html
@@ -2,156 +2,190 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Write restart template for SDA — write_restart.CABLE • PEcAn.CABLE</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Write restart template for SDA — write_restart.CABLE • PEcAn.CABLE
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write restart template for SDA — write_restart.CABLE"
+    />
+
+    <meta property="og:description" content="Write restart files for model" />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
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+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.CABLE</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write restart template for SDA</h1>
-    
-    <div class="hidden name"><code>write_restart.CABLE.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write restart template for SDA</h1>
 
-    <div class="ref-description">
-    
-    <p>Write restart files for model</p>
-    
-    </div>
+            <div class="hidden name"><code>write_restart.CABLE.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>write_restart.CABLE</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
-  <span class='no'>new.state</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>start.time</th>
-      <td><p>Time of current assimilation step</p></td>
-    </tr>
-    <tr>
-      <th>stop.time</th>
-      <td><p>Time of next assimilation step</p></td>
-    </tr>
-    <tr>
-      <th>new.state</th>
-      <td><p>Analysis state matrix returned by <code>sda.enkf</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Write restart files for model</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>write_restart.CABLE</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
+  <span class='no'>new.state</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>start.time</th>
+              <td><p>Time of current assimilation step</p></td>
+            </tr>
+            <tr>
+              <th>stop.time</th>
+              <td><p>Time of next assimilation step</p></td>
+            </tr>
+            <tr>
+              <th>new.state</th>
+              <td>
+                <p>Analysis state matrix returned by <code>sda.enkf</code></p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/clm45/docs/LICENSE-text.html b/models/clm45/docs/LICENSE-text.html
index 2f8cee5..4a5df57 100644
--- a/models/clm45/docs/LICENSE-text.html
+++ b/models/clm45/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-        <a class="navbar-link" href="index.html">PEcAn.CLM45</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.CLM45</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/clm45/docs/authors.html b/models/clm45/docs/authors.html
index 1467914..448eea3 100644
--- a/models/clm45/docs/authors.html
+++ b/models/clm45/docs/authors.html
@@ -2,122 +2,143 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.CLM45</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.CLM45</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/clm45/docs/docsearch.css b/models/clm45/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/clm45/docs/docsearch.css
+++ b/models/clm45/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/clm45/docs/docsearch.js b/models/clm45/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/clm45/docs/docsearch.js
+++ b/models/clm45/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/clm45/docs/index.html b/models/clm45/docs/index.html
index a19b970..70479fc 100644
--- a/models/clm45/docs/index.html
+++ b/models/clm45/docs/index.html
@@ -1,113 +1,169 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of CLM4.5 model • PEcAn.CLM45</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of CLM4.5 model">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn package for integration of CLM4.5 model • PEcAn.CLM45</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of CLM4.5 model"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation. This package provides functions to
-    link the Community Land Model, version 4.5, to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    link the Community Land Model, version 4.5, to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.CLM45</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation. This package provides functions to
-    link the Community Land Model, version 4.5, to PEcAn.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
-
-  </div>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.CLM45</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation. This package
+          provides functions to link the Community Land Model, version 4.5, to
+          PEcAn.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/clm45/docs/pkgdown.css b/models/clm45/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/clm45/docs/pkgdown.css
+++ b/models/clm45/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
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-html, body {
+html,
+body {
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 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
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-  display:inline-block;
+  display: inline-block;
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@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
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+.contents h4 {
   padding-top: 60px;
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 }
@@ -107,7 +110,6 @@ a.anchor {
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 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
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 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/clm45/docs/pkgdown.js b/models/clm45/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/clm45/docs/pkgdown.js
+++ b/models/clm45/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/clm45/docs/reference/index.html b/models/clm45/docs/reference/index.html
index a152492..bac46b8 100644
--- a/models/clm45/docs/reference/index.html
+++ b/models/clm45/docs/reference/index.html
@@ -2,156 +2,203 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.CLM45</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<!-- Font Awesome icons -->
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-<!-- clipboard.js -->
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-<!-- sticky kit -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.CLM45</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Function reference" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.CLM45</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.CLM45</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="met2model.CLM45.html">met2model.CLM45()</a></code> </p>
-        </td>
-        <td><p>met2model for CLM45</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.CLM45.html">model2netcdf.CLM45()</a></code> </p>
-        </td>
-        <td><p>Code to convert CLM45 netcdf output into into CF standard</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.CLM45.html">write.config.CLM45()</a></code> </p>
-        </td>
-        <td><p>Write CLM4.5 configuration files</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.CLM45.html"
+                        >met2model.CLM45()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2model for CLM45</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.CLM45.html"
+                        >model2netcdf.CLM45()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Code to convert CLM45 netcdf output into into CF standard
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.CLM45.html"
+                        >write.config.CLM45()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write CLM4.5 configuration files</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/clm45/docs/reference/met2model.CLM45.html b/models/clm45/docs/reference/met2model.CLM45.html
index c947660..50ad192 100644
--- a/models/clm45/docs/reference/met2model.CLM45.html
+++ b/models/clm45/docs/reference/met2model.CLM45.html
@@ -2,172 +2,214 @@
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.CLM45</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2model for CLM45</h1>
-    
-    <div class="hidden name"><code>met2model.CLM45.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2model for CLM45</h1>
 
-    <div class="ref-description">
-    
-    <p>met2model wrapper for CLM45</p>
-    
-    </div>
+            <div class="hidden name"><code>met2model.CLM45.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2model.CLM45</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>lst</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>...</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>lst</th>
-      <td><p>timezone offset to GMT in hours</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbosefor(year in start_year:end_year)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>met2model wrapper for CLM45</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.CLM45</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>lst</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>...</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lst</th>
+              <td><p>timezone offset to GMT in hours</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  should the function be very verbosefor(year in
+                  start_year:end_year)
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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diff --git a/models/clm45/docs/reference/model2netcdf.CLM45.html b/models/clm45/docs/reference/model2netcdf.CLM45.html
index 754e390..dcb164b 100644
--- a/models/clm45/docs/reference/model2netcdf.CLM45.html
+++ b/models/clm45/docs/reference/model2netcdf.CLM45.html
@@ -2,163 +2,199 @@
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-<!-- Bootstrap -->
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+      model2netcdf.CLM45 • PEcAn.CLM45
+    </title>
+
+    <!-- jquery -->
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
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+    />
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+    />
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+    />
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.CLM45</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Code to convert CLM45 netcdf output into into CF standard</h1>
-    
-    <div class="hidden name"><code>model2netcdf.CLM45.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Code to convert CLM45 netcdf output into into CF standard</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model2netcdf.CLM45</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of CLM45 model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Code to convert CLM45 netcdf output into into CF standard</h1>
+
+            <div class="hidden name"><code>model2netcdf.CLM45.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Code to convert CLM45 netcdf output into into CF standard</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.CLM45</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of CLM45 model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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   </body>
 </html>
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diff --git a/models/clm45/docs/reference/write.config.CLM45.html b/models/clm45/docs/reference/write.config.CLM45.html
index a2a0667..fd2b7f4 100644
--- a/models/clm45/docs/reference/write.config.CLM45.html
+++ b/models/clm45/docs/reference/write.config.CLM45.html
@@ -2,165 +2,204 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Write CLM4.5 configuration files — write.config.CLM45 • PEcAn.CLM45
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write CLM4.5 configuration files — write.config.CLM45"
+    />
+
+    <meta
+      property="og:description"
+      content="Writes config files for use with the Community Land Model model."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.CLM45</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.CLM45</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write CLM4.5 configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.CLM45.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes config files for use with the Community Land Model model.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.CLM45</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>none</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write CLM4.5 configuration files</h1>
+
+            <div class="hidden name"><code>write.config.CLM45.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Writes config files for use with the Community Land Model model.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.CLM45</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>none</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/dalec/docs/LICENSE-text.html b/models/dalec/docs/LICENSE-text.html
index 0ecd3fc..deef736 100644
--- a/models/dalec/docs/LICENSE-text.html
+++ b/models/dalec/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-
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-
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-
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+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.DALEC</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.DALEC</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/dalec/docs/authors.html b/models/dalec/docs/authors.html
index e6df9ab..92aaf49 100644
--- a/models/dalec/docs/authors.html
+++ b/models/dalec/docs/authors.html
@@ -2,126 +2,146 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.DALEC</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.DALEC</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.DALEC</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.DALEC</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Tristan Quaife</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Tristan Quaife</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/dalec/docs/docsearch.css b/models/dalec/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/dalec/docs/docsearch.css
+++ b/models/dalec/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/dalec/docs/docsearch.js b/models/dalec/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/dalec/docs/docsearch.js
+++ b/models/dalec/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/dalec/docs/index.html b/models/dalec/docs/index.html
index 09e53dc..44df740 100644
--- a/models/dalec/docs/index.html
+++ b/models/dalec/docs/index.html
@@ -1,103 +1,160 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the DALEC model • PEcAn.DALEC</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the DALEC model">
-<meta property="og:description" content="This module provides functions to link DALEC to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn package for integration of the DALEC model • PEcAn.DALEC
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the DALEC model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to link DALEC to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.DALEC</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    This module provides functions to link DALEC to PEcAn.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.DALEC</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          This module provides functions to link DALEC to PEcAn.
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/dalec/docs/pkgdown.css b/models/dalec/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/dalec/docs/pkgdown.css
+++ b/models/dalec/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/dalec/docs/pkgdown.js b/models/dalec/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/dalec/docs/pkgdown.js
+++ b/models/dalec/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/dalec/docs/reference/get.model.output.generic.html b/models/dalec/docs/reference/get.model.output.generic.html
index 194136f..eff8e5d 100644
--- a/models/dalec/docs/reference/get.model.output.generic.html
+++ b/models/dalec/docs/reference/get.model.output.generic.html
@@ -2,135 +2,166 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Retrieve model output from local or remote server — get.model.output.generic • PEcAn.DALEC</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Retrieve model output from local or remote server — get.model.output.generic" />
-
-<meta property="og:description" content="Function to retrieve model output from local or remote
-  server" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Retrieve model output from local or remote server</h1>
-    
-    <div class="hidden name"><code>get.model.output.generic.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to retrieve model output from local or remote
-  server</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.model.output.dalec</span>()</pre>
-        
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Retrieve model output from local or remote server</h1>
+
+            <div class="hidden name">
+              <code>get.model.output.generic.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Function to retrieve model output from local or remote server</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.model.output.dalec</span>()</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                </li>
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+
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       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="get.model.output.generic.html">get.model.output.dalec()</a></code> </p>
-        </td>
-        <td><p>Retrieve model output from local or remote server</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2model.DALEC.html">met2model.DALEC()</a></code> </p>
-        </td>
-        <td><p>met2model.DALEC</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.DALEC.html">model2netcdf.DALEC()</a></code> </p>
-        </td>
-        <td><p>Function to convert DALEC model output to standard netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.DALEC.html">write.config.DALEC()</a></code> </p>
-        </td>
-        <td><p>write.config.DALEC</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.model.output.generic.html"
+                        >get.model.output.dalec()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Retrieve model output from local or remote server</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.DALEC.html"
+                        >met2model.DALEC()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2model.DALEC</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.DALEC.html"
+                        >model2netcdf.DALEC()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function to convert DALEC model output to standard netCDF
+                    format
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.DALEC.html"
+                        >write.config.DALEC()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>write.config.DALEC</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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   </body>
 </html>
-
diff --git a/models/dalec/docs/reference/met2model.DALEC.html b/models/dalec/docs/reference/met2model.DALEC.html
index 62695b6..0b2daa5 100644
--- a/models/dalec/docs/reference/met2model.DALEC.html
+++ b/models/dalec/docs/reference/met2model.DALEC.html
@@ -2,169 +2,206 @@
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+                  class="label label-default"
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-<div class="row">
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-    <div class="page-header">
-    <h1>met2model.DALEC</h1>
-    
-    <div class="hidden name"><code>met2model.DALEC.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2model.DALEC</h1>
 
-    <div class="ref-description">
-    
-    <p>met2model for DALEC</p>
-    
-    </div>
+            <div class="hidden name"><code>met2model.DALEC.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>met2model for DALEC</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2model.DALEC</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.DALEC</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>spin_nyear</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>spin_nsample</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>spin_resample</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/models/dalec/docs/reference/model2netcdf.DALEC.html b/models/dalec/docs/reference/model2netcdf.DALEC.html
index eac50bb..5146cf5 100644
--- a/models/dalec/docs/reference/model2netcdf.DALEC.html
+++ b/models/dalec/docs/reference/model2netcdf.DALEC.html
@@ -2,169 +2,206 @@
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+      Function to convert DALEC model output to standard netCDF format —
+      model2netcdf.DALEC • PEcAn.DALEC
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to convert DALEC model output to standard netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.DALEC.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert DALEC output to netCDF</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model2netcdf.DALEC</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of DALEC model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Converts all output contained in a folder to netCDF.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function to convert DALEC model output to standard netCDF format
+            </h1>
+
+            <div class="hidden name"><code>model2netcdf.DALEC.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert DALEC output to netCDF</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.DALEC</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of DALEC model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Converts all output contained in a folder to netCDF.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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diff --git a/models/dalec/docs/reference/write.config.DALEC.html b/models/dalec/docs/reference/write.config.DALEC.html
index 7bceaf5..3aa95ef 100644
--- a/models/dalec/docs/reference/write.config.DALEC.html
+++ b/models/dalec/docs/reference/write.config.DALEC.html
@@ -2,141 +2,172 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+
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+write Dalec Configuration files"
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
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+                type="button"
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.DALEC</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
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+                <li>
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+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>write.config.DALEC</h1>
-    
-    <div class="hidden name"><code>write.config.DALEC.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a configuration files for your model
-write Dalec Configuration files</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.DALEC</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration files</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>write.config.DALEC</h1>
+
+            <div class="hidden name"><code>write.config.DALEC.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Writes a configuration files for your model write Dalec
+              Configuration files
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.DALEC</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration files</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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index 329a72f..16f3638 100644
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@@ -2,97 +2,126 @@
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-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.dvmdostem</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/dvmdostem/docs/authors.html b/models/dvmdostem/docs/authors.html
index 3a1f468..506ce05 100644
--- a/models/dvmdostem/docs/authors.html
+++ b/models/dvmdostem/docs/authors.html
@@ -2,126 +2,146 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.dvmdostem</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.dvmdostem</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.dvmdostem</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.dvmdostem</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Tobey Carman</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Tobey Carman</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/dvmdostem/docs/docsearch.css b/models/dvmdostem/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/dvmdostem/docs/docsearch.css
+++ b/models/dvmdostem/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/dvmdostem/docs/docsearch.js b/models/dvmdostem/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/dvmdostem/docs/docsearch.js
+++ b/models/dvmdostem/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/dvmdostem/docs/index.html b/models/dvmdostem/docs/index.html
index 903f718..a2fece7 100644
--- a/models/dvmdostem/docs/index.html
+++ b/models/dvmdostem/docs/index.html
@@ -1,105 +1,161 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the dvmdostem model • PEcAn.dvmdostem</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the dvmdostem model">
-<meta property="og:description" content="This module provides functions to link the dvmdostem model to
-    PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn package for integration of the dvmdostem model • PEcAn.dvmdostem
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the dvmdostem model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to link the dvmdostem model to
+    PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.dvmdostem</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    This module provides functions to link the dvmdostem model to
-    PEcAn.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.dvmdostem</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          This module provides functions to link the dvmdostem model to PEcAn.
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/dvmdostem/docs/pkgdown.css b/models/dvmdostem/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/dvmdostem/docs/pkgdown.css
+++ b/models/dvmdostem/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/dvmdostem/docs/pkgdown.js b/models/dvmdostem/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/dvmdostem/docs/pkgdown.js
+++ b/models/dvmdostem/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/dvmdostem/docs/reference/convert.samples.dvmdostem.html b/models/dvmdostem/docs/reference/convert.samples.dvmdostem.html
index 9a18fad..d1acaf0 100644
--- a/models/dvmdostem/docs/reference/convert.samples.dvmdostem.html
+++ b/models/dvmdostem/docs/reference/convert.samples.dvmdostem.html
@@ -2,162 +2,212 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Convert samples for dvmdostem — convert.samples.dvmdostem • PEcAn.dvmdostem</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Convert samples for dvmdostem — convert.samples.dvmdostem" />
-
-<meta property="og:description" content="convert parameters, do unit conversions and update parameter names from PEcAn database default
-to units/names within dvmdostem" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Convert samples for dvmdostem — convert.samples.dvmdostem •
+      PEcAn.dvmdostem
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Convert samples for dvmdostem — convert.samples.dvmdostem"
+    />
+
+    <meta
+      property="og:description"
+      content="convert parameters, do unit conversions and update parameter names from PEcAn database default
+to units/names within dvmdostem"
+    />
+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+                type="button"
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+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.dvmdostem</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert samples for dvmdostem</h1>
-    
-    <div class="hidden name"><code>convert.samples.dvmdostem.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>convert parameters, do unit conversions and update parameter names from PEcAn database default
-to units/names within dvmdostem</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>convert.samples.dvmdostem</span>(<span class='no'>trait_values</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>a matrix or dataframe of samples from the trait distribution</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>matrix or dataframe with values transformed</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Performs model specific unit conversions on a a list of trait values,
-such as those provided to write.config</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert samples for dvmdostem</h1>
+
+            <div class="hidden name">
+              <code>convert.samples.dvmdostem.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              convert parameters, do unit conversions and update parameter names
+              from PEcAn database default to units/names within dvmdostem
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>convert.samples.dvmdostem</span>(<span class='no'>trait_values</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.samples</th>
+              <td>
+                <p>
+                  a matrix or dataframe of samples from the trait distribution
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>matrix or dataframe with values transformed</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Performs model specific unit conversions on a a list of trait
+            values, such as those provided to write.config
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, Tobey Carman
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, Tobey Carman
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
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diff --git a/models/dvmdostem/docs/reference/index.html b/models/dvmdostem/docs/reference/index.html
index 2a19349..60251ac 100644
--- a/models/dvmdostem/docs/reference/index.html
+++ b/models/dvmdostem/docs/reference/index.html
@@ -2,156 +2,204 @@
 <!DOCTYPE html>
 <html>
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
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+    <script src="../pkgdown.js"></script>
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
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+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.dvmdostem</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
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+              <ul class="nav navbar-nav">
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="convert.samples.dvmdostem.html">convert.samples.dvmdostem()</a></code> </p>
-        </td>
-        <td><p>Convert samples for dvmdostem</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.dvmdostem.html">model2netcdf.dvmdostem()</a></code> </p>
-        </td>
-        <td><p>Code to convert dvmdostem netcdf output into into CF standard</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.dvmdostem.html">write.config.dvmdostem()</a></code> </p>
-        </td>
-        <td><p>Write dvmdostem model configuration files</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="convert.samples.dvmdostem.html"
+                        >convert.samples.dvmdostem()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Convert samples for dvmdostem</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.dvmdostem.html"
+                        >model2netcdf.dvmdostem()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Code to convert dvmdostem netcdf output into into CF
+                    standard
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.dvmdostem.html"
+                        >write.config.dvmdostem()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write dvmdostem model configuration files</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/dvmdostem/docs/reference/model2netcdf.dvmdostem.html b/models/dvmdostem/docs/reference/model2netcdf.dvmdostem.html
index 6f579d3..606c0b7 100644
--- a/models/dvmdostem/docs/reference/model2netcdf.dvmdostem.html
+++ b/models/dvmdostem/docs/reference/model2netcdf.dvmdostem.html
@@ -2,121 +2,169 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Code to convert dvmdostem netcdf output into into CF standard</h1>
-    
-    <div class="hidden name"><code>model2netcdf.dvmdostem.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Code to convert dvmdostem netcdf output into into CF standard</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model2netcdf.dvmdostem</span>(<span class='no'>outdir</span>, <span class='no'>runstart</span>, <span class='no'>runend</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of dvmdostem model output</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"># NOT RUN {
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Code to convert dvmdostem netcdf output into into CF standard
+            </h1>
+
+            <div class="hidden name">
+              <code>model2netcdf.dvmdostem.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Code to convert dvmdostem netcdf output into into CF standard</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.dvmdostem</span>(<span class='no'>outdir</span>, <span class='no'>runstart</span>, <span class='no'>runend</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of dvmdostem model output</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples">
+# NOT RUN {
  
 # }
 # NOT RUN {
@@ -124,37 +172,34 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 # }
 # NOT RUN {
 # }
-</pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Tobey Carman, Shawn Serbin
-
-  </div>
-</div>
+</pre
+          >
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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-  <p>Developed by .</p>
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-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
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-   </div>
+          <h2>Author</h2>
 
-  
+          Tobey Carman, Shawn Serbin
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diff --git a/models/dvmdostem/docs/reference/write.config.dvmdostem.html b/models/dvmdostem/docs/reference/write.config.dvmdostem.html
index 7946a6d..b4a80c3 100644
--- a/models/dvmdostem/docs/reference/write.config.dvmdostem.html
+++ b/models/dvmdostem/docs/reference/write.config.dvmdostem.html
@@ -2,172 +2,216 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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+      Write dvmdostem model configuration files — write.config.dvmdostem •
+      PEcAn.dvmdostem
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+
+    <!-- pkgdown -->
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+    <script src="../pkgdown.js"></script>
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+      content="Write dvmdostem model configuration files — write.config.dvmdostem"
+    />
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+      content="Writes a dvmdostem PEcAn config file."
+    />
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+    <![endif]-->
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+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.dvmdostem</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write dvmdostem model configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.dvmdostem.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a dvmdostem PEcAn config file.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.dvmdostem</span>(<span class='kw'>defaults</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>trait.values</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>none</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write dvmdostem model configuration files</h1>
+
+            <div class="hidden name">
+              <code>write.config.dvmdostem.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a dvmdostem PEcAn config file.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.dvmdostem</span>(<span class='kw'>defaults</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>trait.values</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>none</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Requires a pft xml object, a list of trait values for a single model
+            run, and the name of the file to create
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Tobey Carman, Shawn Serbin
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Tobey Carman, Shawn Serbin
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-
diff --git a/models/ed/docs/LICENSE-text.html b/models/ed/docs/LICENSE-text.html
index d5a98b9..3325db8 100644
--- a/models/ed/docs/LICENSE-text.html
+++ b/models/ed/docs/LICENSE-text.html
@@ -2,109 +2,146 @@
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 <html>
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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-        <a class="navbar-link" href="index.html">PEcAn.ED2</a>
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-      <a href="articles/running_ed_from_R.html">Running ED from R</a>
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+                class="navbar-toggle collapsed"
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+              </button>
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+                <a class="navbar-link" href="index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -133,27 +170,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/articles/index.html b/models/ed/docs/articles/index.html
index b6a045d..2ae9045 100644
--- a/models/ed/docs/articles/index.html
+++ b/models/ed/docs/articles/index.html
@@ -2,133 +2,166 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
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+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Articles</h1>
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-    <div class="section ">
-      <h3>All vignettes</h3>
-      <p class="section-desc"></p>
+          <div class="section ">
+            <h3>All vignettes</h3>
+            <p class="section-desc"></p>
 
-      <ul>
-        <li><a href="running_ed_from_R.html">Running ED from R</a></li>
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index 9f0d4a2..21ae153 100644
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-    <div class="page-header toc-ignore">
-      <h1>Running ED from R</h1>
-                        <h4 class="author">Alexey Shiklomanov</h4>
-            
-      
-      
-      <div class="hidden name"><code>running_ed_from_R.Rmd</code></div>
+                    <span class="caret"></span>
+                  </a>
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+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
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+              </ul>
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+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header toc-ignore">
+            <h1>Running ED from R</h1>
+            <h4 class="author">Alexey Shiklomanov</h4>
 
-    </div>
+            <div class="hidden name"><code>running_ed_from_R.Rmd</code></div>
+          </div>
 
-    
-    
-<div id="introduction" class="section level1">
-<h1 class="hasAnchor">
-<a href="#introduction" class="anchor"></a>Introduction</h1>
-<p>The <code>PEcAn.ED2</code> package features a number of utilities to facilitate running the ED model from inside R, including working with input files, running the ED executable, and processing the outputs. This tutorial describes these utilites and provides examples of common use cases.</p>
-</div>
-<div id="basic-ed-run" class="section level1">
-<h1 class="hasAnchor">
-<a href="#basic-ed-run" class="anchor"></a>Basic ED run</h1>
-<div id="installing-the-r-package" class="section level2">
-<h2 class="hasAnchor">
-<a href="#installing-the-r-package" class="anchor"></a>Installing the R package</h2>
-<p>The <code>PEcAn.ED2</code> package and its PEcAn dependencies can be installed from GitHub as follows (all CRAN package dependencies should be installed automatically):</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"base/logger"</span>)
+          <div id="introduction" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#introduction" class="anchor"></a>Introduction
+            </h1>
+            <p>
+              The <code>PEcAn.ED2</code> package features a number of utilities
+              to facilitate running the ED model from inside R, including
+              working with input files, running the ED executable, and
+              processing the outputs. This tutorial describes these utilites and
+              provides examples of common use cases.
+            </p>
+          </div>
+          <div id="basic-ed-run" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#basic-ed-run" class="anchor"></a>Basic ED run
+            </h1>
+            <div id="installing-the-r-package" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#installing-the-r-package" class="anchor"></a
+                >Installing the R package
+              </h2>
+              <p>
+                The <code>PEcAn.ED2</code> package and its PEcAn dependencies
+                can be installed from GitHub as follows (all CRAN package
+                dependencies should be installed automatically):
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"base/logger"</span>)
 devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"base/utils"</span>)
 devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"base/settings"</span>)
 devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"modules/data.atmosphere"</span>)
 devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"models/ed"</span>)
 
-<span class="kw">library</span>(PEcAn.ED2)</code></pre></div>
-</div>
-<div id="installing-the-ed2-model" class="section level2">
-<h2 class="hasAnchor">
-<a href="#installing-the-ed2-model" class="anchor"></a>Installing the ED2 model</h2>
-<p>The source code for the ED2 model is available <a href="https://github.com/edmodel/ed2">on GitHub</a>.</p>
-<p>Alternatively, if you have <a href="https://singularity.lbl.gov">Singularity</a> container software installed, you can use a pre-built Singularity container available on <a href="https://www.singularity-hub.org/collections/642">Singularity Hub</a>:</p>
-<pre><code>singularity pull --name ed2.simg shub://ashiklom/ED2</code></pre>
-</div>
-<div id="ed-inputs" class="section level2">
-<h2 class="hasAnchor">
-<a href="#ed-inputs" class="anchor"></a>ED inputs</h2>
-<div id="edi" class="section level3">
-<h3 class="hasAnchor">
-<a href="#edi" class="anchor"></a>EDI</h3>
-<p>ED requires a global land use database to determine its land-sea mask, as well as a vegetation “thermal sums” database. These can be customized to some extent, but this package provides a version of the most common inputs. These inputs, stored in an “EDI” directory, can be downloaded via the <code>download_edi</code> function:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(here)
+<span class="kw">library</span>(PEcAn.ED2)</code></pre>
+              </div>
+            </div>
+            <div id="installing-the-ed2-model" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#installing-the-ed2-model" class="anchor"></a
+                >Installing the ED2 model
+              </h2>
+              <p>
+                The source code for the ED2 model is available
+                <a href="https://github.com/edmodel/ed2">on GitHub</a>.
+              </p>
+              <p>
+                Alternatively, if you have
+                <a href="https://singularity.lbl.gov">Singularity</a> container
+                software installed, you can use a pre-built Singularity
+                container available on
+                <a href="https://www.singularity-hub.org/collections/642"
+                  >Singularity Hub</a
+                >:
+              </p>
+              <pre><code>singularity pull --name ed2.simg shub://ashiklom/ED2</code></pre>
+            </div>
+            <div id="ed-inputs" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#ed-inputs" class="anchor"></a>ED inputs
+              </h2>
+              <div id="edi" class="section level3">
+                <h3 class="hasAnchor"><a href="#edi" class="anchor"></a>EDI</h3>
+                <p>
+                  ED requires a global land use database to determine its
+                  land-sea mask, as well as a vegetation “thermal sums”
+                  database. These can be customized to some extent, but this
+                  package provides a version of the most common inputs. These
+                  inputs, stored in an “EDI” directory, can be downloaded via
+                  the <code>download_edi</code> function:
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw">library</span>(here)
 rundir &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/here/topics/here">here</a></span>(<span class="st">"vignettes"</span>, <span class="st">"ed_run_data"</span>)
 <span class="kw">dir.create</span>(rundir, <span class="dt">showWarnings =</span> <span class="ot">FALSE</span>)
 
@@ -123,14 +217,30 @@ <h3 class="hasAnchor">
   <span class="kw"><a href="../reference/download_edi.html">download_edi</a></span>(edi_dir)
 } <span class="cf">else</span> {
   <span class="kw">message</span>(<span class="st">"EDI directory already exists. Skipping download."</span>)
-}</code></pre></div>
-</div>
-<div id="meteorological-data" class="section level3">
-<h3 class="hasAnchor">
-<a href="#meteorological-data" class="anchor"></a>Meteorological data</h3>
-<p>To do the ED run described here, we’ll need some meteorological data. ED meteorological data are typically stored in HDF5 format and are described by a plain text header file (typically called <code>ED_MET_DRIVER_HEADER</code>).</p>
-<p>To download the meteorological data, we’ll use the <code>PEcAn.data.atmosphere</code> package. Here, we grab the data for the first week of July 2005 and Harvard Forest, for which we’ll be running the simulation.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">start_date &lt;-<span class="st"> "2006-07-01"</span>
+}</code></pre>
+                </div>
+              </div>
+              <div id="meteorological-data" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#meteorological-data" class="anchor"></a
+                  >Meteorological data
+                </h3>
+                <p>
+                  To do the ED run described here, we’ll need some
+                  meteorological data. ED meteorological data are typically
+                  stored in HDF5 format and are described by a plain text header
+                  file (typically called <code>ED_MET_DRIVER_HEADER</code>).
+                </p>
+                <p>
+                  To download the meteorological data, we’ll use the
+                  <code>PEcAn.data.atmosphere</code> package. Here, we grab the
+                  data for the first week of July 2005 and Harvard Forest, for
+                  which we’ll be running the simulation.
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">start_date &lt;-<span class="st"> "2006-07-01"</span>
 end_date &lt;-<span class="st"> "2006-07-08"</span>
 latitude &lt;-<span class="st"> </span><span class="fl">42.53</span>
 longitude &lt;-<span class="st"> </span><span class="op">-</span><span class="fl">72.19</span>
@@ -142,9 +252,13 @@ <h3 class="hasAnchor">
   <span class="dt">site_id =</span> <span class="ot">NULL</span>,
   <span class="dt">lat.in =</span> latitude,
   <span class="dt">lon.in =</span> longitude
-)</code></pre></div>
-<p>Next, we convert this raw data to the ED-specific format.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">ed_met &lt;-<span class="st"> </span><span class="kw"><a href="../reference/met2model.ED2.html">met2model.ED2</a></span>(
+)</code></pre>
+                </div>
+                <p>Next, we convert this raw data to the ED-specific format.</p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">ed_met &lt;-<span class="st"> </span><span class="kw"><a href="../reference/met2model.ED2.html">met2model.ED2</a></span>(
   <span class="dt">in.path =</span> <span class="kw">dirname</span>(raw_met<span class="op">$</span>file),
   <span class="dt">in.prefix =</span> <span class="st">"CRUNCEP"</span>,
   <span class="dt">outfolder =</span> <span class="kw">file.path</span>(rundir, <span class="st">"ed_met"</span>),
@@ -153,51 +267,108 @@ <h3 class="hasAnchor">
   <span class="dt">lat =</span> latitude,
   <span class="dt">lon =</span> longitude,
   <span class="dt">overwrite =</span> <span class="ot">TRUE</span>
-)</code></pre></div>
-<p>If you already have ED-specific meteorology available, <code>PEcAn.ED2</code> provides utilities to interact with that file directly:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">met_driver_raw &lt;-<span class="st"> "/path/to/ED_MET_DRIVER_HEADER"</span>
+)</code></pre>
+                </div>
+                <p>
+                  If you already have ED-specific meteorology available,
+                  <code>PEcAn.ED2</code> provides utilities to interact with
+                  that file directly:
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">met_driver_raw &lt;-<span class="st"> "/path/to/ED_MET_DRIVER_HEADER"</span>
 met_driver_obj &lt;-<span class="st"> </span><span class="kw"><a href="../reference/read_ed_metheader.html">read_ed_metheader</a></span>(met_driver_raw, <span class="dt">check =</span> <span class="ot">FALSE</span>)
 met_driver_obj[[<span class="dv">1</span>]]<span class="op">$</span>path_prefix &lt;-<span class="st"> "/path/to/new/location"</span>
 met_driver_obj[[<span class="dv">1</span>]]<span class="op">$</span>xmin &lt;-<span class="st"> </span><span class="op">-</span><span class="dv">90</span>
 met_driver_obj[[<span class="dv">1</span>]]<span class="op">$</span>ymin &lt;-<span class="st"> </span><span class="dv">43</span>
 
 met_driver_path &lt;-<span class="st"> </span><span class="kw">file.path</span>(rundir, <span class="st">"ED_MET_DRIVER_HEADER"</span>)
-<span class="kw"><a href="../reference/write_ed_metheader.html">write_ed_metheader</a></span>(met_driver_obj, met_driver_path)</code></pre></div>
-</div>
-<div id="vegetation-inputs" class="section level3">
-<h3 class="hasAnchor">
-<a href="#vegetation-inputs" class="anchor"></a>Vegetation inputs</h3>
-<p>A common way to initialize ED is through three interrelated vegetation initial condition files:</p>
-<ul>
-<li>
-<code>css</code> – Cohort file, which describes all plant cohorts located within a patch, including its PFT, DBH, and stand density</li>
-<li>
-<code>pss</code> – Patch file, which describes each patch within a site (single, plot-scale runs will often have only one patch)</li>
-<li>
-<code>site</code> – Site file, which describes each site (single, plot-scale runs will often have only one site)</li>
-</ul>
-<p>The package ships with simple functional examples of these objects (<code>example_css/pss/site</code>) and functions for quickly creating custom objects based on these examples (<code>create_css/pss/site</code>). Below, we create a <code>css</code> file with a single PFT with a specific DBH, but stick to the unmodified example <code>pss</code> and <code>site</code> files.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">css &lt;-<span class="st"> </span><span class="kw"><a href="../reference/create_css.html">create_css</a></span>(<span class="kw">list</span>(<span class="dt">pft =</span> <span class="dv">11</span>, <span class="dt">dbh =</span> <span class="fl">18.00</span>))
+<span class="kw"><a href="../reference/write_ed_metheader.html">write_ed_metheader</a></span>(met_driver_obj, met_driver_path)</code></pre>
+                </div>
+              </div>
+              <div id="vegetation-inputs" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#vegetation-inputs" class="anchor"></a>Vegetation
+                  inputs
+                </h3>
+                <p>
+                  A common way to initialize ED is through three interrelated
+                  vegetation initial condition files:
+                </p>
+                <ul>
+                  <li>
+                    <code>css</code> – Cohort file, which describes all plant
+                    cohorts located within a patch, including its PFT, DBH, and
+                    stand density
+                  </li>
+                  <li>
+                    <code>pss</code> – Patch file, which describes each patch
+                    within a site (single, plot-scale runs will often have only
+                    one patch)
+                  </li>
+                  <li>
+                    <code>site</code> – Site file, which describes each site
+                    (single, plot-scale runs will often have only one site)
+                  </li>
+                </ul>
+                <p>
+                  The package ships with simple functional examples of these
+                  objects (<code>example_css/pss/site</code>) and functions for
+                  quickly creating custom objects based on these examples
+                  (<code>create_css/pss/site</code>). Below, we create a
+                  <code>css</code> file with a single PFT with a specific DBH,
+                  but stick to the unmodified example <code>pss</code> and
+                  <code>site</code> files.
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">css &lt;-<span class="st"> </span><span class="kw"><a href="../reference/create_css.html">create_css</a></span>(<span class="kw">list</span>(<span class="dt">pft =</span> <span class="dv">11</span>, <span class="dt">dbh =</span> <span class="fl">18.00</span>))
 pss &lt;-<span class="st"> </span>example_pss
 site &lt;-<span class="st"> </span>example_site
 veg_input &lt;-<span class="st"> </span><span class="kw"><a href="../reference/create_ed_veg.html">create_ed_veg</a></span>(css, pss, site, latitude, longitude, <span class="dt">check =</span> <span class="ot">TRUE</span>)
 
 veg_prefix &lt;-<span class="st"> </span><span class="kw">file.path</span>(rundir, <span class="st">"veg_input"</span>, <span class="st">"test_veg"</span>)
-<span class="kw"><a href="../reference/write_ed_veg.html">write_ed_veg</a></span>(veg_input, veg_prefix)</code></pre></div>
-<p>As with meteorology, <code>PEcAn.ED2</code> also provides utilities for working with existing vegetation inputs.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">veg_prefix &lt;-<span class="st"> "/path/to/site/files/prefix"</span>
+<span class="kw"><a href="../reference/write_ed_veg.html">write_ed_veg</a></span>(veg_input, veg_prefix)</code></pre>
+                </div>
+                <p>
+                  As with meteorology, <code>PEcAn.ED2</code> also provides
+                  utilities for working with existing vegetation inputs.
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">veg_prefix &lt;-<span class="st"> "/path/to/site/files/prefix"</span>
 latitude &lt;-<span class="st"> </span><span class="fl">43.3724</span>
 longitude &lt;-<span class="st"> </span><span class="op">-</span><span class="fl">89.9071</span>
-veg_input &lt;-<span class="st"> </span><span class="kw"><a href="../reference/read_ed_veg.html">read_ed_veg</a></span>(veg_prefix, <span class="dt">latitude =</span> latitude, <span class="dt">longitude =</span> longitude)</code></pre></div>
-</div>
-<div id="ed-configuration-file" class="section level3">
-<h3 class="hasAnchor">
-<a href="#ed-configuration-file" class="anchor"></a>ED configuration file</h3>
-<p>Now that all inputs are taken care of, the final step is to create the ED configuration file (typically called <code>ED2IN</code>).</p>
-<p>First, read a <code>ED2IN</code> template file:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">ed2in_raw &lt;-<span class="st"> </span><span class="kw"><a href="../reference/read_ed2in.html">read_ed2in</a></span>(<span class="kw">system.file</span>(<span class="st">"ED2IN.rgit"</span>, <span class="dt">package =</span> <span class="st">"PEcAn.ED2"</span>))</code></pre></div>
-<p>Then, set up the <code>ED2IN</code> with the required components.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">ed2in &lt;-<span class="st"> </span><span class="kw"><a href="../reference/modify_ed2in.html">modify_ed2in</a></span>(
+veg_input &lt;-<span class="st"> </span><span class="kw"><a href="../reference/read_ed_veg.html">read_ed_veg</a></span>(veg_prefix, <span class="dt">latitude =</span> latitude, <span class="dt">longitude =</span> longitude)</code></pre>
+                </div>
+              </div>
+              <div id="ed-configuration-file" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#ed-configuration-file" class="anchor"></a>ED
+                  configuration file
+                </h3>
+                <p>
+                  Now that all inputs are taken care of, the final step is to
+                  create the ED configuration file (typically called
+                  <code>ED2IN</code>).
+                </p>
+                <p>First, read a <code>ED2IN</code> template file:</p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">ed2in_raw &lt;-<span class="st"> </span><span class="kw"><a href="../reference/read_ed2in.html">read_ed2in</a></span>(<span class="kw">system.file</span>(<span class="st">"ED2IN.rgit"</span>, <span class="dt">package =</span> <span class="st">"PEcAn.ED2"</span>))</code></pre>
+                </div>
+                <p>
+                  Then, set up the <code>ED2IN</code> with the required
+                  components.
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">ed2in &lt;-<span class="st"> </span><span class="kw"><a href="../reference/modify_ed2in.html">modify_ed2in</a></span>(
   ed2in_raw,
   <span class="dt">veg_prefix =</span> veg_prefix,
   <span class="dt">latitude =</span> latitude,
@@ -210,56 +381,92 @@ <h3 class="hasAnchor">
   <span class="dt">output_dir =</span> <span class="kw">file.path</span>(rundir, <span class="st">"out"</span>),
   <span class="dt">runtype =</span> <span class="st">"INITIAL"</span>,
   <span class="dt">EXPNME =</span> <span class="st">"ED test run"</span>
-)</code></pre></div>
-<p>It is also a good idea to check the <code>ED2IN</code> file for internal consistency.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/check_ed2in.html">check_ed2in</a></span>(ed2in)</code></pre></div>
-<p>Assuming the <code>ed2in</code> object is valid, you then write it to a file to a desired directory. This doesn’t have to be the run directory (nor does the file have to be named <code>ED2IN</code>), but it’s a good idea to keep the <code>ED2IN</code> file close to the run outputs, as it provides useful metadata for the run.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">ed2in_path &lt;-<span class="st"> </span><span class="kw">file.path</span>(rundir, <span class="st">"ED2IN"</span>)
-<span class="kw"><a href="../reference/write_ed2in.html">write_ed2in</a></span>(ed2in, ed2in_path)</code></pre></div>
-</div>
-<div id="running-ed" class="section level3">
-<h3 class="hasAnchor">
-<a href="#running-ed" class="anchor"></a>Running ED</h3>
-<p>Assuming all of the inputs are correct, running ED is as simple as calling the <code>run_ed_singularity</code> function, which requires paths to the Singularity image and ED2IN file.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">img_path &lt;-<span class="st"> "~/Projects/ED2/ed2.simg"</span>
-<span class="kw"><a href="../reference/run_ed_singularity.html">run_ed_singularity</a></span>(img_path, ed2in_path)</code></pre></div>
-</div>
-</div>
-</div>
-  </div>
+)</code></pre>
+                </div>
+                <p>
+                  It is also a good idea to check the <code>ED2IN</code> file
+                  for internal consistency.
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw"><a href="../reference/check_ed2in.html">check_ed2in</a></span>(ed2in)</code></pre>
+                </div>
+                <p>
+                  Assuming the <code>ed2in</code> object is valid, you then
+                  write it to a file to a desired directory. This doesn’t have
+                  to be the run directory (nor does the file have to be named
+                  <code>ED2IN</code>), but it’s a good idea to keep the
+                  <code>ED2IN</code> file close to the run outputs, as it
+                  provides useful metadata for the run.
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">ed2in_path &lt;-<span class="st"> </span><span class="kw">file.path</span>(rundir, <span class="st">"ED2IN"</span>)
+<span class="kw"><a href="../reference/write_ed2in.html">write_ed2in</a></span>(ed2in, ed2in_path)</code></pre>
+                </div>
+              </div>
+              <div id="running-ed" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#running-ed" class="anchor"></a>Running ED
+                </h3>
+                <p>
+                  Assuming all of the inputs are correct, running ED is as
+                  simple as calling the
+                  <code>run_ed_singularity</code> function, which requires paths
+                  to the Singularity image and ED2IN file.
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">img_path &lt;-<span class="st"> "~/Projects/ED2/ed2.simg"</span>
+<span class="kw"><a href="../reference/run_ed_singularity.html">run_ed_singularity</a></span>(img_path, ed2in_path)</code></pre>
+                </div>
+              </div>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#introduction">Introduction</a></li>
-      <li>
-<a href="#basic-ed-run">Basic ED run</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#installing-the-r-package">Installing the R package</a></li>
-      <li><a href="#installing-the-ed2-model">Installing the ED2 model</a></li>
-      <li><a href="#ed-inputs">ED inputs</a></li>
-      </ul>
-</li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li><a href="#introduction">Introduction</a></li>
+              <li>
+                <a href="#basic-ed-run">Basic ED run</a>
+                <ul class="nav nav-pills nav-stacked">
+                  <li>
+                    <a href="#installing-the-r-package"
+                      >Installing the R package</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#installing-the-ed2-model"
+                      >Installing the ED2 model</a
+                    >
+                  </li>
+                  <li><a href="#ed-inputs">ED inputs</a></li>
+                </ul>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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index daf8990..b2c4f25 100644
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@@ -2,162 +2,184 @@
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+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Alexey Shiklomanov</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Alexey Shiklomanov</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/docsearch.css b/models/ed/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/ed/docs/docsearch.css
+++ b/models/ed/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/ed/docs/docsearch.js b/models/ed/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/ed/docs/docsearch.js
+++ b/models/ed/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/ed/docs/index.html b/models/ed/docs/index.html
index b1a01b4..7b49665 100644
--- a/models/ed/docs/index.html
+++ b/models/ed/docs/index.html
@@ -1,125 +1,189 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of ED2 model • PEcAn.ED2</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of ED2 model">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn package for integration of ED2 model • PEcAn.ED2</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of ED2 model"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation. This package provides functions to
-    link the Ecosystem Demography Model, version 2, to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    link the Ecosystem Demography Model, version 2, to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/running_ed_from_R.html">Running ED from R</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation. This package provides functions to
-    link the Ecosystem Demography Model, version 2, to PEcAn.
-  </div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation. This package
+          provides functions to link the Ecosystem Demography Model, version 2,
+          to PEcAn.
+        </div>
 
-  </div>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/ed/docs/pkgdown.css b/models/ed/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/ed/docs/pkgdown.css
+++ b/models/ed/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
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-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
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@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
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@@ -107,7 +110,6 @@ a.anchor {
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-
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 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/ed/docs/pkgdown.js b/models/ed/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/ed/docs/pkgdown.js
+++ b/models/ed/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/ed/docs/reference/between.html b/models/ed/docs/reference/between.html
index 8e1faa7..ea487ab 100644
--- a/models/ed/docs/reference/between.html
+++ b/models/ed/docs/reference/between.html
@@ -2,163 +2,206 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Check if value is between (inclusive) a range — between • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<!-- sticky kit -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Check if value is between (inclusive) a range — between" />
-
-<meta property="og:description" content="Check if value is between (inclusive) a range" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Check if value is between (inclusive) a range — between • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Check if value is between (inclusive) a range — between"
+    />
+
+    <meta
+      property="og:description"
+      content="Check if value is between (inclusive) a range"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check if value is between (inclusive) a range</h1>
-    
-    <div class="hidden name"><code>between.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check if value is between (inclusive) a range</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>between</span>(<span class='no'>x</span>, <span class='no'>lower</span>, <span class='no'>upper</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>Value to check</p></td>
-    </tr>
-    <tr>
-      <th>lower</th>
-      <td><p>Lower limit</p></td>
-    </tr>
-    <tr>
-      <th>upper</th>
-      <td><p>Upper limit</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check if value is between (inclusive) a range</h1>
+
+            <div class="hidden name"><code>between.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check if value is between (inclusive) a range</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>between</span>(<span class='no'>x</span>, <span class='no'>lower</span>, <span class='no'>upper</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>Value to check</p></td>
+            </tr>
+            <tr>
+              <th>lower</th>
+              <td><p>Lower limit</p></td>
+            </tr>
+            <tr>
+              <th>upper</th>
+              <td><p>Upper limit</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/check_css.html b/models/ed/docs/reference/check_css.html
index 9395570..49ff852 100644
--- a/models/ed/docs/reference/check_css.html
+++ b/models/ed/docs/reference/check_css.html
@@ -2,175 +2,232 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Check individual ED input files — check_css • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
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+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+                  >1.6.0</span
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+
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+                  <a href="../index.html">
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+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
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+              </ul>
+
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check individual ED input files</h1>
-    
-    <div class="hidden name"><code>check_css.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check individual ED input files</h1>
 
-    <div class="ref-description">
-    
-    <p>Check internal file formatting, and optionally check for compatibility
-against related files.</p>
-    
-    </div>
+            <div class="hidden name"><code>check_css.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>check_css</span>(<span class='no'>css</span>, <span class='kw'>pss</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
+          <div class="ref-description">
+            <p>
+              Check internal file formatting, and optionally check for
+              compatibility against related files.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_css</span>(<span class='no'>css</span>, <span class='kw'>pss</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
 
 <span class='fu'>check_pss</span>(<span class='no'>pss</span>, <span class='kw'>site</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
 
 <span class='fu'>check_site</span>(<span class='no'>site</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>css</th>
-      <td><p>css data object (see <a href='read_css.html'>read_css</a>)</p></td>
-    </tr>
-    <tr>
-      <th>pss</th>
-      <td><p>pss data object (see <a href='read_css.html'>read_pss</a>)</p></td>
-    </tr>
-    <tr>
-      <th>site</th>
-      <td><p>site data object (see <a href='read_css.html'>read_site</a>)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>NULL</code> (invisibly)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>css</th>
+              <td>
+                <p>
+                  css data object (see <a href="read_css.html">read_css</a>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pss</th>
+              <td>
+                <p>
+                  pss data object (see <a href="read_css.html">read_pss</a>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>site</th>
+              <td>
+                <p>
+                  site data object (see <a href="read_css.html">read_site</a>)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>NULL</code> (invisibly)</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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diff --git a/models/ed/docs/reference/check_ed2in.html b/models/ed/docs/reference/check_ed2in.html
index 2b8c59d..08f40eb 100644
--- a/models/ed/docs/reference/check_ed2in.html
+++ b/models/ed/docs/reference/check_ed2in.html
@@ -2,159 +2,204 @@
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 <html>
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+
+    <meta
+      property="og:description"
+      content="Check the basic structure of ed2in object, as well as consistency among
 arguments (e.g. run dates and coordinates are within the range of vegetation
-and meteorology data)." />
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+    />
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+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                </li>
+                <li class="dropdown">
+                  <a
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
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+                  >
+                    Articles
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+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check ED2IN</h1>
-    
-    <div class="hidden name"><code>check_ed2in.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check the basic structure of <code>ed2in</code> object, as well as consistency among
-arguments (e.g. run dates and coordinates are within the range of vegetation
-and meteorology data).</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check_ed2in</span>(<span class='no'>ed2in</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ed2in</th>
-      <td><p>Named list of ED2IN tag-value pairs. See <a href='read_ed2in.html'>read_ed2in</a>.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check ED2IN</h1>
+
+            <div class="hidden name"><code>check_ed2in.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Check the basic structure of <code>ed2in</code> object, as well as
+              consistency among arguments (e.g. run dates and coordinates are
+              within the range of vegetation and meteorology data).
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_ed2in</span>(<span class='no'>ed2in</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ed2in</th>
+              <td>
+                <p>
+                  Named list of ED2IN tag-value pairs. See
+                  <a href="read_ed2in.html">read_ed2in</a>.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/check_ed_metfile.html b/models/ed/docs/reference/check_ed_metfile.html
index cce04e9..d4cefc4 100644
--- a/models/ed/docs/reference/check_ed_metfile.html
+++ b/models/ed/docs/reference/check_ed_metfile.html
@@ -2,165 +2,210 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Check individual ED metfile — check_ed_metfile"
+    />
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+    <meta property="og:description" content="Check individual ED metfile" />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+    <![endif]-->
   </head>
 
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-
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-  <a href="../index.html">
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-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
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-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
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-        
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check individual ED metfile</h1>
-    
-    <div class="hidden name"><code>check_ed_metfile.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check individual ED metfile</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check_ed_metfile</span>(<span class='no'>metfile</span>, <span class='no'>variables</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>metfile</th>
-      <td><p>Path to meteorology file</p></td>
-    </tr>
-    <tr>
-      <th>variables</th>
-      <td><p>Variables table from <a href='read_ed_metheader.html'>ed_metheader</a> object</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>NULL</code>, invisibly, if successful or throw an error</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check individual ED metfile</h1>
+
+            <div class="hidden name"><code>check_ed_metfile.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Check individual ED metfile</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_ed_metfile</span>(<span class='no'>metfile</span>, <span class='no'>variables</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>metfile</th>
+              <td><p>Path to meteorology file</p></td>
+            </tr>
+            <tr>
+              <th>variables</th>
+              <td>
+                <p>
+                  Variables table from
+                  <a href="read_ed_metheader.html">ed_metheader</a> object
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>NULL</code>, invisibly, if successful or throw an error</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/check_ed_metheader.html b/models/ed/docs/reference/check_ed_metheader.html
index 83f3cd5..74795ba 100644
--- a/models/ed/docs/reference/check_ed_metheader.html
+++ b/models/ed/docs/reference/check_ed_metheader.html
@@ -2,178 +2,235 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    />
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+      property="og:description"
+      content="Check that the object has all components, and throw an error if anything is
 wrong. Optionally, do some basic checks of actualy meteorology files as
-well." />
-<meta name="twitter:card" content="summary" />
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+    />
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-        
-      </ul>
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+                  >1.6.0</span
+                >
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check ED met header object</h1>
-    
-    <div class="hidden name"><code>check_ed_metheader.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check ED met header object</h1>
 
-    <div class="ref-description">
-    
-    <p>Check that the object has all components, and throw an error if anything is
-wrong. Optionally, do some basic checks of actualy meteorology files as
-well.</p>
-    
-    </div>
+            <div class="hidden name"><code>check_ed_metheader.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Check that the object has all components, and throw an error if
+              anything is wrong. Optionally, do some basic checks of actualy
+              meteorology files as well.
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>check_ed_metheader</span>(<span class='no'>ed_metheader</span>, <span class='kw'>check_files</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+          <pre
+            class="usage"
+          ><span class='fu'>check_ed_metheader</span>(<span class='no'>ed_metheader</span>, <span class='kw'>check_files</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 
 <span class='fu'>check_ed_metheader_format</span>(<span class='no'>ed_metheader_format</span>, <span class='kw'>check_files</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ed_metheader</th>
-      <td><p>ED meteorology header object (see <a href='read_ed_metheader.html'>read_ed_metheader</a>)</p></td>
-    </tr>
-    <tr>
-      <th>check_files</th>
-      <td><p>Logical. If <code>TRUE</code>, perform basic diagnostics on met
-files as well.</p></td>
-    </tr>
-    <tr>
-      <th>ed_metheader_format</th>
-      <td><p>A single format inside the met header object</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><code>check_ed_metheader_format</code> checks an individual format (one item in the
-<code>ed_metheader</code> list). <code>check_ed_metheader</code> applies these checks to each item
-in the format list.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ed_metheader</th>
+              <td>
+                <p>
+                  ED meteorology header object (see
+                  <a href="read_ed_metheader.html">read_ed_metheader</a>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>check_files</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code>, perform basic diagnostics on
+                  met files as well.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ed_metheader_format</th>
+              <td><p>A single format inside the met header object</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            <code>check_ed_metheader_format</code> checks an individual format
+            (one item in the <code>ed_metheader</code> list).
+            <code>check_ed_metheader</code> applies these checks to each item in
+            the format list.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/models/ed/docs/reference/convert.samples.ED.html b/models/ed/docs/reference/convert.samples.ED.html
index c2249dc..211c85f 100644
--- a/models/ed/docs/reference/convert.samples.ED.html
+++ b/models/ed/docs/reference/convert.samples.ED.html
@@ -2,167 +2,222 @@
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+      convert parameters from PEcAn database default units to ED defaults —
+      convert.samples.ED • PEcAn.ED2
+    </title>
+
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+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+such as those provided to write.config"
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
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+                  </a>
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+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>convert parameters from PEcAn database default units to ED defaults</h1>
-    
-    <div class="hidden name"><code>convert.samples.ED.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Performs model specific unit conversions on a a list of trait values,
-such as those provided to write.config</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>convert.samples.ED</span>(<span class='no'>trait.samples</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>a matrix or dataframe of samples from the trait distribution</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>matrix or dataframe with values transformed</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              convert parameters from PEcAn database default units to ED
+              defaults
+            </h1>
+
+            <div class="hidden name"><code>convert.samples.ED.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Performs model specific unit conversions on a a list of trait
+              values, such as those provided to write.config
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>convert.samples.ED</span>(<span class='no'>trait.samples</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.samples</th>
+              <td>
+                <p>
+                  a matrix or dataframe of samples from the trait distribution
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>matrix or dataframe with values transformed</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, David LeBauer, Carl Davidson, Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, David LeBauer, Carl Davidson, Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/models/ed/docs/reference/create_css.html b/models/ed/docs/reference/create_css.html
index a636f71..81f75db 100644
--- a/models/ed/docs/reference/create_css.html
+++ b/models/ed/docs/reference/create_css.html
@@ -2,169 +2,227 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Create css, pss, and site files from examples — create_css • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Create css, pss, and site files from examples — create_css"
+    />
+
+    <meta
+      property="og:description"
+      content="Create css, pss, and site files from examples"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
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+                <li class="dropdown">
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+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
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+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create css, pss, and site files from examples</h1>
-    
-    <div class="hidden name"><code>create_css.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create css, pss, and site files from examples</h1>
 
-    <div class="ref-description">
-    
-    <p>Create css, pss, and site files from examples</p>
-    
-    </div>
+            <div class="hidden name"><code>create_css.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>create_css</span>(<span class='no'>input</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+          <div class="ref-description">
+            <p>Create css, pss, and site files from examples</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>create_css</span>(<span class='no'>input</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 
 <span class='fu'>create_pss</span>(<span class='no'>input</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 
 <span class='fu'>create_site</span>(<span class='no'>input</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>input</th>
-      <td><p>Named <code>list</code> or <code>data.frame</code> containing columns to replace in examples</p></td>
-    </tr>
-    <tr>
-      <th>check</th>
-      <td><p>Logical. If <code>TRUE</code> (default), also check files for validity.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>css, pss, or site object (<code>data.frame</code>, possibly with attributes)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>input</th>
+              <td>
+                <p>
+                  Named <code>list</code> or <code>data.frame</code> containing
+                  columns to replace in examples
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>check</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code> (default), also check files for
+                  validity.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            css, pss, or site object (<code>data.frame</code>, possibly with
+            attributes)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
-
diff --git a/models/ed/docs/reference/create_ed_veg.html b/models/ed/docs/reference/create_ed_veg.html
index 4829f74..fe7536d 100644
--- a/models/ed/docs/reference/create_ed_veg.html
+++ b/models/ed/docs/reference/create_ed_veg.html
@@ -2,179 +2,242 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Create full ED vegetation input object — create_ed_veg" />
-
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-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Create full ED vegetation input object — create_ed_veg • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Create full ED vegetation input object — create_ed_veg"
+    />
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+      property="og:description"
+      content="Create full ED vegetation input object"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create full ED vegetation input object</h1>
-    
-    <div class="hidden name"><code>create_ed_veg.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Create full ED vegetation input object</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>create_ed_veg</span>(<span class='no'>css</span>, <span class='no'>pss</span>, <span class='no'>site</span>, <span class='no'>latitude</span>, <span class='no'>longitude</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>css</th>
-      <td><p><a href='read_css.html'>css</a> object (<code>data.frame</code>)</p></td>
-    </tr>
-    <tr>
-      <th>pss</th>
-      <td><p><a href='read_css.html'>pss</a> object (<code>data.frame</code>)</p></td>
-    </tr>
-    <tr>
-      <th>site</th>
-      <td><p><a href='read_css.html'>site</a> object (<code>data.frame</code>)</p></td>
-    </tr>
-    <tr>
-      <th>latitude</th>
-      <td><p>Latitude coordinate</p></td>
-    </tr>
-    <tr>
-      <th>longitude</th>
-      <td><p>Longitude coordinate</p></td>
-    </tr>
-    <tr>
-      <th>check</th>
-      <td><p>Logical. If <code>TRUE</code> (default), also check files for validity.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional objects to store in list</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create full ED vegetation input object</h1>
+
+            <div class="hidden name"><code>create_ed_veg.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Create full ED vegetation input object</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>create_ed_veg</span>(<span class='no'>css</span>, <span class='no'>pss</span>, <span class='no'>site</span>, <span class='no'>latitude</span>, <span class='no'>longitude</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>css</th>
+              <td>
+                <p>
+                  <a href="read_css.html">css</a> object
+                  (<code>data.frame</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pss</th>
+              <td>
+                <p>
+                  <a href="read_css.html">pss</a> object
+                  (<code>data.frame</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>site</th>
+              <td>
+                <p>
+                  <a href="read_css.html">site</a> object
+                  (<code>data.frame</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>latitude</th>
+              <td><p>Latitude coordinate</p></td>
+            </tr>
+            <tr>
+              <th>longitude</th>
+              <td><p>Longitude coordinate</p></td>
+            </tr>
+            <tr>
+              <th>check</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code> (default), also check files for
+                  validity.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>Additional objects to store in list</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/models/ed/docs/reference/dates_in_month.html b/models/ed/docs/reference/dates_in_month.html
index 8c99456..c2087fa 100644
--- a/models/ed/docs/reference/dates_in_month.html
+++ b/models/ed/docs/reference/dates_in_month.html
@@ -2,163 +2,208 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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-
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-
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Get all the dates in a month — dates_in_month • PEcAn.ED2</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      content="Get all the dates in a month — dates_in_month"
+    />
+
+    <meta
+      property="og:description"
+      content="For a given date, figure out its month and return all of the dates for that
+month."
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+    <![endif]-->
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get all the dates in a month</h1>
-    
-    <div class="hidden name"><code>dates_in_month.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>For a given date, figure out its month and return all of the dates for that
-month.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>dates_in_month</span>(<span class='no'>date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>date</th>
-      <td><p>Date as string or date object</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Sequence of dates from the first to the last day of the month.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get all the dates in a month</h1>
+
+            <div class="hidden name"><code>dates_in_month.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              For a given date, figure out its month and return all of the dates
+              for that month.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dates_in_month</span>(<span class='no'>date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>date</th>
+              <td><p>Date as string or date object</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Sequence of dates from the first to the last day of the month.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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+          <p>Developed by .</p>
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diff --git a/models/ed/docs/reference/download_edi.html b/models/ed/docs/reference/download_edi.html
index 4ce5c2d..ab02339 100644
--- a/models/ed/docs/reference/download_edi.html
+++ b/models/ed/docs/reference/download_edi.html
@@ -2,172 +2,221 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+    <meta property="og:title" content="Download ED inputs — download_edi" />
+
+    <meta
+      property="og:description"
+      content="Download and unzip common ED inputs from a public Open Science Framework
 (OSF) repository (https://osf.io/b6umf). Inputs include the Olson Global
-Ecosystems (OGE) database (oge2OLD) and the chd and dgd databases." />
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-<![endif]-->
+Ecosystems (OGE) database (oge2OLD) and the chd and dgd databases."
+    />
+    <meta name="twitter:card" content="summary" />
 
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
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+                        >Running ED from R</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download ED inputs</h1>
-    
-    <div class="hidden name"><code>download_edi.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Download and unzip common ED inputs from a public Open Science Framework
-(OSF) repository (https://osf.io/b6umf). Inputs include the Olson Global
-Ecosystems (OGE) database (<code>oge2OLD</code>) and the <code>chd</code> and <code>dgd</code> databases.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>download_edi</span>(<span class='no'>directory</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>directory</th>
-      <td><p>Target directory for unzipping files. Will be created if it
-doesn't exist.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>TRUE</code>, invisibly</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>The total download size around 28 MB.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download ED inputs</h1>
+
+            <div class="hidden name"><code>download_edi.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Download and unzip common ED inputs from a public Open Science
+              Framework (OSF) repository (https://osf.io/b6umf). Inputs include
+              the Olson Global Ecosystems (OGE) database (<code>oge2OLD</code>)
+              and the <code>chd</code> and <code>dgd</code> databases.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>download_edi</span>(<span class='no'>directory</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>directory</th>
+              <td>
+                <p>
+                  Target directory for unzipping files. Will be created if it
+                  doesn't exist.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>TRUE</code>, invisibly</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>The total download size around 28 MB.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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diff --git a/models/ed/docs/reference/ed.var.html b/models/ed/docs/reference/ed.var.html
index 54b85ef..234bd58 100644
--- a/models/ed/docs/reference/ed.var.html
+++ b/models/ed/docs/reference/ed.var.html
@@ -2,150 +2,194 @@
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+      list, readvar variables to read from file, expr if any derivation is
+      needed — ed.var • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    />
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+returns out list, readvar variables to read from file, expr if any derivation is needed — ed.var"
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+returns out list, readvar variables to read from file, expr if any derivation is needed"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Lookup function for translating commonly used ED variables
-returns out list, readvar variables to read from file, expr if any derivation is needed</h1>
-    
-    <div class="hidden name"><code>ed.var.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Lookup function for translating commonly used ED variables
-returns out list, readvar variables to read from file, expr if any derivation is needed</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>ed.var</span>(<span class='no'>varname</span>)</pre>
-        
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Lookup function for translating commonly used ED variables returns
+              out list, readvar variables to read from file, expr if any
+              derivation is needed
+            </h1>
+
+            <div class="hidden name"><code>ed.var.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Lookup function for translating commonly used ED variables returns
+              out list, readvar variables to read from file, expr if any
+              derivation is needed
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>ed.var</span>(<span class='no'>varname</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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diff --git a/models/ed/docs/reference/ed2in2time.html b/models/ed/docs/reference/ed2in2time.html
index 2dfe1ca..11233b5 100644
--- a/models/ed/docs/reference/ed2in2time.html
+++ b/models/ed/docs/reference/ed2in2time.html
@@ -2,161 +2,209 @@
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+      Convert ED2IN <code>ITIMEA/Z</code> string to hour and minute — ed2in2time
+      • PEcAn.ED2
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert ED2IN <code>ITIMEA/Z</code> string to hour and minute</h1>
-    
-    <div class="hidden name"><code>ed2in2time.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert ED2IN <code>ITIMEA/Z</code> string to hour and minute</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>ed2in2time</span>(<span class='no'>itimea</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>itimea</th>
-      <td><p>ED2IN time string, e.g. "1200"</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>List containing numeric values of hour and minute</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Convert ED2IN <code>ITIMEA/Z</code> string to hour and minute
+            </h1>
+
+            <div class="hidden name"><code>ed2in2time.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert ED2IN <code>ITIMEA/Z</code> string to hour and minute</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>ed2in2time</span>(<span class='no'>itimea</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>itimea</th>
+              <td><p>ED2IN time string, e.g. "1200"</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>List containing numeric values of hour and minute</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
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-
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+        </div>
+      </div>
 
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index a63fce4..4fe443a 100644
--- a/models/ed/docs/reference/example_css.html
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@@ -2,155 +2,194 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Example css, pss, and site objects</h1>
-    
-    <div class="hidden name"><code>example_css.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Example css, pss, and site objects</h1>
 
-    <div class="ref-description">
-    
-    <p>Example css, pss, and site objects</p>
-    
-    </div>
+            <div class="hidden name"><code>example_css.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='no'>example_css</span>
+          <div class="ref-description">
+            <p>Example css, pss, and site objects</p>
+          </div>
+
+          <pre class="usage"><span class='no'>example_css</span>
 
 <span class='no'>example_pss</span>
 
 <span class='no'>example_site</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 1 rows and 10 columns.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
+
+          <p>
+            An object of class <code>tbl_df</code> (inherits from
+            <code>tbl</code>, <code>data.frame</code>) with 1 rows and 10
+            columns.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/get.model.output.ED2.html b/models/ed/docs/reference/get.model.output.ED2.html
index ff0ade1..cf8cd14 100644
--- a/models/ed/docs/reference/get.model.output.ED2.html
+++ b/models/ed/docs/reference/get.model.output.ED2.html
@@ -2,151 +2,190 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<script src="../pkgdown.js"></script>
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-<meta name="twitter:card" content="summary" />
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-<!-- mathjax -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Retrieve ED2 HDF model output from local or remote server —
+      get.model.output.ED2 • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Retrieve ED2 HDF model output from local or remote server — get.model.output.ED2"
+    />
+
+    <meta
+      property="og:description"
+      content="Function to retrieve ED2 HDF model output from local or remote server"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="../reference/index.html">Reference</a>
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-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
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-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Retrieve ED2 HDF model output from local or remote server</h1>
-    
-    <div class="hidden name"><code>get.model.output.ED2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to retrieve ED2 HDF model output from local or remote server</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Retrieve ED2 HDF model output from local or remote server</h1>
 
-    <pre class="usage"><span class='fu'>get.model.output.ED2</span>(<span class='no'>settings</span>)</pre>
-        
+            <div class="hidden name"><code>get.model.output.ED2.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>
+              Function to retrieve ED2 HDF model output from local or remote
+              server
+            </p>
+          </div>
 
-    <h2>Author</h2>
-    
-Shawn Serbin
+          <pre
+            class="usage"
+          ><span class='fu'>get.model.output.ED2</span>(<span class='no'>settings</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
-
diff --git a/models/ed/docs/reference/get_configxml.ED2.html b/models/ed/docs/reference/get_configxml.ED2.html
index cb22bd8..75ad6c1 100644
--- a/models/ed/docs/reference/get_configxml.ED2.html
+++ b/models/ed/docs/reference/get_configxml.ED2.html
@@ -2,163 +2,206 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Get ED2 config.xml file — get_configxml.ED2 • PEcAn.ED2</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+        <!--/.navbar -->
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get ED2 config.xml file</h1>
-    
-    <div class="hidden name"><code>get_configxml.ED2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get ED2 config.xml file</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_configxml.ED2</span>(<span class='no'>rundir</span>, <span class='no'>runid</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>rundir</th>
-      <td><p>Model run directory. Usually <code>&lt;workflowID&gt;/run</code></p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>PEcAn run ID</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get ED2 config.xml file</h1>
+
+            <div class="hidden name"><code>get_configxml.ED2.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get ED2 config.xml file</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_configxml.ED2</span>(<span class='no'>rundir</span>, <span class='no'>runid</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>rundir</th>
+              <td>
+                <p>
+                  Model run directory. Usually
+                  <code>&lt;workflowID&gt;/run</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>PEcAn run ID</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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diff --git a/models/ed/docs/reference/get_ed2in_dates.html b/models/ed/docs/reference/get_ed2in_dates.html
index d76c471..9ff449c 100644
--- a/models/ed/docs/reference/get_ed2in_dates.html
+++ b/models/ed/docs/reference/get_ed2in_dates.html
@@ -2,161 +2,211 @@
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+
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+                        >Running ED from R</a
+                      >
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+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Extract sequence of dates from ED2IN file</h1>
-    
-    <div class="hidden name"><code>get_ed2in_dates.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Extract sequence of dates from ED2IN file</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_ed2in_dates</span>(<span class='no'>ed2in</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ed2in</th>
-      <td><p>Named list of ED2IN tag-value pairs. See <a href='read_ed2in.html'>read_ed2in</a>.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Vector of dates from start date to end date by 1 day</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Extract sequence of dates from ED2IN file</h1>
+
+            <div class="hidden name"><code>get_ed2in_dates.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Extract sequence of dates from ED2IN file</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_ed2in_dates</span>(<span class='no'>ed2in</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ed2in</th>
+              <td>
+                <p>
+                  Named list of ED2IN tag-value pairs. See
+                  <a href="read_ed2in.html">read_ed2in</a>.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Vector of dates from start date to end date by 1 day</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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diff --git a/models/ed/docs/reference/get_latlon.html b/models/ed/docs/reference/get_latlon.html
index f3bd35f..9233d4b 100644
--- a/models/ed/docs/reference/get_latlon.html
+++ b/models/ed/docs/reference/get_latlon.html
@@ -2,170 +2,219 @@
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+    />
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+      property="og:description"
+      content="Automatically determine latitude or longitude from an ED input filepath. If
 the latitude/longitude regular expression isn't matched, this will throw an
-error." />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Parse latitude or longitude</h1>
-    
-    <div class="hidden name"><code>get_latlon.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Automatically determine latitude or longitude from an ED input filepath. If
-the latitude/longitude regular expression isn't matched, this will throw an
-error.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_latlon</span>(<span class='no'>filepath</span>, <span class='no'>latlon</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>filepath</th>
-      <td><p>Path to a css, pss, or site file</p></td>
-    </tr>
-    <tr>
-      <th>latlon</th>
-      <td><p>Which value to retrieve, either "lat" for latitude or "lon"
-for longitude</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Numeric value of latitude or longitude</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Parse latitude or longitude</h1>
+
+            <div class="hidden name"><code>get_latlon.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Automatically determine latitude or longitude from an ED input
+              filepath. If the latitude/longitude regular expression isn't
+              matched, this will throw an error.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_latlon</span>(<span class='no'>filepath</span>, <span class='no'>latlon</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>filepath</th>
+              <td><p>Path to a css, pss, or site file</p></td>
+            </tr>
+            <tr>
+              <th>latlon</th>
+              <td>
+                <p>
+                  Which value to retrieve, either "lat" for latitude or "lon"
+                  for longitude
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Numeric value of latitude or longitude</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
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diff --git a/models/ed/docs/reference/get_met_dates.html b/models/ed/docs/reference/get_met_dates.html
index ffa877e..a95d176 100644
--- a/models/ed/docs/reference/get_met_dates.html
+++ b/models/ed/docs/reference/get_met_dates.html
@@ -2,163 +2,210 @@
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    <script src="../pkgdown.js"></script>
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+the matching file names."
+    />
+    <meta name="twitter:card" content="summary" />
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+                  >1.6.0</span
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get meteorology dates</h1>
-    
-    <div class="hidden name"><code>get_met_dates.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Figure out the dates for which a given meteorology is available by parsing
-the matching file names.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_met_dates</span>(<span class='no'>ed_metheader</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ed_metheader</th>
-      <td><p>ED meteorlogy header object (see <a href='read_ed_metheader.html'>read_ed_metheader</a>)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Vector of dates for a run</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get meteorology dates</h1>
+
+            <div class="hidden name"><code>get_met_dates.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Figure out the dates for which a given meteorology is available by
+              parsing the matching file names.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_met_dates</span>(<span class='no'>ed_metheader</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ed_metheader</th>
+              <td>
+                <p>
+                  ED meteorlogy header object (see
+                  <a href="read_ed_metheader.html">read_ed_metheader</a>)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Vector of dates for a run</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/models/ed/docs/reference/get_restartfile.ED2.html b/models/ed/docs/reference/get_restartfile.ED2.html
index c70aac0..eb8d599 100644
--- a/models/ed/docs/reference/get_restartfile.ED2.html
+++ b/models/ed/docs/reference/get_restartfile.ED2.html
@@ -2,168 +2,215 @@
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+
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+    <script
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+      crossorigin="anonymous"
+    ></script>
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+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+                <span
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get ED history restart file path</h1>
-    
-    <div class="hidden name"><code>get_restartfile.ED2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get ED history restart file path</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_restartfile.ED2</span>(<span class='no'>mod_outdir</span>, <span class='no'>runid</span>, <span class='no'>file.time</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mod_outdir</th>
-      <td><p>Directory where PEcAn stores ensemble outputs. Usually
-<code>&lt;workflowID&gt;/out</code></p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>PEcAn run ID</p></td>
-    </tr>
-    <tr>
-      <th>file.time</th>
-      <td><p>Start or end time from SDA analysis</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get ED history restart file path</h1>
+
+            <div class="hidden name"><code>get_restartfile.ED2.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get ED history restart file path</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_restartfile.ED2</span>(<span class='no'>mod_outdir</span>, <span class='no'>runid</span>, <span class='no'>file.time</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mod_outdir</th>
+              <td>
+                <p>
+                  Directory where PEcAn stores ensemble outputs. Usually
+                  <code>&lt;workflowID&gt;/out</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>PEcAn run ID</p></td>
+            </tr>
+            <tr>
+              <th>file.time</th>
+              <td><p>Start or end time from SDA analysis</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
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diff --git a/models/ed/docs/reference/index.html b/models/ed/docs/reference/index.html
index 5202361..fbe52a6 100644
--- a/models/ed/docs/reference/index.html
+++ b/models/ed/docs/reference/index.html
@@ -2,495 +2,812 @@
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-<title>Function reference • PEcAn.ED2</title>
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+    ></script>
+    <!-- Bootstrap -->
 
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
 
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+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-      
-      </header>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
 
-    <table class="ref-index">
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="between.html">between()</a></code> </p>
-        </td>
-        <td><p>Check if value is between (inclusive) a range</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_css.html">check_css()</a></code> <code><a href="check_css.html">check_pss()</a></code> <code><a href="check_css.html">check_site()</a></code> </p>
-        </td>
-        <td><p>Check individual ED input files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_ed2in.html">check_ed2in()</a></code> </p>
-        </td>
-        <td><p>Check ED2IN</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_ed_metfile.html">check_ed_metfile()</a></code> </p>
-        </td>
-        <td><p>Check individual ED metfile</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_ed_metheader.html">check_ed_metheader()</a></code> <code><a href="check_ed_metheader.html">check_ed_metheader_format()</a></code> </p>
-        </td>
-        <td><p>Check ED met header object</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="convert.samples.ED.html">convert.samples.ED()</a></code> </p>
-        </td>
-        <td><p>convert parameters from PEcAn database default units to ED defaults</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="create_css.html">create_css()</a></code> <code><a href="create_css.html">create_pss()</a></code> <code><a href="create_css.html">create_site()</a></code> </p>
-        </td>
-        <td><p>Create css, pss, and site files from examples</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="create_ed_veg.html">create_ed_veg()</a></code> </p>
-        </td>
-        <td><p>Create full ED vegetation input object</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dates_in_month.html">dates_in_month()</a></code> </p>
-        </td>
-        <td><p>Get all the dates in a month</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download_edi.html">download_edi()</a></code> </p>
-        </td>
-        <td><p>Download ED inputs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ed.var.html">ed.var()</a></code> </p>
-        </td>
-        <td><p>Lookup function for translating commonly used ED variables
-returns out list, readvar variables to read from file, expr if any derivation is needed</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ed2in2time.html">ed2in2time()</a></code> </p>
-        </td>
-        <td><p>Convert ED2IN <code>ITIMEA/Z</code> string to hour and minute</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="example_css.html">example_css</a></code> <code><a href="example_css.html">example_pss</a></code> <code><a href="example_css.html">example_site</a></code> </p>
-        </td>
-        <td><p>Example css, pss, and site objects</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.model.output.ED2.html">get.model.output.ED2()</a></code> </p>
-        </td>
-        <td><p>Retrieve ED2 HDF model output from local or remote server</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_configxml.ED2.html">get_configxml.ED2()</a></code> </p>
-        </td>
-        <td><p>Get ED2 config.xml file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_ed2in_dates.html">get_ed2in_dates()</a></code> </p>
-        </td>
-        <td><p>Extract sequence of dates from ED2IN file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_latlon.html">get_latlon()</a></code> </p>
-        </td>
-        <td><p>Parse latitude or longitude</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_met_dates.html">get_met_dates()</a></code> </p>
-        </td>
-        <td><p>Get meteorology dates</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_restartfile.ED2.html">get_restartfile.ED2()</a></code> </p>
-        </td>
-        <td><p>Get ED history restart file path</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="is.ed2in.html">is.ed2in()</a></code> </p>
-        </td>
-        <td><p>Check if object is <code>ed2in</code></p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="list.files.nodir.html">list.files.nodir()</a></code> </p>
-        </td>
-        <td><p>List only files in a directory</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2model.ED2.html">met2model.ED2()</a></code> </p>
-        </td>
-        <td><p>met2model wrapper for ED2</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met_flag_description.html">met_flag_description</a></code> </p>
-        </td>
-        <td><p>Description of meteorology flags</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met_variable_description.html">met_variable_description</a></code> </p>
-        </td>
-        <td><p>Description of meteorology variables</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.ED2.html">model2netcdf.ED2()</a></code> </p>
-        </td>
-        <td><p>Code to convert ED2's -T- HDF5 output into netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="modify_df.html">modify_df()</a></code> </p>
-        </td>
-        <td><p>Modify a reference <code>data.frame</code></p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="modify_ed2in.html">modify_ed2in()</a></code> </p>
-        </td>
-        <td><p>Modify an ED2IN object</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="parse.history.html">parse.history()</a></code> </p>
-        </td>
-        <td><p>Create a CSV from history.xml outputed by ED</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="patch_cohort_index.html">patch_cohort_index()</a></code> </p>
-        </td>
-        <td><p>Generate ED2 cohort to patch mapping vector</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="prepare_ed_veg_filename.html">prepare_ed_veg_filename()</a></code> </p>
-        </td>
-        <td><p>Format file name for ED vegetation inputs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="print.ed2in.html">print(<i>&lt;ed2in&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Print method for <code>ed2in</code></p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="put_E_values.html">put_E_values()</a></code> </p>
-        </td>
-        <td><p>Function for put -E- values to nc_var list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="put_T_values.html">put_T_values()</a></code> </p>
-        </td>
-        <td><p>Function for put -T- values to nc_var list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.output.ED2.html">read.output.ED2()</a></code> </p>
-        </td>
-        <td><p>Read ED output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.output.file.ed.html">read.output.file.ed()</a></code> </p>
-        </td>
-        <td><p>read output - ED</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_E_files.html">read_E_files()</a></code> </p>
-        </td>
-        <td><p>Function for reading -E- files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_S_files.html">read_S_files()</a></code> </p>
-        </td>
-        <td><p>S-file contents are not written to standard netcdfs but are used by read_restart
-from SDA's perspective it doesn't make sense to write and read to ncdfs because ED restarts from history files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_T_files.html">read_T_files()</a></code> </p>
-        </td>
-        <td><p>Function for reading -T- files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_css.html">read_css()</a></code> <code><a href="read_css.html">read_pss()</a></code> <code><a href="read_css.html">read_site()</a></code> </p>
-        </td>
-        <td><p>Read individual css, pss, and site files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_ed2in.html">read_ed2in()</a></code> </p>
-        </td>
-        <td><p>Read ED2IN file to named list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_ed_metheader.html">read_ed_metheader()</a></code> </p>
-        </td>
-        <td><p>Read ED meteorology header file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_ed_veg.html">read_ed_veg()</a></code> </p>
-        </td>
-        <td><p>Read ED2 vegetation inputs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_restart.ED2.html">read_restart.ED2()</a></code> </p>
-        </td>
-        <td><p>State data assimilation read-restart for ED2</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="remove.config.ED2.html">remove.config.ED2()</a></code> </p>
-        </td>
-        <td><p>Clear out old config and ED model run files.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="run_ed_singularity.html">run_ed_singularity()</a></code> </p>
-        </td>
-        <td><p>Run ED singularity container</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="tags2char.html">tags2char()</a></code> </p>
-        </td>
-        <td><p>Format ED2IN tag-value list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="translate_vars_ed.html">translate_vars_ed()</a></code> </p>
-        </td>
-        <td><p>Function translating pecan vars to ED vars
-var.names &lt;- c("DBH", "AGB", "AbvGrndWood")</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="veg2model.ED2.html">veg2model.ED2()</a></code> </p>
-        </td>
-        <td><p>Writes ED specific IC files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.ED2.html">write.config.ED2()</a></code> </p>
-        </td>
-        <td><p>Write ED configuration files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.jobsh.ED2.html">write.config.jobsh.ED2()</a></code> </p>
-        </td>
-        <td><p>Write ED2 config.xml file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.xml.ED2.html">write.config.xml.ED2()</a></code> </p>
-        </td>
-        <td><p>Write ED2 config.xml file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_css.html">write_css()</a></code> <code><a href="write_css.html">write_pss()</a></code> <code><a href="write_css.html">write_site()</a></code> </p>
-        </td>
-        <td><p>Write individual ED inputs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_ed2in.html">write_ed2in()</a></code> </p>
-        </td>
-        <td><p>Write ED2IN list to file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_ed_metheader.html">write_ed_metheader()</a></code> </p>
-        </td>
-        <td><p>Write ED meteorlogy header</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_ed_veg.html">write_ed_veg()</a></code> </p>
-        </td>
-        <td><p>Write ED inputs to directory</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_restart.ED2.html">write_restart.ED2()</a></code> </p>
-        </td>
-        <td><p>Write ED2 restart file from SDA results</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="zz.imports.html">zz.imports</a></code> </p>
-        </td>
-        <td><p>Imports from other packages</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="between.html">between()</a></code>
+                  </p>
+                </td>
+                <td><p>Check if value is between (inclusive) a range</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="check_css.html">check_css()</a></code>
+                    <code><a href="check_css.html">check_pss()</a></code>
+                    <code><a href="check_css.html">check_site()</a></code>
+                  </p>
+                </td>
+                <td><p>Check individual ED input files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="check_ed2in.html">check_ed2in()</a></code>
+                  </p>
+                </td>
+                <td><p>Check ED2IN</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check_ed_metfile.html"
+                        >check_ed_metfile()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check individual ED metfile</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check_ed_metheader.html"
+                        >check_ed_metheader()</a
+                      ></code
+                    >
+                    <code
+                      ><a href="check_ed_metheader.html"
+                        >check_ed_metheader_format()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check ED met header object</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="convert.samples.ED.html"
+                        >convert.samples.ED()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    convert parameters from PEcAn database default units to ED
+                    defaults
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="create_css.html">create_css()</a></code>
+                    <code><a href="create_css.html">create_pss()</a></code>
+                    <code><a href="create_css.html">create_site()</a></code>
+                  </p>
+                </td>
+                <td><p>Create css, pss, and site files from examples</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="create_ed_veg.html">create_ed_veg()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create full ED vegetation input object</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="dates_in_month.html">dates_in_month()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get all the dates in a month</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="download_edi.html">download_edi()</a></code>
+                  </p>
+                </td>
+                <td><p>Download ED inputs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ed.var.html">ed.var()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Lookup function for translating commonly used ED variables
+                    returns out list, readvar variables to read from file, expr
+                    if any derivation is needed
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ed2in2time.html">ed2in2time()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Convert ED2IN <code>ITIMEA/Z</code> string to hour and
+                    minute
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="example_css.html">example_css</a></code>
+                    <code><a href="example_css.html">example_pss</a></code>
+                    <code><a href="example_css.html">example_site</a></code>
+                  </p>
+                </td>
+                <td><p>Example css, pss, and site objects</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.model.output.ED2.html"
+                        >get.model.output.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Retrieve ED2 HDF model output from local or remote server
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_configxml.ED2.html"
+                        >get_configxml.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get ED2 config.xml file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_ed2in_dates.html"
+                        >get_ed2in_dates()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Extract sequence of dates from ED2IN file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get_latlon.html">get_latlon()</a></code>
+                  </p>
+                </td>
+                <td><p>Parse latitude or longitude</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_met_dates.html">get_met_dates()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get meteorology dates</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_restartfile.ED2.html"
+                        >get_restartfile.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get ED history restart file path</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="is.ed2in.html">is.ed2in()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Check if object is <code>ed2in</code></p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="list.files.nodir.html"
+                        >list.files.nodir()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>List only files in a directory</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.ED2.html">met2model.ED2()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2model wrapper for ED2</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met_flag_description.html"
+                        >met_flag_description</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Description of meteorology flags</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met_variable_description.html"
+                        >met_variable_description</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Description of meteorology variables</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.ED2.html"
+                        >model2netcdf.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Code to convert ED2's -T- HDF5 output into netCDF format
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="modify_df.html">modify_df()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Modify a reference <code>data.frame</code></p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="modify_ed2in.html">modify_ed2in()</a></code>
+                  </p>
+                </td>
+                <td><p>Modify an ED2IN object</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="parse.history.html">parse.history()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create a CSV from history.xml outputed by ED</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="patch_cohort_index.html"
+                        >patch_cohort_index()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Generate ED2 cohort to patch mapping vector</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="prepare_ed_veg_filename.html"
+                        >prepare_ed_veg_filename()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Format file name for ED vegetation inputs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="print.ed2in.html"
+                        >print(<i>&lt;ed2in&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Print method for <code>ed2in</code></p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="put_E_values.html">put_E_values()</a></code>
+                  </p>
+                </td>
+                <td><p>Function for put -E- values to nc_var list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="put_T_values.html">put_T_values()</a></code>
+                  </p>
+                </td>
+                <td><p>Function for put -T- values to nc_var list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.output.ED2.html"
+                        >read.output.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read ED output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.output.file.ed.html"
+                        >read.output.file.ed()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>read output - ED</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="read_E_files.html">read_E_files()</a></code>
+                  </p>
+                </td>
+                <td><p>Function for reading -E- files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="read_S_files.html">read_S_files()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    S-file contents are not written to standard netcdfs but are
+                    used by read_restart from SDA's perspective it doesn't make
+                    sense to write and read to ncdfs because ED restarts from
+                    history files
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="read_T_files.html">read_T_files()</a></code>
+                  </p>
+                </td>
+                <td><p>Function for reading -T- files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="read_css.html">read_css()</a></code>
+                    <code><a href="read_css.html">read_pss()</a></code>
+                    <code><a href="read_css.html">read_site()</a></code>
+                  </p>
+                </td>
+                <td><p>Read individual css, pss, and site files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="read_ed2in.html">read_ed2in()</a></code>
+                  </p>
+                </td>
+                <td><p>Read ED2IN file to named list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read_ed_metheader.html"
+                        >read_ed_metheader()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read ED meteorology header file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="read_ed_veg.html">read_ed_veg()</a></code>
+                  </p>
+                </td>
+                <td><p>Read ED2 vegetation inputs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read_restart.ED2.html"
+                        >read_restart.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>State data assimilation read-restart for ED2</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="remove.config.ED2.html"
+                        >remove.config.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Clear out old config and ED model run files.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="run_ed_singularity.html"
+                        >run_ed_singularity()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Run ED singularity container</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="tags2char.html">tags2char()</a></code>
+                  </p>
+                </td>
+                <td><p>Format ED2IN tag-value list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="translate_vars_ed.html"
+                        >translate_vars_ed()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function translating pecan vars to ED vars var.names &lt;-
+                    c("DBH", "AGB", "AbvGrndWood")
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="veg2model.ED2.html">veg2model.ED2()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Writes ED specific IC files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.ED2.html"
+                        >write.config.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write ED configuration files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.jobsh.ED2.html"
+                        >write.config.jobsh.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write ED2 config.xml file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.xml.ED2.html"
+                        >write.config.xml.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write ED2 config.xml file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="write_css.html">write_css()</a></code>
+                    <code><a href="write_css.html">write_pss()</a></code>
+                    <code><a href="write_css.html">write_site()</a></code>
+                  </p>
+                </td>
+                <td><p>Write individual ED inputs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="write_ed2in.html">write_ed2in()</a></code>
+                  </p>
+                </td>
+                <td><p>Write ED2IN list to file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write_ed_metheader.html"
+                        >write_ed_metheader()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write ED meteorlogy header</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="write_ed_veg.html">write_ed_veg()</a></code>
+                  </p>
+                </td>
+                <td><p>Write ED inputs to directory</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write_restart.ED2.html"
+                        >write_restart.ED2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write ED2 restart file from SDA results</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="zz.imports.html">zz.imports</a></code>
+                  </p>
+                </td>
+                <td><p>Imports from other packages</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
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-  </div>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
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+        <div class="copyright">
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index 3576b63..0396c50 100644
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@@ -2,155 +2,198 @@
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check if object is <code>ed2in</code></h1>
-    
-    <div class="hidden name"><code>is.ed2in.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Simple test if object inheirts from class <code>"ed2in"</code>.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>is.ed2in</span>(<span class='no'>x</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>Object to be tested</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check if object is <code>ed2in</code></h1>
+
+            <div class="hidden name"><code>is.ed2in.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Simple test if object inheirts from class <code>"ed2in"</code>.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>is.ed2in</span>(<span class='no'>x</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>Object to be tested</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/list.files.nodir.html b/models/ed/docs/reference/list.files.nodir.html
index 99a4628..2d0434a 100644
--- a/models/ed/docs/reference/list.files.nodir.html
+++ b/models/ed/docs/reference/list.files.nodir.html
@@ -2,162 +2,204 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>List only files in a directory — list.files.nodir • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="List only files in a directory — list.files.nodir" />
-
-<meta property="og:description" content="List only files in a directory" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>List only files in a directory — list.files.nodir • PEcAn.ED2</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="List only files in a directory — list.files.nodir"
+    />
+
+    <meta property="og:description" content="List only files in a directory" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>List only files in a directory</h1>
-    
-    <div class="hidden name"><code>list.files.nodir.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>List only files in a directory</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>list.files.nodir</span>(<span class='no'>path</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>path</th>
-      <td><p>a character vector of full path names; the default
-    corresponds to the working directory, <code>getwd()</code>.  Tilde
-    expansion (see <code>path.expand</code>) is performed.  Missing
-    values will be ignored.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>List only files in a directory</h1>
+
+            <div class="hidden name"><code>list.files.nodir.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>List only files in a directory</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>list.files.nodir</span>(<span class='no'>path</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>path</th>
+              <td>
+                <p>
+                  a character vector of full path names; the default corresponds
+                  to the working directory, <code>getwd()</code>. Tilde
+                  expansion (see <code>path.expand</code>) is performed. Missing
+                  values will be ignored.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/met2model.ED2.html b/models/ed/docs/reference/met2model.ED2.html
index 141798e..6e9b8fe 100644
--- a/models/ed/docs/reference/met2model.ED2.html
+++ b/models/ed/docs/reference/met2model.ED2.html
@@ -2,195 +2,254 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>met2model wrapper for ED2 — met2model.ED2 • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="met2model wrapper for ED2 — met2model.ED2" />
-
-<meta property="og:description" content="If files already exist in 'Outfolder', the default function is NOT to
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>met2model wrapper for ED2 — met2model.ED2 • PEcAn.ED2</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="met2model wrapper for ED2 — met2model.ED2"
+    />
+
+    <meta
+      property="og:description"
+      content="If files already exist in 'Outfolder', the default function is NOT to
 overwrite them and only gives user the notice that file already exists. If
 user wants to overwrite the existing files, just change overwrite statement
-below to TRUE." />
-<meta name="twitter:card" content="summary" />
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-
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+              </button>
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+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2model wrapper for ED2</h1>
-    
-    <div class="hidden name"><code>met2model.ED2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>If files already exist in 'Outfolder', the default function is NOT to
-overwrite them and only gives user the notice that file already exists. If
-user wants to overwrite the existing files, just change overwrite statement
-below to TRUE.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>met2model.ED2</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2model wrapper for ED2</h1>
+
+            <div class="hidden name"><code>met2model.ED2.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              If files already exist in 'Outfolder', the default function is NOT
+              to overwrite them and only gives user the notice that file already
+              exists. If user wants to overwrite the existing files, just change
+              overwrite statement below to TRUE.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.ED2</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>lst</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>lat</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>lon</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>leap_year</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>lst</th>
-      <td><p>timezone offset to GMT in hours</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    <tr>
-      <th>leap_year</th>
-      <td><p>Enforce Leap-years? If set to TRUE, will require leap years to have 366 days. If set to false, will require all years to have 365 days. Default = TRUE.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lst</th>
+              <td><p>timezone offset to GMT in hours</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+            <tr>
+              <th>leap_year</th>
+              <td>
+                <p>
+                  Enforce Leap-years? If set to TRUE, will require leap years to
+                  have 366 days. If set to false, will require all years to have
+                  365 days. Default = TRUE.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/met_flag_description.html b/models/ed/docs/reference/met_flag_description.html
index e984a8e..bc3c01a 100644
--- a/models/ed/docs/reference/met_flag_description.html
+++ b/models/ed/docs/reference/met_flag_description.html
@@ -2,160 +2,208 @@
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 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Description of meteorology flags — met_flag_description • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Description of meteorology flags — met_flag_description"
+    />
+
+    <meta
+      property="og:description"
+      content="Descriptions of ED met header variable flags."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
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-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+            <div class="navbar-header">
+              <button
+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Description of meteorology flags</h1>
-    
-    <div class="hidden name"><code>met_flag_description.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Descriptions of ED met header variable flags.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='no'>met_flag_description</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 5 rows and 2 columns.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><code>data.frame</code> with the following columns:</p><ul>
-<li><p><code>flag</code> -- Numeric flag (in header file)</p></li>
-<li><p><code>flag_description</code> -- Description of flag</p></li>
-</ul>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Description of meteorology flags</h1>
+
+            <div class="hidden name"><code>met_flag_description.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Descriptions of ED met header variable flags.</p>
+          </div>
+
+          <pre class="usage"><span class='no'>met_flag_description</span></pre>
+
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
+
+          <p>
+            An object of class <code>tbl_df</code> (inherits from
+            <code>tbl</code>, <code>data.frame</code>) with 5 rows and 2
+            columns.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p><code>data.frame</code> with the following columns:</p>
+          <ul>
+            <li>
+              <p><code>flag</code> -- Numeric flag (in header file)</p>
+            </li>
+            <li>
+              <p><code>flag_description</code> -- Description of flag</p>
+            </li>
           </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
 
-  </div>
-</div>
+            <li><a href="#details">Details</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/models/ed/docs/reference/met_variable_description.html b/models/ed/docs/reference/met_variable_description.html
index 4687202..030f6cd 100644
--- a/models/ed/docs/reference/met_variable_description.html
+++ b/models/ed/docs/reference/met_variable_description.html
@@ -2,161 +2,219 @@
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+      PEcAn.ED2
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Description of meteorology variables</h1>
-    
-    <div class="hidden name"><code>met_variable_description.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Helpful information about ED_MET_DRIVER files.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='no'>met_variable_description</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 15 rows and 3 columns.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><code>data.frame</code> with the following columns:</p><ul>
-<li><p><code>variable</code> -- Variable name</p></li>
-<li><p><code>description</code> -- Variable description</p></li>
-<li><p><code>unit</code> -- Variable unit (character, parse-able by <code>udunints2</code>)</p></li>
-</ul>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Description of meteorology variables</h1>
+
+            <div class="hidden name">
+              <code>met_variable_description.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Helpful information about ED_MET_DRIVER files.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='no'>met_variable_description</span></pre>
+
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
+
+          <p>
+            An object of class <code>tbl_df</code> (inherits from
+            <code>tbl</code>, <code>data.frame</code>) with 15 rows and 3
+            columns.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p><code>data.frame</code> with the following columns:</p>
+          <ul>
+            <li>
+              <p><code>variable</code> -- Variable name</p>
+            </li>
+            <li>
+              <p><code>description</code> -- Variable description</p>
+            </li>
+            <li>
+              <p>
+                <code>unit</code> -- Variable unit (character, parse-able by
+                <code>udunints2</code>)
+              </p>
+            </li>
           </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
 
-  </div>
-</div>
+            <li><a href="#details">Details</a></li>
+          </ul>
+        </div>
+      </div>
 
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index 6d98b16..b9237a7 100644
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+++ b/models/ed/docs/reference/model2netcdf.ED2.html
@@ -2,180 +2,227 @@
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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-        
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Code to convert ED2's -T- HDF5 output into netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.ED2.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Code to convert ED2's -T- HDF5 output into netCDF format</h1>
 
-    <div class="ref-description">
-    
-    <p>Modified from Code to convert ED2.1's HDF5 output into the NACP Intercomparison format (ALMA using netCDF)</p>
-    
-    </div>
+            <div class="hidden name"><code>model2netcdf.ED2.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>model2netcdf.ED2</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>pft_names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of ED model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>pft_names</th>
-      <td><p>Names of PFTs used in the run, vector</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze, Shawn Serbin, Rob Kooper, Toni Viskari, Istem Fer
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Modified from Code to convert ED2.1's HDF5 output into the NACP
+              Intercomparison format (ALMA using netCDF)
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.ED2</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>pft_names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of ED model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>pft_names</th>
+              <td><p>Names of PFTs used in the run, vector</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze, Shawn Serbin, Rob Kooper, Toni Viskari, Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/modify_df.html b/models/ed/docs/reference/modify_df.html
index 6e84565..ec2c06b 100644
--- a/models/ed/docs/reference/modify_df.html
+++ b/models/ed/docs/reference/modify_df.html
@@ -2,167 +2,219 @@
 <!DOCTYPE html>
 <html>
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-
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-
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-<![endif]-->
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+    <meta charset="utf-8" />
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Modify a reference <code>data.frame</code> — modify_df • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      content="Modify a reference <code>data.frame</code> — modify_df"
+    />
+
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+only a single column."
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
   </head>
 
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="../reference/index.html">Reference</a>
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-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
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-  </a>
-  <ul class="dropdown-menu" role="menu">
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-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
-    </li>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Modify a reference <code>data.frame</code></h1>
-    
-    <div class="hidden name"><code>modify_df.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Wrapper around <code>modifyList</code> to allow expanding a <code>data.frame</code> by modifying
-only a single column.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>modify_df</span>(<span class='no'>input</span>, <span class='no'>base</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>input</th>
-      <td><p>Named <code>list</code> or <code>data.frame</code> containing columns to replace in <code>base</code></p></td>
-    </tr>
-    <tr>
-      <th>base</th>
-      <td><p>Reference object to modify</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Modified <code>data.frame</code></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Modify a reference <code>data.frame</code></h1>
+
+            <div class="hidden name"><code>modify_df.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Wrapper around <code>modifyList</code> to allow expanding a
+              <code>data.frame</code> by modifying only a single column.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>modify_df</span>(<span class='no'>input</span>, <span class='no'>base</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>input</th>
+              <td>
+                <p>
+                  Named <code>list</code> or <code>data.frame</code> containing
+                  columns to replace in <code>base</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>base</th>
+              <td><p>Reference object to modify</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Modified <code>data.frame</code></p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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 </html>
-
diff --git a/models/ed/docs/reference/modify_ed2in.html b/models/ed/docs/reference/modify_ed2in.html
index dc9235d..2aecb94 100644
--- a/models/ed/docs/reference/modify_ed2in.html
+++ b/models/ed/docs/reference/modify_ed2in.html
@@ -2,270 +2,423 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      content='This is a convenience function for modifying an ed2in list object.
 Arguments passed in all caps are assumed to be ED2IN namelist parameters and
 are inserted directly into the ed2in list objects. Lowercase arguments are
-defined explicitly (see &quot;Parameters&quot;), and those that do not match explicit
+defined explicitly (see "Parameters"), and those that do not match explicit
 arguments will be ignored with a warning. Because the lowercase arguments
 come with additional validity checks, they are recommended over modifying
-the ED2IN file directly via uppercase arguments." />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Modify an ED2IN object</h1>
-    
-    <div class="hidden name"><code>modify_ed2in.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This is a convenience function for modifying an <code>ed2in</code> list object.
-Arguments passed in all caps are assumed to be ED2IN namelist parameters and
-are inserted directly into the <code>ed2in</code> list objects. Lowercase arguments are
-defined explicitly (see "Parameters"), and those that do not match explicit
-arguments will be ignored with a warning. Because the lowercase arguments
-come with additional validity checks, they are recommended over modifying
-the ED2IN file directly via uppercase arguments.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>modify_ed2in</span>(<span class='no'>ed2in</span>, <span class='no'>...</span>, <span class='kw'>veg_prefix</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Modify an ED2IN object</h1>
+
+            <div class="hidden name"><code>modify_ed2in.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This is a convenience function for modifying an
+              <code>ed2in</code> list object. Arguments passed in all caps are
+              assumed to be ED2IN namelist parameters and are inserted directly
+              into the <code>ed2in</code> list objects. Lowercase arguments are
+              defined explicitly (see "Parameters"), and those that do not match
+              explicit arguments will be ignored with a warning. Because the
+              lowercase arguments come with additional validity checks, they are
+              recommended over modifying the ED2IN file directly via uppercase
+              arguments.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>modify_ed2in</span>(<span class='no'>ed2in</span>, <span class='no'>...</span>, <span class='kw'>veg_prefix</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>met_driver</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>end_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>EDI_path</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>output_types</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>output_dir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>run_dir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>runtype</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>run_name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>pecan_defaults</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>add_if_missing</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>check_paths</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>.dots</span> <span class='kw'>=</span> <span class='fu'>list</span>())</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>...</th>
-      <td><p>Namelist arguments (see Description and Details)</p></td>
-    </tr>
-    <tr>
-      <th>veg_prefix</th>
-      <td><p>Vegetation file prefix (<code>SFILIN</code>). If <code>lat</code> and <code>lon</code> are part of the prefix,</p></td>
-    </tr>
-    <tr>
-      <th>latitude</th>
-      <td><p>Run latitude coordinate. If <code>veg_prefix</code> is also provided,
-pass to <a href='read_ed_veg.html'>read_ed_veg</a>, otherwise set in ED2IN directly. Should be omitted if
-<code>lat</code> and <code>lon</code> are already part of <code>veg_prefix</code>.</p></td>
-    </tr>
-    <tr>
-      <th>longitude</th>
-      <td><p>Run longitude coordinate. If <code>veg_prefix</code> is also provided,
-pass to <a href='read_ed_veg.html'>read_ed_veg</a>, otherwise set in ED2IN directly. Should be omitted if
-<code>lat</code> and <code>lon</code> are already part of <code>veg_prefix</code>.</p></td>
-    </tr>
-    <tr>
-      <th>met_driver</th>
-      <td><p>Path and filename of met driver header
-(<code>ED_MET_DRIVER_DB</code>)</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Run start date (<code>IMONTHA</code>, <code>IDATEA</code>, <code>IYEARA</code>, <code>ITIMEA</code>)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>Run end date (<code>IMONTHZ</code>, <code>IDATEZ</code>, <code>IYEARZ</code> <code>ITIMEZ</code>)</p></td>
-    </tr>
-    <tr>
-      <th>EDI_path</th>
-      <td><p>Path to <code>EDI</code> directory, which often has the <code>VEG_DATABASE</code>
-and <code>THSUMS_DATABASE</code> files.</p></td>
-    </tr>
-    <tr>
-      <th>output_types</th>
-      <td><p>Character vector of output types (see Details)</p></td>
-    </tr>
-    <tr>
-      <th>output_dir</th>
-      <td><p>Output directory, for <code>FFILOUT</code> (analysis) and <code>SFILOUT</code>
-(history) files</p></td>
-    </tr>
-    <tr>
-      <th>run_dir</th>
-      <td><p>Directory in which to store run-related config files (e.g. <code>config.xml</code>).</p></td>
-    </tr>
-    <tr>
-      <th>runtype</th>
-      <td><p>ED initialization mode; either "INITIAL" or "HISTORY"</p></td>
-    </tr>
-    <tr>
-      <th>pecan_defaults</th>
-      <td><p>Logical. If <code>TRUE</code>, set common <code>ED2IN</code> defaults.</p></td>
-    </tr>
-    <tr>
-      <th>add_if_missing</th>
-      <td><p>Logical. If <code>TRUE</code>, all-caps arguments not found in
-existing <code>ed2in</code> list will be added to the end.  Default = <code>FALSE</code>.</p></td>
-    </tr>
-    <tr>
-      <th>check_paths</th>
-      <td><p>Logical. If <code>TRUE</code> (default), for any parameters that
-expect files, check that files exist and throw an error if they don't.</p></td>
-    </tr>
-    <tr>
-      <th>.dots</th>
-      <td><p>A list of <code>...</code> arguments.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>Modified <code>ed2in</code> list object. See <a href='read_ed2in.html'>read_ed2in</a>.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Namelist arguments are applied last, and will silently overwrite any
-arguments set by special case arguments.</p>
-<p>Namelist arguments can be stored in a list and passed in via the <code>.dots</code>
-argument (e.g. <code>.dots = list(SFILIN = "/path/prefix_", ...)</code>), or using the
-<code>rlang::!!!</code> splicing operator. If both are provided, they will be spliced
-together, with the <code>...</code> taking precedence.</p>
-<p>For <code>output_types</code>, select one or more of the following:</p><ul>
-<li><p>"fast" -- Fast analysis; mostly polygon-level averages (<code>IFOUTPUT</code>)</p></li>
-<li><p>"daily -- Daily means (one file per day) (<code>IDOUTPUT</code>)</p></li>
-<li><p>"monthly" -- Monthly means (one file per month) (<code>IMOUTPUT</code>)</p></li>
-<li><p>"monthly_diurnal" -- Monthly means of the diurnal cycle (one file per
-month) (<code>IQOUTPUT</code>)</p></li>
-<li><p>"annual" -- Annual (one file per year) (<code>IYOUTPUT</code>)</p></li>
-<li><p>"instant" -- Instantaneous fluxes, mostly polygon-level variables, one
-file per year (<code>ITOUTPUT</code>)</p></li>
-<li><p>"restart" -- Restart file for HISTORY runs. (<code>ISOUTPUT</code>)</p></li>
-<li><p>"all" -- All output types</p></li>
-</ul>
-    
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>...</th>
+              <td><p>Namelist arguments (see Description and Details)</p></td>
+            </tr>
+            <tr>
+              <th>veg_prefix</th>
+              <td>
+                <p>
+                  Vegetation file prefix (<code>SFILIN</code>). If
+                  <code>lat</code> and <code>lon</code> are part of the prefix,
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>latitude</th>
+              <td>
+                <p>
+                  Run latitude coordinate. If <code>veg_prefix</code> is also
+                  provided, pass to <a href="read_ed_veg.html">read_ed_veg</a>,
+                  otherwise set in ED2IN directly. Should be omitted if
+                  <code>lat</code> and <code>lon</code> are already part of
+                  <code>veg_prefix</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>longitude</th>
+              <td>
+                <p>
+                  Run longitude coordinate. If <code>veg_prefix</code> is also
+                  provided, pass to <a href="read_ed_veg.html">read_ed_veg</a>,
+                  otherwise set in ED2IN directly. Should be omitted if
+                  <code>lat</code> and <code>lon</code> are already part of
+                  <code>veg_prefix</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>met_driver</th>
+              <td>
+                <p>
+                  Path and filename of met driver header
+                  (<code>ED_MET_DRIVER_DB</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  Run start date (<code>IMONTHA</code>, <code>IDATEA</code>,
+                  <code>IYEARA</code>, <code>ITIMEA</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  Run end date (<code>IMONTHZ</code>, <code>IDATEZ</code>,
+                  <code>IYEARZ</code> <code>ITIMEZ</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>EDI_path</th>
+              <td>
+                <p>
+                  Path to <code>EDI</code> directory, which often has the
+                  <code>VEG_DATABASE</code> and
+                  <code>THSUMS_DATABASE</code> files.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>output_types</th>
+              <td><p>Character vector of output types (see Details)</p></td>
+            </tr>
+            <tr>
+              <th>output_dir</th>
+              <td>
+                <p>
+                  Output directory, for <code>FFILOUT</code> (analysis) and
+                  <code>SFILOUT</code> (history) files
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>run_dir</th>
+              <td>
+                <p>
+                  Directory in which to store run-related config files (e.g.
+                  <code>config.xml</code>).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>runtype</th>
+              <td>
+                <p>ED initialization mode; either "INITIAL" or "HISTORY"</p>
+              </td>
+            </tr>
+            <tr>
+              <th>pecan_defaults</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code>, set common
+                  <code>ED2IN</code> defaults.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>add_if_missing</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code>, all-caps arguments not found in
+                  existing <code>ed2in</code> list will be added to the end.
+                  Default = <code>FALSE</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>check_paths</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code> (default), for any parameters
+                  that expect files, check that files exist and throw an error
+                  if they don't.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>.dots</th>
+              <td>
+                <p>A list of <code>...</code> arguments.</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Modified <code>ed2in</code> list object. See
+            <a href="read_ed2in.html">read_ed2in</a>.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Namelist arguments are applied last, and will silently overwrite any
+            arguments set by special case arguments.
+          </p>
+          <p>
+            Namelist arguments can be stored in a list and passed in via the
+            <code>.dots</code> argument (e.g.
+            <code>.dots = list(SFILIN = "/path/prefix_", ...)</code>), or using
+            the <code>rlang::!!!</code> splicing operator. If both are provided,
+            they will be spliced together, with the <code>...</code> taking
+            precedence.
+          </p>
+          <p>
+            For <code>output_types</code>, select one or more of the following:
+          </p>
+          <ul>
+            <li>
+              <p>
+                "fast" -- Fast analysis; mostly polygon-level averages
+                (<code>IFOUTPUT</code>)
+              </p>
+            </li>
+            <li>
+              <p>
+                "daily -- Daily means (one file per day) (<code>IDOUTPUT</code>)
+              </p>
+            </li>
+            <li>
+              <p>
+                "monthly" -- Monthly means (one file per month)
+                (<code>IMOUTPUT</code>)
+              </p>
+            </li>
+            <li>
+              <p>
+                "monthly_diurnal" -- Monthly means of the diurnal cycle (one
+                file per month) (<code>IQOUTPUT</code>)
+              </p>
+            </li>
+            <li>
+              <p>
+                "annual" -- Annual (one file per year) (<code>IYOUTPUT</code>)
+              </p>
+            </li>
+            <li>
+              <p>
+                "instant" -- Instantaneous fluxes, mostly polygon-level
+                variables, one file per year (<code>ITOUTPUT</code>)
+              </p>
+            </li>
+            <li>
+              <p>
+                "restart" -- Restart file for HISTORY runs.
+                (<code>ISOUTPUT</code>)
+              </p>
+            </li>
+            <li><p>"all" -- All output types</p></li>
+          </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+            <li><a href="#value">Value</a></li>
 
-      <li><a href="#details">Details</a></li>
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/parse.history.html b/models/ed/docs/reference/parse.history.html
index 4ce5721..05469d2 100644
--- a/models/ed/docs/reference/parse.history.html
+++ b/models/ed/docs/reference/parse.history.html
@@ -2,167 +2,217 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Create a CSV from history.xml outputed by ED — parse.history • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Create a CSV from history.xml outputed by ED — parse.history"
+    />
+
+    <meta
+      property="og:description"
+      content="This will generate the CSV file needed by write configs to write the
 config.xml. This is a hack right now, all this information should be
-in the PEcAn DB." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<![endif]-->
+in the PEcAn DB."
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-    <div class="navbar-header">
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create a CSV from history.xml outputed by ED</h1>
-    
-    <div class="hidden name"><code>parse.history.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This will generate the CSV file needed by write configs to write the
-config.xml. This is a hack right now, all this information should be
-in the PEcAn DB.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>parse.history</span>(<span class='no'>historyfile</span>, <span class='kw'>outfile</span> <span class='kw'>=</span> <span class='st'>""</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>historyfile</th>
-      <td><p>filename of history file generated by ED.</p></td>
-    </tr>
-    <tr>
-      <th>outfile</th>
-      <td><p>location where to write output, if no specified it will write to the console.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create a CSV from history.xml outputed by ED</h1>
+
+            <div class="hidden name"><code>parse.history.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This will generate the CSV file needed by write configs to write
+              the config.xml. This is a hack right now, all this information
+              should be in the PEcAn DB.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>parse.history</span>(<span class='no'>historyfile</span>, <span class='kw'>outfile</span> <span class='kw'>=</span> <span class='st'>""</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>historyfile</th>
+              <td><p>filename of history file generated by ED.</p></td>
+            </tr>
+            <tr>
+              <th>outfile</th>
+              <td>
+                <p>
+                  location where to write output, if no specified it will write
+                  to the console.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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   </body>
 </html>
-
diff --git a/models/ed/docs/reference/patch_cohort_index.html b/models/ed/docs/reference/patch_cohort_index.html
index c0d46fc..b2b0c48 100644
--- a/models/ed/docs/reference/patch_cohort_index.html
+++ b/models/ed/docs/reference/patch_cohort_index.html
@@ -2,161 +2,210 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-cohort vectors onto patches, for instance for use with tapply." />
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Generate ED2 cohort to patch mapping vector — patch_cohort_index •
+      PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
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+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Generate ED2 cohort to patch mapping vector — patch_cohort_index"
+    />
+
+    <meta
+      property="og:description"
+      content="Generate a vector of integer indices for mapping ED state
+cohort vectors onto patches, for instance for use with tapply."
+    />
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+                <span
+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
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+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate ED2 cohort to patch mapping vector</h1>
-    
-    <div class="hidden name"><code>patch_cohort_index.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generate a vector of integer indices for mapping ED state
-cohort vectors onto patches, for instance for use with <code>tapply</code>.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>patch_cohort_index</span>(<span class='no'>nc</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>nc</th>
-      <td><p><code>ncdf4</code> object for ED history restart file.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generate ED2 cohort to patch mapping vector</h1>
+
+            <div class="hidden name"><code>patch_cohort_index.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Generate a vector of integer indices for mapping ED state cohort
+              vectors onto patches, for instance for use with
+              <code>tapply</code>.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>patch_cohort_index</span>(<span class='no'>nc</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>nc</th>
+              <td>
+                <p><code>ncdf4</code> object for ED history restart file.</p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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+          </p>
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diff --git a/models/ed/docs/reference/prepare_ed_veg_filename.html b/models/ed/docs/reference/prepare_ed_veg_filename.html
index b2c7f93..fc20fd1 100644
--- a/models/ed/docs/reference/prepare_ed_veg_filename.html
+++ b/models/ed/docs/reference/prepare_ed_veg_filename.html
@@ -2,180 +2,236 @@
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+      PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+      property="og:description"
+      content="Adds the latitude and longitude, or checks if they are formatted correctly.
 Then, splits the prefix into the directory and base name, appends the suffix
 to the base name (adding a starting dot, if necessary), and returns the
-filename as a character." />
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-<![endif]-->
+filename as a character."
+    />
+    <meta name="twitter:card" content="summary" />
 
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+                    role="button"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Format file name for ED vegetation inputs</h1>
-    
-    <div class="hidden name"><code>prepare_ed_veg_filename.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Adds the latitude and longitude, or checks if they are formatted correctly.
-Then, splits the prefix into the directory and base name, appends the suffix
-to the base name (adding a starting dot, if necessary), and returns the
-filename as a character.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>prepare_ed_veg_filename</span>(<span class='no'>path_prefix</span>, <span class='no'>suffix</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Format file name for ED vegetation inputs</h1>
+
+            <div class="hidden name">
+              <code>prepare_ed_veg_filename.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Adds the latitude and longitude, or checks if they are formatted
+              correctly. Then, splits the prefix into the directory and base
+              name, appends the suffix to the base name (adding a starting dot,
+              if necessary), and returns the filename as a character.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>prepare_ed_veg_filename</span>(<span class='no'>path_prefix</span>, <span class='no'>suffix</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>path_prefix</th>
-      <td><p>Desired path and prefix (without latitude and longitude)</p></td>
-    </tr>
-    <tr>
-      <th>suffix</th>
-      <td><p>Character string of filename suffix.</p></td>
-    </tr>
-    <tr>
-      <th>latitude</th>
-      <td><p>Site latitude coordinate (default = <code>NULL</code>)</p></td>
-    </tr>
-    <tr>
-      <th>longitude</th>
-      <td><p>Site longitude coordinate (default = <code>NULL</code>)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Character string of full formatted file path</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>path_prefix</th>
+              <td>
+                <p>Desired path and prefix (without latitude and longitude)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>suffix</th>
+              <td><p>Character string of filename suffix.</p></td>
+            </tr>
+            <tr>
+              <th>latitude</th>
+              <td>
+                <p>Site latitude coordinate (default = <code>NULL</code>)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>longitude</th>
+              <td>
+                <p>Site longitude coordinate (default = <code>NULL</code>)</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Character string of full formatted file path</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/models/ed/docs/reference/print.ed2in.html b/models/ed/docs/reference/print.ed2in.html
index 5469f0c..19ae743 100644
--- a/models/ed/docs/reference/print.ed2in.html
+++ b/models/ed/docs/reference/print.ed2in.html
@@ -2,160 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Print method for <code>ed2in</code></h1>
-    
-    <div class="hidden name"><code>print.ed2in.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Print method for <code>ed2in</code></h1>
 
-    <div class="ref-description">
-    
-    <p>Sets attributes to <code>NULL</code> before printing, so the output isn't as messy.</p>
-    
-    </div>
+            <div class="hidden name"><code>print.ed2in.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for ed2in</span>
-<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>an object used to select a method.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>further arguments passed to or from other methods.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Sets attributes to <code>NULL</code> before printing, so the
+              output isn't as messy.
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for ed2in</span>
+<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>an object used to select a method.</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>further arguments passed to or from other methods.</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/models/ed/docs/reference/put_E_values.html b/models/ed/docs/reference/put_E_values.html
index b5a7cc5..1518869 100644
--- a/models/ed/docs/reference/put_E_values.html
+++ b/models/ed/docs/reference/put_E_values.html
@@ -2,145 +2,182 @@
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-    <h1>Function for put -E- values to nc_var list</h1>
-    
-    <div class="hidden name"><code>put_E_values.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function for put -E- values to nc_var list</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Function for put -E- values to nc_var list</h1>
 
-    <pre class="usage"><span class='fu'>put_E_values</span>(<span class='no'>yr</span>, <span class='no'>nc_var</span>, <span class='no'>out</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>begins</span>, <span class='no'>ends</span>, <span class='no'>pft_names</span>, <span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>put_E_values.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Function for put -E- values to nc_var list</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>put_E_values</span>(<span class='no'>yr</span>, <span class='no'>nc_var</span>, <span class='no'>out</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>begins</span>, <span class='no'>ends</span>, <span class='no'>pft_names</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
-
diff --git a/models/ed/docs/reference/put_T_values.html b/models/ed/docs/reference/put_T_values.html
index 40be673..cb5ba07 100644
--- a/models/ed/docs/reference/put_T_values.html
+++ b/models/ed/docs/reference/put_T_values.html
@@ -2,145 +2,182 @@
 <!DOCTYPE html>
 <html>
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+      Function for put -T- values to nc_var list — put_T_values • PEcAn.ED2
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Function for put -T- values to nc_var list — put_T_values"
+    />
+
+    <meta
+      property="og:description"
+      content="Function for put -T- values to nc_var list"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+                  >1.6.0</span
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+            </div>
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function for put -T- values to nc_var list</h1>
-    
-    <div class="hidden name"><code>put_T_values.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function for put -T- values to nc_var list</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Function for put -T- values to nc_var list</h1>
 
-    <pre class="usage"><span class='fu'>put_T_values</span>(<span class='no'>yr</span>, <span class='no'>nc_var</span>, <span class='no'>out</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>begins</span>, <span class='no'>ends</span>, <span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>put_T_values.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Function for put -T- values to nc_var list</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>put_T_values</span>(<span class='no'>yr</span>, <span class='no'>nc_var</span>, <span class='no'>out</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>begins</span>, <span class='no'>ends</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
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-
diff --git a/models/ed/docs/reference/read.output.ED2.html b/models/ed/docs/reference/read.output.ED2.html
index 5dbb7b6..cd1e946 100644
--- a/models/ed/docs/reference/read.output.ED2.html
+++ b/models/ed/docs/reference/read.output.ED2.html
@@ -2,164 +2,206 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<![endif]-->
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+    <meta charset="utf-8" />
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+
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read ED output</h1>
-    
-    <div class="hidden name"><code>read.output.ED2.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read ED output</h1>
 
-    <div class="ref-description">
+            <div class="hidden name"><code>read.output.ED2.Rd</code></div>
+          </div>
 
-    </div>
+          <div class="ref-description"></div>
 
-    <pre class="usage"><span class='fu'>read.output.ED2</span>(<span class='no'>run.id</span>, <span class='no'>outdir</span>, <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>read.output.ED2</span>(<span class='no'>run.id</span>, <span class='no'>outdir</span>, <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
   <span class='kw'>variables</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"AGB_CO"</span>, <span class='st'>"NPLANT"</span>), <span class='kw'>output.type</span> <span class='kw'>=</span> <span class='st'>"Y"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>run.id</th>
-      <td><p>the id distiguishing the model run</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>the directory that the model's output was sent to</p></td>
-    </tr>
-    <tr>
-      <th>start.year</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>output.type</th>
-      <td><p>type of output file to read, can be '-Y-' for annual output, '-M-' for monthly means, '-D-' for daily means, '-T-' for instantaneous fluxes. Output types are set in the ED2IN namelist as NL<!-- %I\link{DMYT}OUTPUT} --></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>run.id</th>
+              <td><p>the id distiguishing the model run</p></td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>the directory that the model's output was sent to</p></td>
+            </tr>
+            <tr>
+              <th>start.year</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>output.type</th>
+              <td>
+                <p>
+                  type of output file to read, can be '-Y-' for annual output,
+                  '-M-' for monthly means, '-D-' for daily means, '-T-' for
+                  instantaneous fluxes. Output types are set in the ED2IN
+                  namelist as NL<!-- %I\link{DMYT}OUTPUT} -->
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/read.output.file.ed.html b/models/ed/docs/reference/read.output.file.ed.html
index 7aa2630..ac17c0f 100644
--- a/models/ed/docs/reference/read.output.file.ed.html
+++ b/models/ed/docs/reference/read.output.file.ed.html
@@ -2,169 +2,215 @@
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+    ></script>
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+    <script src="../pkgdown.js"></script>
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+      content="read output - ED — read.output.file.ed"
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+    <meta name="twitter:card" content="summary" />
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-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
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-        
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
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+                type="button"
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+                data-toggle="collapse"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>read output - ED</h1>
-    
-    <div class="hidden name"><code>read.output.file.ed.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Extract ED output for specific variables from an hdf5 file</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read.output.file.ed</span>(<span class='no'>filename</span>, <span class='kw'>variables</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"AGB_CO"</span>, <span class='st'>"NPLANT"</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>filename</th>
-      <td><p>string, name of file with data</p></td>
-    </tr>
-    <tr>
-      <th>variables</th>
-      <td><p>variables to extract from file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>single value of output variable from filename. In the case of AGB, it is summed across all plants</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>read output - ED</h1>
+
+            <div class="hidden name"><code>read.output.file.ed.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Extract ED output for specific variables from an hdf5 file</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read.output.file.ed</span>(<span class='no'>filename</span>, <span class='kw'>variables</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"AGB_CO"</span>, <span class='st'>"NPLANT"</span>))</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>filename</th>
+              <td><p>string, name of file with data</p></td>
+            </tr>
+            <tr>
+              <th>variables</th>
+              <td><p>variables to extract from file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            single value of output variable from filename. In the case of AGB,
+            it is summed across all plants
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Carl Davidson
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
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diff --git a/models/ed/docs/reference/read_E_files.html b/models/ed/docs/reference/read_E_files.html
index e53eb14..9646ae1 100644
--- a/models/ed/docs/reference/read_E_files.html
+++ b/models/ed/docs/reference/read_E_files.html
@@ -2,175 +2,228 @@
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-    <div class="page-header">
-    <h1>Function for reading -E- files</h1>
-    
-    <div class="hidden name"><code>read_E_files.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Function for reading -E- files</h1>
 
-    <div class="ref-description">
-    
-    <p>Function for reading -E- files</p>
-    
-    </div>
+            <div class="hidden name"><code>read_E_files.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>read_E_files</span>(<span class='no'>yr</span>, <span class='no'>yfiles</span>, <span class='no'>efiles</span>, <span class='no'>outdir</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>pft_names</span>,
+          <div class="ref-description">
+            <p>Function for reading -E- files</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_E_files</span>(<span class='no'>yr</span>, <span class='no'>yfiles</span>, <span class='no'>efiles</span>, <span class='no'>outdir</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>pft_names</span>,
   <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>yr</th>
-      <td><p>the year being processed</p></td>
-    </tr>
-    <tr>
-      <th>yfiles</th>
-      <td><p>the years on the filenames, will be used to matched efiles for that year</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>e.g.     yr = 1999
-yfiles = 1999 1999 1999 1999 1999 1999 1999 2000 2000 2000 2000
-efiles = "analysis-E-1999-06-00-000000-g01.h5" "analysis-E-1999-07-00-000000-g01.h5"
-"analysis-E-1999-08-00-000000-g01.h5" "analysis-E-1999-09-00-000000-g01.h5"
-"analysis-E-1999-10-00-000000-g01.h5" "analysis-E-1999-11-00-000000-g01.h5"
-"analysis-E-1999-12-00-000000-g01.h5" "analysis-E-2000-01-00-000000-g01.h5"
-"analysis-E-2000-02-00-000000-g01.h5" "analysis-E-2000-03-00-000000-g01.h5"
-"analysis-E-2000-04-00-000000-g01.h5"</p>
-<p>pft_names  : character vector with names of PFTs
-pft_names &lt;- c("temperate.Early_Hardwood", "temperate.Late_Hardwood")</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>yr</th>
+              <td><p>the year being processed</p></td>
+            </tr>
+            <tr>
+              <th>yfiles</th>
+              <td>
+                <p>
+                  the years on the filenames, will be used to matched efiles for
+                  that year
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            e.g. yr = 1999 yfiles = 1999 1999 1999 1999 1999 1999 1999 2000 2000
+            2000 2000 efiles = "analysis-E-1999-06-00-000000-g01.h5"
+            "analysis-E-1999-07-00-000000-g01.h5"
+            "analysis-E-1999-08-00-000000-g01.h5"
+            "analysis-E-1999-09-00-000000-g01.h5"
+            "analysis-E-1999-10-00-000000-g01.h5"
+            "analysis-E-1999-11-00-000000-g01.h5"
+            "analysis-E-1999-12-00-000000-g01.h5"
+            "analysis-E-2000-01-00-000000-g01.h5"
+            "analysis-E-2000-02-00-000000-g01.h5"
+            "analysis-E-2000-03-00-000000-g01.h5"
+            "analysis-E-2000-04-00-000000-g01.h5"
+          </p>
+          <p>
+            pft_names : character vector with names of PFTs pft_names &lt;-
+            c("temperate.Early_Hardwood", "temperate.Late_Hardwood")
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+          </ul>
+        </div>
+      </div>
 
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index b39ce29..c7cbbe9 100644
--- a/models/ed/docs/reference/read_S_files.html
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+      PEcAn.ED2
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>S-file contents are not written to standard netcdfs but are used by read_restart
-from SDA's perspective it doesn't make sense to write and read to ncdfs because ED restarts from history files</h1>
-    
-    <div class="hidden name"><code>read_S_files.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>S-file contents are not written to standard netcdfs but are used by read_restart
-from SDA's perspective it doesn't make sense to write and read to ncdfs because ED restarts from history files</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_S_files</span>(<span class='no'>sfile</span>, <span class='no'>outdir</span>, <span class='no'>pft_names</span>, <span class='kw'>pecan_names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sfile</th>
-      <td><p>history file name e.g. "history-S-1961-01-01-000000-g01.h5"</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>path to run outdir, where the -S- file is</p></td>
-    </tr>
-    <tr>
-      <th>pft_names</th>
-      <td><p>string vector, names of ED2 pfts in the run, e.g. c("temperate.Early_Hardwood", "temperate.Late_Conifer")</p></td>
-    </tr>
-    <tr>
-      <th>pecan_names</th>
-      <td><p>string vector, pecan names of requested variables, e.g. c("AGB", "AbvGrndWood")</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              S-file contents are not written to standard netcdfs but are used
+              by read_restart from SDA's perspective it doesn't make sense to
+              write and read to ncdfs because ED restarts from history files
+            </h1>
+
+            <div class="hidden name"><code>read_S_files.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              S-file contents are not written to standard netcdfs but are used
+              by read_restart from SDA's perspective it doesn't make sense to
+              write and read to ncdfs because ED restarts from history files
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_S_files</span>(<span class='no'>sfile</span>, <span class='no'>outdir</span>, <span class='no'>pft_names</span>, <span class='kw'>pecan_names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sfile</th>
+              <td>
+                <p>
+                  history file name e.g. "history-S-1961-01-01-000000-g01.h5"
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>path to run outdir, where the -S- file is</p></td>
+            </tr>
+            <tr>
+              <th>pft_names</th>
+              <td>
+                <p>
+                  string vector, names of ED2 pfts in the run, e.g.
+                  c("temperate.Early_Hardwood", "temperate.Late_Conifer")
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pecan_names</th>
+              <td>
+                <p>
+                  string vector, pecan names of requested variables, e.g.
+                  c("AGB", "AbvGrndWood")
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/models/ed/docs/reference/read_T_files.html b/models/ed/docs/reference/read_T_files.html
index f9e633c..8ffe6bf 100644
--- a/models/ed/docs/reference/read_T_files.html
+++ b/models/ed/docs/reference/read_T_files.html
@@ -2,167 +2,214 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Function for reading -T- files — read_T_files"
+    />
+
+    <meta property="og:description" content="Function for reading -T- files" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+    <![endif]-->
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function for reading -T- files</h1>
-    
-    <div class="hidden name"><code>read_T_files.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function for reading -T- files</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_T_files</span>(<span class='no'>yr</span>, <span class='no'>yfiles</span>, <span class='no'>tfiles</span>, <span class='no'>outdir</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>yr</th>
-      <td><p>the year being processed</p></td>
-    </tr>
-    <tr>
-      <th>yfiles</th>
-      <td><p>the years on the filenames, will be used to matched tfiles for that year</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>e.g.    yr = 1999
-yfiles = 1999 2000
-tfiles = "analysis-T-1999-00-00-000000-g01.h5" "analysis-T-2000-00-00-000000-g01.h5"</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Function for reading -T- files</h1>
+
+            <div class="hidden name"><code>read_T_files.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Function for reading -T- files</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_T_files</span>(<span class='no'>yr</span>, <span class='no'>yfiles</span>, <span class='no'>tfiles</span>, <span class='no'>outdir</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>yr</th>
+              <td><p>the year being processed</p></td>
+            </tr>
+            <tr>
+              <th>yfiles</th>
+              <td>
+                <p>
+                  the years on the filenames, will be used to matched tfiles for
+                  that year
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            e.g. yr = 1999 yfiles = 1999 2000 tfiles =
+            "analysis-T-1999-00-00-000000-g01.h5"
+            "analysis-T-2000-00-00-000000-g01.h5"
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/models/ed/docs/reference/read_css.html b/models/ed/docs/reference/read_css.html
index 081754f..b21d95d 100644
--- a/models/ed/docs/reference/read_css.html
+++ b/models/ed/docs/reference/read_css.html
@@ -2,173 +2,231 @@
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-
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+      Read individual css, pss, and site files — read_css • PEcAn.ED2
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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+
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+    <script src="../pkgdown.js"></script>
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+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
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+
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read individual css, pss, and site files</h1>
-    
-    <div class="hidden name"><code>read_css.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read individual css, pss, and site files</h1>
 
-    <div class="ref-description">
-    
-    <p>Read files into objects usable by other PEcAn.ED2 utilities, and optionally check for errors.</p>
-    
-    </div>
+            <div class="hidden name"><code>read_css.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>read_css</span>(<span class='no'>filepath</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
+          <div class="ref-description">
+            <p>
+              Read files into objects usable by other PEcAn.ED2 utilities, and
+              optionally check for errors.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_css</span>(<span class='no'>filepath</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
 
 <span class='fu'>read_pss</span>(<span class='no'>filepath</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 
 <span class='fu'>read_site</span>(<span class='no'>filepath</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>filepath</th>
-      <td><p>Full path to css, pss, or site file</p></td>
-    </tr>
-    <tr>
-      <th>check</th>
-      <td><p>Logical. If <code>TRUE</code> (default), <a href='check_css.html'>check</a> that file is valid.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional arguments to <a href='check_css.html'>check functions</a>.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>data.frame</code> containing</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>filepath</th>
+              <td><p>Full path to css, pss, or site file</p></td>
+            </tr>
+            <tr>
+              <th>check</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code> (default),
+                  <a href="check_css.html">check</a> that file is valid.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  Additional arguments to
+                  <a href="check_css.html">check functions</a>.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>data.frame</code> containing</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/models/ed/docs/reference/read_ed2in.html b/models/ed/docs/reference/read_ed2in.html
index 57256c3..1eae803 100644
--- a/models/ed/docs/reference/read_ed2in.html
+++ b/models/ed/docs/reference/read_ed2in.html
@@ -2,161 +2,204 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<![endif]-->
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+    <meta charset="utf-8" />
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <script src="../pkgdown.js"></script>
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+      content="Read ED2IN file to named list — read_ed2in"
+    />
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+      content="Parse an ED2IN file to a named list."
+    />
+    <meta name="twitter:card" content="summary" />
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+
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+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read ED2IN file to named list</h1>
-    
-    <div class="hidden name"><code>read_ed2in.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Parse an ED2IN file to a named list.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_ed2in</span>(<span class='no'>filename</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>filename</th>
-      <td><p>Full path to ED2IN file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Named list of <code>tag = value</code></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read ED2IN file to named list</h1>
+
+            <div class="hidden name"><code>read_ed2in.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Parse an ED2IN file to a named list.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_ed2in</span>(<span class='no'>filename</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>filename</th>
+              <td><p>Full path to ED2IN file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Named list of <code>tag = value</code></p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+        <div class="copyright">
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diff --git a/models/ed/docs/reference/read_ed_metheader.html b/models/ed/docs/reference/read_ed_metheader.html
index f2b3397..b1be045 100644
--- a/models/ed/docs/reference/read_ed_metheader.html
+++ b/models/ed/docs/reference/read_ed_metheader.html
@@ -2,209 +2,321 @@
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 <html>
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+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+    <!-- clipboard.js -->
+    <script
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+    ></script>
+
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+    />
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+manipulated within R. Returns a list of file formats."
+    />
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+                <span
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+              <ul class="nav navbar-nav">
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+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
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+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read ED meteorology header file</h1>
-    
-    <div class="hidden name"><code>read_ed_metheader.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Read a ED_MET_DRIVER_HEADER file into a list-like object that can be
-manipulated within R. Returns a list of file formats.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_ed_metheader</span>(<span class='no'>filename</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check_files</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>filename</th>
-      <td><p>File name (including path) of met driver header file, as
-character</p></td>
-    </tr>
-    <tr>
-      <th>check</th>
-      <td><p>Logical, whether or not to check file for correctness (default
-= <code>TRUE</code>)</p></td>
-    </tr>
-    <tr>
-      <th>check_files</th>
-      <td><p>Logical. If <code>TRUE</code>, perform basic diagnostics on met
-files as well.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>List of ED met input parameters. See Details.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>The output is an unnamed list with each element corresponding to a single
-file format. Each file format contains the following elements:</p><ul>
-<li><p><code>path_prefix</code> -- Path and prefix of files</p></li>
-<li><p><code>nlon</code> -- Number of longitude grid cells</p></li>
-<li><p><code>nlat</code> -- Number of latitude grid cells</p></li>
-<li><p><code>dx</code> -- Size of longitude grid cell</p></li>
-<li><p><code>dy</code> -- Size of latitude grid cell</p></li>
-<li><p><code>xmin</code> -- Minimum longitude</p></li>
-<li><p><code>ymin</code> -- Minimum latitude</p></li>
-<li><p><code>variables</code> -- Data frame of variables, with the columns described below.
-Starred columns are required for writing. This table is left joined with
-<a href='met_variable_description.html'>met_variable_description</a> and <a href='met_flag_description.html'>met_flag_description</a>.</p><ul>
-<li><p><code>variable</code> -- Variable name</p></li>
-<li><p><code>description</code> -- Variable description</p></li>
-<li><p><code>unit</code> -- Variable unit</p></li>
-<li><p><code>update_frequency</code> -- Update frequency (seconds) or scalar values if
-<code>flag=4</code></p></li>
-<li><p><code>flag</code> -- Variable flags.</p></li>
-<li><p><code>flag_description</code> -- Description of variable flag</p></li>
-</ul></li>
-</ul>
-    <p>The formatting of a meteorlogy header file is as follows (from the ED GitHub Wiki):</p><pre>&lt;number of file formats&gt;    # Repeat lines below this number of times
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read ED meteorology header file</h1>
+
+            <div class="hidden name"><code>read_ed_metheader.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Read a ED_MET_DRIVER_HEADER file into a list-like object that can
+              be manipulated within R. Returns a list of file formats.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_ed_metheader</span>(<span class='no'>filename</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check_files</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>filename</th>
+              <td>
+                <p>
+                  File name (including path) of met driver header file, as
+                  character
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>check</th>
+              <td>
+                <p>
+                  Logical, whether or not to check file for correctness (default
+                  = <code>TRUE</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>check_files</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code>, perform basic diagnostics on
+                  met files as well.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>List of ED met input parameters. See Details.</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            The output is an unnamed list with each element corresponding to a
+            single file format. Each file format contains the following
+            elements:
+          </p>
+          <ul>
+            <li>
+              <p><code>path_prefix</code> -- Path and prefix of files</p>
+            </li>
+            <li>
+              <p><code>nlon</code> -- Number of longitude grid cells</p>
+            </li>
+            <li>
+              <p><code>nlat</code> -- Number of latitude grid cells</p>
+            </li>
+            <li>
+              <p><code>dx</code> -- Size of longitude grid cell</p>
+            </li>
+            <li>
+              <p><code>dy</code> -- Size of latitude grid cell</p>
+            </li>
+            <li>
+              <p><code>xmin</code> -- Minimum longitude</p>
+            </li>
+            <li>
+              <p><code>ymin</code> -- Minimum latitude</p>
+            </li>
+            <li>
+              <p>
+                <code>variables</code> -- Data frame of variables, with the
+                columns described below. Starred columns are required for
+                writing. This table is left joined with
+                <a href="met_variable_description.html"
+                  >met_variable_description</a
+                >
+                and
+                <a href="met_flag_description.html">met_flag_description</a>.
+              </p>
+              <ul>
+                <li>
+                  <p><code>variable</code> -- Variable name</p>
+                </li>
+                <li>
+                  <p><code>description</code> -- Variable description</p>
+                </li>
+                <li>
+                  <p><code>unit</code> -- Variable unit</p>
+                </li>
+                <li>
+                  <p>
+                    <code>update_frequency</code> -- Update frequency (seconds)
+                    or scalar values if <code>flag=4</code>
+                  </p>
+                </li>
+                <li>
+                  <p><code>flag</code> -- Variable flags.</p>
+                </li>
+                <li>
+                  <p>
+                    <code>flag_description</code> -- Description of variable
+                    flag
+                  </p>
+                </li>
+              </ul>
+            </li>
+          </ul>
+          <p>
+            The formatting of a meteorlogy header file is as follows (from the
+            ED GitHub Wiki):
+          </p>
+          <pre>
+&lt;number of file formats&gt;    # Repeat lines below this number of times
 &lt;path and prefix of files&gt;
 &lt;nlon&gt;, &lt;nlat&gt;, &lt;dx&gt;, &lt;dy&gt;, &lt;xmin&gt;, &lt;ymin&gt;
 &lt;number of variables&gt;
 &lt;list of variable names&gt;
 &lt;list of update frequencies (seconds) or scalar values if flag=4&gt;
 &lt;list of variable flags&gt;
-</pre>
-    <p>The variables in the third row are defined as follows:</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+</pre
+          >
+          <p>The variables in the third row are defined as follows:</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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diff --git a/models/ed/docs/reference/read_ed_veg.html b/models/ed/docs/reference/read_ed_veg.html
index 9569515..2003d15 100644
--- a/models/ed/docs/reference/read_ed_veg.html
+++ b/models/ed/docs/reference/read_ed_veg.html
@@ -2,177 +2,240 @@
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 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read ED2 vegetation inputs</h1>
-    
-    <div class="hidden name"><code>read_ed_veg.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read ED2 vegetation inputs</h1>
 
-    <div class="ref-description">
-    
-    <p>Read ED2 css, pss, and site files into a single ED input object.</p>
-    
-    </div>
+            <div class="hidden name"><code>read_ed_veg.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>read_ed_veg</span>(<span class='no'>path_prefix</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>
+              Read ED2 css, pss, and site files into a single ED input object.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_ed_veg</span>(<span class='no'>path_prefix</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>path_prefix</th>
-      <td><p>Full path and prefix to initial condition files.</p></td>
-    </tr>
-    <tr>
-      <th>latitude</th>
-      <td><p>Run latitude (default = <code>NULL</code>). If <code>NULL</code>, deduced from file name.</p></td>
-    </tr>
-    <tr>
-      <th>longitude</th>
-      <td><p>Run longitude (default = <code>NULL</code>). If <code>NULL</code>, deduced from file name.</p></td>
-    </tr>
-    <tr>
-      <th>check</th>
-      <td><p>Whether or not to check css, pss, and site files for validity.
-Default = <code>TRUE</code>.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>List containing <code>css</code>, <code>pss</code>, and <code>site</code> objects, <code>latitude</code> and
-<code>longitude</code>, and <code>orig_paths</code>, a list of paths to the original <code>css</code>, <code>pss</code>,
-and <code>site</code> files.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>path_prefix</th>
+              <td><p>Full path and prefix to initial condition files.</p></td>
+            </tr>
+            <tr>
+              <th>latitude</th>
+              <td>
+                <p>
+                  Run latitude (default = <code>NULL</code>). If
+                  <code>NULL</code>, deduced from file name.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>longitude</th>
+              <td>
+                <p>
+                  Run longitude (default = <code>NULL</code>). If
+                  <code>NULL</code>, deduced from file name.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>check</th>
+              <td>
+                <p>
+                  Whether or not to check css, pss, and site files for validity.
+                  Default = <code>TRUE</code>.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            List containing <code>css</code>, <code>pss</code>, and
+            <code>site</code> objects, <code>latitude</code> and
+            <code>longitude</code>, and <code>orig_paths</code>, a list of paths
+            to the original <code>css</code>, <code>pss</code>, and
+            <code>site</code> files.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/models/ed/docs/reference/read_restart.ED2.html b/models/ed/docs/reference/read_restart.ED2.html
index 569cacb..bb339ac 100644
--- a/models/ed/docs/reference/read_restart.ED2.html
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>State data assimilation read-restart for ED2</h1>
-    
-    <div class="hidden name"><code>read_restart.ED2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>State data assimilation read-restart for ED2</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_restart.ED2</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>, <span class='no'>var.names</span>, <span class='no'>params</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Output directory</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>Run ID</p></td>
-    </tr>
-    <tr>
-      <th>stop.time</th>
-      <td><p>Year that is being read</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>var.names</th>
-      <td><p>Variable names to be extracted</p></td>
-    </tr>
-    <tr>
-      <th>params</th>
-      <td><p>Any parameters required for state calculations</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>State data assimilation read-restart for ED2</h1>
+
+            <div class="hidden name"><code>read_restart.ED2.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>State data assimilation read-restart for ED2</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_restart.ED2</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>, <span class='no'>var.names</span>, <span class='no'>params</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Output directory</p></td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>Run ID</p></td>
+            </tr>
+            <tr>
+              <th>stop.time</th>
+              <td><p>Year that is being read</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>var.names</th>
+              <td><p>Variable names to be extracted</p></td>
+            </tr>
+            <tr>
+              <th>params</th>
+              <td><p>Any parameters required for state calculations</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='no'>outdir</span> <span class='kw'>&lt;-</span> <span class='st'>"~/sda-hackathon/outputs"</span>
   <span class='no'>runid</span> <span class='kw'>&lt;-</span> <span class='st'>"99000000020"</span>
   <span class='no'>settings_file</span> <span class='kw'>&lt;-</span> <span class='st'>"outputs/pecan.CONFIGS.xml"</span>
@@ -157,36 +208,32 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov, Istem Fer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Alexey Shiklomanov, Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/remove.config.ED2.html b/models/ed/docs/reference/remove.config.ED2.html
index 838ccef..b995096 100644
--- a/models/ed/docs/reference/remove.config.ED2.html
+++ b/models/ed/docs/reference/remove.config.ED2.html
@@ -2,155 +2,195 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Clear out old config and ED model run files. — remove.config.ED2 •
+      PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Clear out old config and ED model run files. — remove.config.ED2"
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+      content="Clear out old config and ED model run files."
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
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-    <span class="caret"></span>
-  </a>
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-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
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-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Clear out old config and ED model run files.</h1>
-    
-    <div class="hidden name"><code>remove.config.ED2.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Clear out old config and ED model run files.</h1>
 
-    <div class="ref-description">
-    
-    <p>Clear out old config and ED model run files.</p>
-    
-    </div>
+            <div class="hidden name"><code>remove.config.ED2.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>remove.config.ED2</span>(<span class='kw'>main.outdir</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>outdir</span>, <span class='no'>settings</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <div class="ref-description">
+            <p>Clear out old config and ED model run files.</p>
+          </div>
 
-    <p>nothing, removes config files as side effect</p>
-    
+          <pre
+            class="usage"
+          ><span class='fu'>remove.config.ED2</span>(<span class='kw'>main.outdir</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>outdir</span>, <span class='no'>settings</span>)</pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing, removes config files as side effect</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, David LeBauer, Alexey Shikomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, David LeBauer, Alexey Shikomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/run_ed_singularity.html b/models/ed/docs/reference/run_ed_singularity.html
index f1258c1..3cdf0cf 100644
--- a/models/ed/docs/reference/run_ed_singularity.html
+++ b/models/ed/docs/reference/run_ed_singularity.html
@@ -2,187 +2,267 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Run ED singularity container — run_ed_singularity • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Run ED singularity container</h1>
-    
-    <div class="hidden name"><code>run_ed_singularity.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Uses <a href='http://www.rdocumentation.org/packages/base/topics/system2'>base::system2</a> to run ED or EDR via a Singularity container.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>run_ed_singularity</span>(<span class='no'>img_path</span>, <span class='no'>ed2in_path</span>, <span class='kw'>app</span> <span class='kw'>=</span> <span class='st'>"ED"</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Run ED singularity container</h1>
+
+            <div class="hidden name"><code>run_ed_singularity.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Uses
+              <a
+                href="http://www.rdocumentation.org/packages/base/topics/system2"
+                >base::system2</a
+              >
+              to run ED or EDR via a Singularity container.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>run_ed_singularity</span>(<span class='no'>img_path</span>, <span class='no'>ed2in_path</span>, <span class='kw'>app</span> <span class='kw'>=</span> <span class='st'>"ED"</span>,
   <span class='kw'>singularity_args</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>img_path</th>
-      <td><p>Path to Singularity container (usually a <code>.simg</code> file)</p></td>
-    </tr>
-    <tr>
-      <th>ed2in_path</th>
-      <td><p>Path to ED2IN file.</p></td>
-    </tr>
-    <tr>
-      <th>app</th>
-      <td><p>Singularity "app" to run. Either "ED" or "EDR".</p></td>
-    </tr>
-    <tr>
-      <th>singularity_args</th>
-      <td><p>Additional arguments to be passed to <code>singularity run</code> (before)</p></td>
-    </tr>
-    <tr>
-      <th>Additional</th>
-      <td><p>arguments to <a href='http://www.rdocumentation.org/packages/base/topics/system2'>base::system2</a></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>On some systems, to run Singularity properly, you will need to bind
-additional paths. To do this, pass the arguments as a character vector to
-<code>singularity_args</code>. For instance:</p><pre>bindpaths &lt;- c("/scratch", "/data")
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>img_path</th>
+              <td>
+                <p>
+                  Path to Singularity container (usually a
+                  <code>.simg</code> file)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ed2in_path</th>
+              <td><p>Path to ED2IN file.</p></td>
+            </tr>
+            <tr>
+              <th>app</th>
+              <td><p>Singularity "app" to run. Either "ED" or "EDR".</p></td>
+            </tr>
+            <tr>
+              <th>singularity_args</th>
+              <td>
+                <p>
+                  Additional arguments to be passed to
+                  <code>singularity run</code> (before)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>Additional</th>
+              <td>
+                <p>
+                  arguments to
+                  <a
+                    href="http://www.rdocumentation.org/packages/base/topics/system2"
+                    >base::system2</a
+                  >
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            On some systems, to run Singularity properly, you will need to bind
+            additional paths. To do this, pass the arguments as a character
+            vector to <code>singularity_args</code>. For instance:
+          </p>
+          <pre>
+bindpaths &lt;- c("/scratch", "/data")
 run_ed_singularity(..., singularity_args = paste("--bind", bindpaths))
-</pre>
-    <p>By default, <a href='http://www.rdocumentation.org/packages/base/topics/system2'>base::system2</a> prints the output to the console. To store
-standard ED output in a variable as a character vector, set <code>stdout = TRUE</code>.
-To redirect all output to the variable, including GCC exceptions, use
-<code>stderr = TRUE</code> (this will automatically set <code>stdout = TRUE</code> as well).
-Output can also be redirected to a file via <code>stderr = "/path/to/file.log"</code>.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+</pre
+          >
+          <p>
+            By default,
+            <a href="http://www.rdocumentation.org/packages/base/topics/system2"
+              >base::system2</a
+            >
+            prints the output to the console. To store standard ED output in a
+            variable as a character vector, set <code>stdout = TRUE</code>. To
+            redirect all output to the variable, including GCC exceptions, use
+            <code>stderr = TRUE</code> (this will automatically set
+            <code>stdout = TRUE</code> as well). Output can also be redirected
+            to a file via <code>stderr = "/path/to/file.log"</code>.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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diff --git a/models/ed/docs/reference/tags2char.html b/models/ed/docs/reference/tags2char.html
index 8b9a5cb..ce2e787 100644
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+    />
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+    />
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Format ED2IN tag-value list</h1>
-    
-    <div class="hidden name"><code>tags2char.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Converts an <code>ed2in</code>-like list to an ED2IN-formatted character vector.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>tags2char</span>(<span class='no'>ed2in</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ed2in</th>
-      <td><p>Named list of ED2IN tag-value pairs. See <a href='read_ed2in.html'>read_ed2in</a>.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Format ED2IN tag-value list</h1>
+
+            <div class="hidden name"><code>tags2char.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Converts an <code>ed2in</code>-like list to an ED2IN-formatted
+              character vector.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>tags2char</span>(<span class='no'>ed2in</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ed2in</th>
+              <td>
+                <p>
+                  Named list of ED2IN tag-value pairs. See
+                  <a href="read_ed2in.html">read_ed2in</a>.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/translate_vars_ed.html b/models/ed/docs/reference/translate_vars_ed.html
index 48c94f7..8581a5b 100644
--- a/models/ed/docs/reference/translate_vars_ed.html
+++ b/models/ed/docs/reference/translate_vars_ed.html
@@ -2,150 +2,188 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function translating pecan vars to ED vars
-var.names &lt;- c("DBH", "AGB", "AbvGrndWood") — translate_vars_ed • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
-<!-- clipboard.js -->
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-
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-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Function translating pecan vars to ED vars
-var.names &lt;- c("DBH", "AGB", "AbvGrndWood") — translate_vars_ed" />
-
-<meta property="og:description" content="Function translating pecan vars to ED vars
-var.names &amp;lt;- c(&quot;DBH&quot;, &quot;AGB&quot;, &quot;AbvGrndWood&quot;)" />
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-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Function translating pecan vars to ED vars var.names &lt;- c("DBH", "AGB",
+      "AbvGrndWood") — translate_vars_ed • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Function translating pecan vars to ED
+    vars var.names &lt;- c("DBH", "AGB", "AbvGrndWood") — translate_vars_ed" />
+
+    <meta
+      property="og:description"
+      content='Function translating pecan vars to ED vars
+var.names &amp;lt;- c("DBH", "AGB", "AbvGrndWood")'
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function translating pecan vars to ED vars
-var.names &lt;- c("DBH", "AGB", "AbvGrndWood")</h1>
-    
-    <div class="hidden name"><code>translate_vars_ed.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function translating pecan vars to ED vars
-var.names &lt;- c("DBH", "AGB", "AbvGrndWood")</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>translate_vars_ed</span>(<span class='no'>varnames</span>)</pre>
-        
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function translating pecan vars to ED vars var.names &lt;-
+              c("DBH", "AGB", "AbvGrndWood")
+            </h1>
+
+            <div class="hidden name"><code>translate_vars_ed.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function translating pecan vars to ED vars var.names &lt;-
+              c("DBH", "AGB", "AbvGrndWood")
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>translate_vars_ed</span>(<span class='no'>varnames</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
-
diff --git a/models/ed/docs/reference/veg2model.ED2.html b/models/ed/docs/reference/veg2model.ED2.html
index 0d0e710..15603ec 100644
--- a/models/ed/docs/reference/veg2model.ED2.html
+++ b/models/ed/docs/reference/veg2model.ED2.html
@@ -2,165 +2,205 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
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-
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-<![endif]-->
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+    <meta charset="utf-8" />
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
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+      crossorigin="anonymous"
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+    <![endif]-->
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-        
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
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+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Writes ED specific IC files</h1>
-    
-    <div class="hidden name"><code>veg2model.ED2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes ED specific IC files</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>veg2model.ED2</span>(<span class='no'>outfolder</span>, <span class='no'>veg_info</span>, <span class='no'>start_date</span>, <span class='no'>new_site</span>, <span class='no'>source</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>where to write files</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>filenames</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Writes ED specific IC files</h1>
+
+            <div class="hidden name"><code>veg2model.ED2.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes ED specific IC files</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>veg2model.ED2</span>(<span class='no'>outfolder</span>, <span class='no'>veg_info</span>, <span class='no'>start_date</span>, <span class='no'>new_site</span>, <span class='no'>source</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>where to write files</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>filenames</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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-   </div>
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   </body>
 </html>
-
diff --git a/models/ed/docs/reference/write.config.ED2.html b/models/ed/docs/reference/write.config.ED2.html
index 634755a..f4ea822 100644
--- a/models/ed/docs/reference/write.config.ED2.html
+++ b/models/ed/docs/reference/write.config.ED2.html
@@ -2,187 +2,244 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Write ED configuration files — write.config.ED2 • PEcAn.ED2</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
+    <!-- sticky kit -->
+    <script
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+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
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+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write ED configuration files — write.config.ED2"
+    />
+
+    <meta
+      property="og:description"
+      content="Writes an xml and ED2IN config files for use with the Ecological Demography
 model. Requires a pft xml object, a list of trait values for a single model
-run, and the name of the file to create" />
-<meta name="twitter:card" content="summary" />
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+run, and the name of the file to create"
+    />
+    <meta name="twitter:card" content="summary" />
 
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-        
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write ED configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.ED2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes an xml and ED2IN config files for use with the Ecological Demography
-model. Requires a pft xml object, a list of trait values for a single model
-run, and the name of the file to create</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.ED2</span>(<span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write ED configuration files</h1>
+
+            <div class="hidden name"><code>write.config.ED2.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Writes an xml and ED2IN config files for use with the Ecological
+              Demography model. Requires a pft xml object, a list of trait
+              values for a single model run, and the name of the file to create
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.ED2</span>(<span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>,
   <span class='kw'>defaults</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>constants</span>, <span class='kw'>check</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.values</th>
-      <td><p>Named list of trait values, with names corresponding to PFT</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process. Default=settings$constants</p></td>
-    </tr>
-    <tr>
-      <th>check</th>
-      <td><p>Logical. If <code>TRUE</code>, check ED2IN validity before running and
-throw an error if anything is wrong (default = <code>FALSE</code>)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file and ED2IN namelist for given run</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.values</th>
+              <td>
+                <p>
+                  Named list of trait values, with names corresponding to PFT
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>defaults</th>
+              <td>
+                <p>list of defaults to process. Default=settings$constants</p>
+              </td>
+            </tr>
+            <tr>
+              <th>check</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code>, check ED2IN validity before
+                  running and throw an error if anything is wrong (default =
+                  <code>FALSE</code>)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file and ED2IN namelist for given run</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov, Istem
+          Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/write.config.jobsh.ED2.html b/models/ed/docs/reference/write.config.jobsh.ED2.html
index 8a89e22..b4e4d22 100644
--- a/models/ed/docs/reference/write.config.jobsh.ED2.html
+++ b/models/ed/docs/reference/write.config.jobsh.ED2.html
@@ -2,179 +2,235 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Write ED2 config.xml file — write.config.jobsh.ED2 • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Write ED2 config.xml file — write.config.jobsh.ED2" />
-
-<meta property="og:description" content="Function for writing job.sh file for ED2 runs" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Write ED2 config.xml file — write.config.jobsh.ED2 • PEcAn.ED2
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write ED2 config.xml file — write.config.jobsh.ED2"
+    />
+
+    <meta
+      property="og:description"
+      content="Function for writing job.sh file for ED2 runs"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-  <a href="../reference/index.html">Reference</a>
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-    Articles
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-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
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-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write ED2 config.xml file</h1>
-    
-    <div class="hidden name"><code>write.config.jobsh.ED2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function for writing job.sh file for ED2 runs</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.jobsh.ED2</span>(<span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings list. For this function, need the following:
-run$host$rundir, run$host$outdir, run$host$scratchdir,
-run$host$clearscratch, model$jobtemplate, model$job.sh, run$host$job.sh,
-run$site$lat, run$site$lon, run$inputs$met$path, run$start.date,
-run$end.date, model$binary</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>PEcAn run ID</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Character vector containing job.sh file</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Refactored by Alexey Shiklomanov to allow use in PEcAn RTM module.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write ED2 config.xml file</h1>
+
+            <div class="hidden name">
+              <code>write.config.jobsh.ED2.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Function for writing job.sh file for ED2 runs</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.jobsh.ED2</span>(<span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  PEcAn settings list. For this function, need the following:
+                  run$host$rundir, run$host$outdir, run$host$scratchdir,
+                  run$host$clearscratch, model$jobtemplate, model$job.sh,
+                  run$host$job.sh, run$site$lat, run$site$lon,
+                  run$inputs$met$path, run$start.date, run$end.date,
+                  model$binary
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>PEcAn run ID</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Character vector containing job.sh file</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Refactored by Alexey Shiklomanov to allow use in PEcAn RTM module.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/write.config.xml.ED2.html b/models/ed/docs/reference/write.config.xml.ED2.html
index 637f889..80e7806 100644
--- a/models/ed/docs/reference/write.config.xml.ED2.html
+++ b/models/ed/docs/reference/write.config.xml.ED2.html
@@ -2,180 +2,233 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Write ED2 config.xml file — write.config.xml.ED2 • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Write ED2 config.xml file — write.config.xml.ED2" />
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-<meta name="twitter:card" content="summary" />
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-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Write ED2 config.xml file — write.config.xml.ED2 • PEcAn.ED2</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write ED2 config.xml file — write.config.xml.ED2"
+    />
+
+    <meta property="og:description" content="Write ED2 config.xml file" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write ED2 config.xml file</h1>
-    
-    <div class="hidden name"><code>write.config.xml.ED2.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write ED2 config.xml file</h1>
 
-    <div class="ref-description">
-    
-    <p>Write ED2 config.xml file</p>
-    
-    </div>
+            <div class="hidden name"><code>write.config.xml.ED2.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Write ED2 config.xml file</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>write.config.xml.ED2</span>(<span class='no'>settings</span>, <span class='no'>trait.values</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.xml.ED2</span>(<span class='no'>settings</span>, <span class='no'>trait.values</span>,
   <span class='kw'>defaults</span> <span class='kw'>=</span> <span class='no'>settings</span>$<span class='no'>constants</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings file. Settings required for this script are: model$revision, model$config.header, constants</p></td>
-    </tr>
-    <tr>
-      <th>trait.values</th>
-      <td><p>List of trait values with which to replace defaults</p></td>
-    </tr>
-    <tr>
-      <th>defaults</th>
-      <td><p>List of defaults to process. Default = settings$constants</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>R XML object containing full ED2 XML file</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Refactored by Alexey Shiklomanov to allow use in PEcAn RTM module.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  PEcAn settings file. Settings required for this script are:
+                  model$revision, model$config.header, constants
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>trait.values</th>
+              <td>
+                <p>List of trait values with which to replace defaults</p>
+              </td>
+            </tr>
+            <tr>
+              <th>defaults</th>
+              <td>
+                <p>List of defaults to process. Default = settings$constants</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>R XML object containing full ED2 XML file</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Refactored by Alexey Shiklomanov to allow use in PEcAn RTM module.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin, Carl Davidson, Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/write_css.html b/models/ed/docs/reference/write_css.html
index b32cb18..d85cc52 100644
--- a/models/ed/docs/reference/write_css.html
+++ b/models/ed/docs/reference/write_css.html
@@ -2,194 +2,258 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Write individual ED inputs — write_css • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-
-<meta property="og:title" content="Write individual ED inputs — write_css" />
-
-<meta property="og:description" content="Functions for writing css, pss, and site files from their respective objects." />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Write individual ED inputs — write_css • PEcAn.ED2</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write individual ED inputs — write_css"
+    />
+
+    <meta
+      property="og:description"
+      content="Functions for writing css, pss, and site files from their respective objects."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write individual ED inputs</h1>
-    
-    <div class="hidden name"><code>write_css.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write individual ED inputs</h1>
 
-    <div class="ref-description">
-    
-    <p>Functions for writing css, pss, and site files from their respective objects.</p>
-    
-    </div>
+            <div class="hidden name"><code>write_css.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>write_css</span>(<span class='no'>css</span>, <span class='no'>path_prefix</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
+          <div class="ref-description">
+            <p>
+              Functions for writing css, pss, and site files from their
+              respective objects.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write_css</span>(<span class='no'>css</span>, <span class='no'>path_prefix</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
 
 <span class='fu'>write_pss</span>(<span class='no'>pss</span>, <span class='no'>path_prefix</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
 
 <span class='fu'>write_site</span>(<span class='no'>site</span>, <span class='no'>path_prefix</span>, <span class='kw'>latitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>longitude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>css</th>
-      <td><p>css object (see <a href='read_css.html'>read_css</a>)</p></td>
-    </tr>
-    <tr>
-      <th>path_prefix</th>
-      <td><p>Desired path and prefix (without latitude and longitude)</p></td>
-    </tr>
-    <tr>
-      <th>latitude</th>
-      <td><p>Site latitude coordinate (default = <code>NULL</code>)</p></td>
-    </tr>
-    <tr>
-      <th>longitude</th>
-      <td><p>Site longitude coordinate (default = <code>NULL</code>)</p></td>
-    </tr>
-    <tr>
-      <th>pss</th>
-      <td><p>pss object (see <a href='read_css.html'>read_pss</a>)</p></td>
-    </tr>
-    <tr>
-      <th>site</th>
-      <td><p>site object (see <a href='read_css.html'>read_site</a>)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Full file path as character, invisibly</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Latitude and longitude coordinates will be converted directly to character,
-without any changes to their precision. If they are <code>NULL</code> (default), the
-function assumes that <code>lat</code> and <code>lon</code> are already in the <code>path_prefix</code>, and
-if they are absent, the function will throw an error.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>css</th>
+              <td>
+                <p>css object (see <a href="read_css.html">read_css</a>)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>path_prefix</th>
+              <td>
+                <p>Desired path and prefix (without latitude and longitude)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>latitude</th>
+              <td>
+                <p>Site latitude coordinate (default = <code>NULL</code>)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>longitude</th>
+              <td>
+                <p>Site longitude coordinate (default = <code>NULL</code>)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>pss</th>
+              <td>
+                <p>pss object (see <a href="read_css.html">read_pss</a>)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>site</th>
+              <td>
+                <p>site object (see <a href="read_css.html">read_site</a>)</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Full file path as character, invisibly</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Latitude and longitude coordinates will be converted directly to
+            character, without any changes to their precision. If they are
+            <code>NULL</code> (default), the function assumes that
+            <code>lat</code> and <code>lon</code> are already in the
+            <code>path_prefix</code>, and if they are absent, the function will
+            throw an error.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
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 </html>
-
diff --git a/models/ed/docs/reference/write_ed2in.html b/models/ed/docs/reference/write_ed2in.html
index 9df6707..407acc1 100644
--- a/models/ed/docs/reference/write_ed2in.html
+++ b/models/ed/docs/reference/write_ed2in.html
@@ -2,126 +2,171 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Write ED2IN list to file — write_ed2in • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Write ED2IN list to file — write_ed2in" />
-
-<meta property="og:description" content="This writes a ED2IN file from an ed2in list. Default method writes a
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Write ED2IN list to file — write_ed2in • PEcAn.ED2</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write ED2IN list to file — write_ed2in"
+    />
+
+    <meta
+      property="og:description"
+      content="This writes a ED2IN file from an ed2in list. Default method writes a
 barebones file without comments. S3 method for ed2in objects extracts
 comments and their locations from the object attributes (if barebones is
-FALSE)." />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+FALSE)."
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
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-    <span class="caret"></span>
-  </a>
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-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
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-      <ul class="nav navbar-nav navbar-right">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write ED2IN list to file</h1>
-    
-    <div class="hidden name"><code>write_ed2in.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This writes a ED2IN file from an <code>ed2in</code> list. Default method writes a
-barebones file without comments. S3 method for <code>ed2in</code> objects extracts
-comments and their locations from the object attributes (if <code>barebones</code> is
-<code>FALSE</code>).</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write_ed2in</span>(<span class='no'>ed2in</span>, <span class='no'>filename</span>, <span class='kw'>custom_header</span> <span class='kw'>=</span> <span class='fu'>character</span>(),
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write ED2IN list to file</h1>
+
+            <div class="hidden name"><code>write_ed2in.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This writes a ED2IN file from an <code>ed2in</code> list. Default
+              method writes a barebones file without comments. S3 method for
+              <code>ed2in</code> objects extracts comments and their locations
+              from the object attributes (if <code>barebones</code> is
+              <code>FALSE</code>).
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write_ed2in</span>(<span class='no'>ed2in</span>, <span class='no'>filename</span>, <span class='kw'>custom_header</span> <span class='kw'>=</span> <span class='fu'>character</span>(),
   <span class='kw'>barebones</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
 
 <span class='co'># S3 method for ed2in</span>
@@ -131,54 +176,67 @@ <h1>Write ED2IN list to file</h1>
 <span class='co'># S3 method for default</span>
 <span class='fu'>write_ed2in</span>(<span class='no'>ed2in</span>, <span class='no'>filename</span>,
   <span class='kw'>custom_header</span> <span class='kw'>=</span> <span class='fu'>character</span>(), <span class='kw'>barebones</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ed2in</th>
-      <td><p>Named list of ED2IN tag-value pairs. See <a href='read_ed2in.html'>read_ed2in</a>.</p></td>
-    </tr>
-    <tr>
-      <th>filename</th>
-      <td><p>Target file name</p></td>
-    </tr>
-    <tr>
-      <th>custom_header</th>
-      <td><p>Character vector for additional header comments. Each
-item gets its own line.</p></td>
-    </tr>
-    <tr>
-      <th>barebones</th>
-      <td><p>Logical. If <code>TRUE</code>, omit comments and only write tag-value pairs.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ed2in</th>
+              <td>
+                <p>
+                  Named list of ED2IN tag-value pairs. See
+                  <a href="read_ed2in.html">read_ed2in</a>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>filename</th>
+              <td><p>Target file name</p></td>
+            </tr>
+            <tr>
+              <th>custom_header</th>
+              <td>
+                <p>
+                  Character vector for additional header comments. Each item
+                  gets its own line.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>barebones</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code>, omit comments and only write
+                  tag-value pairs.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/write_ed_metheader.html b/models/ed/docs/reference/write_ed_metheader.html
index 6554df8..1a72877 100644
--- a/models/ed/docs/reference/write_ed_metheader.html
+++ b/models/ed/docs/reference/write_ed_metheader.html
@@ -2,165 +2,215 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<script src="../pkgdown.js"></script>
-
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-
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-<meta name="twitter:card" content="summary" />
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Write ED meteorlogy header — write_ed_metheader"
+    />
+
+    <meta
+      property="og:description"
+      content="Write ED met driver header from R met driver list object"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../index.html">
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-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
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-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write ED meteorlogy header</h1>
-    
-    <div class="hidden name"><code>write_ed_metheader.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write ED meteorlogy header</h1>
 
-    <div class="ref-description">
-    
-    <p>Write ED met driver header from R met driver list object</p>
-    
-    </div>
+            <div class="hidden name"><code>write_ed_metheader.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>write_ed_metheader</span>(<span class='no'>ed_metheader</span>, <span class='no'>filename</span>,
-  <span class='kw'>header_line</span> <span class='kw'>=</span> <span class='fu'>shQuote</span>(<span class='st'>"header"</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ed_metheader</th>
-      <td><p>ED meteorlogy header object (see <a href='read_ed_metheader.html'>read_ed_metheader</a>)</p></td>
-    </tr>
-    <tr>
-      <th>filename</th>
-      <td><p>Full file name (including path) of ED met header</p></td>
-    </tr>
-    <tr>
-      <th>header_line</th>
-      <td><p>Character string for top line of output file. Default is
-<code>'header'</code>.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Write ED met driver header from R met driver list object</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>write_ed_metheader</span>(<span class='no'>ed_metheader</span>, <span class='no'>filename</span>,
+  <span class='kw'>header_line</span> <span class='kw'>=</span> <span class='fu'>shQuote</span>(<span class='st'>"header"</span>))</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ed_metheader</th>
+              <td>
+                <p>
+                  ED meteorlogy header object (see
+                  <a href="read_ed_metheader.html">read_ed_metheader</a>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>filename</th>
+              <td><p>Full file name (including path) of ED met header</p></td>
+            </tr>
+            <tr>
+              <th>header_line</th>
+              <td>
+                <p>
+                  Character string for top line of output file. Default is
+                  <code>'header'</code>.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/write_ed_veg.html b/models/ed/docs/reference/write_ed_veg.html
index d0f353e..ed445e0 100644
--- a/models/ed/docs/reference/write_ed_veg.html
+++ b/models/ed/docs/reference/write_ed_veg.html
@@ -2,167 +2,224 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Write ED inputs to directory — write_ed_veg • PEcAn.ED2</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Write ED inputs to directory — write_ed_veg" />
-
-<meta property="og:description" content="Write a complete ED inputs object to disk. css, pss, and
-site files are automatically named and correctly formatted." />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Write ED inputs to directory — write_ed_veg • PEcAn.ED2</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write ED inputs to directory — write_ed_veg"
+    />
+
+    <meta
+      property="og:description"
+      content="Write a complete ED inputs object to disk. css, pss, and
+site files are automatically named and correctly formatted."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-
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-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/running_ed_from_R.html">Running ED from R</a>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ED2</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write ED inputs to directory</h1>
-    
-    <div class="hidden name"><code>write_ed_veg.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Write a complete <a href='read_ed_veg.html'>ED inputs object</a> to disk. <code>css</code>, <code>pss</code>, and
-<code>site</code> files are automatically named and correctly formatted.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write_ed_veg</span>(<span class='no'>ed_veg</span>, <span class='no'>path_prefix</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ed_veg</th>
-      <td><p>ED vegetation inputs object (see <a href='read_ed_veg.html'>read_ed_veg</a>).</p></td>
-    </tr>
-    <tr>
-      <th>path_prefix</th>
-      <td><p>Desired path and prefix (without latitude and longitude)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Named list (<code>css</code>, <code>pss</code>, <code>site</code>) of full file paths, invisibly</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write ED inputs to directory</h1>
+
+            <div class="hidden name"><code>write_ed_veg.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Write a complete
+              <a href="read_ed_veg.html">ED inputs object</a> to disk.
+              <code>css</code>, <code>pss</code>, and <code>site</code> files
+              are automatically named and correctly formatted.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write_ed_veg</span>(<span class='no'>ed_veg</span>, <span class='no'>path_prefix</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ed_veg</th>
+              <td>
+                <p>
+                  ED vegetation inputs object (see
+                  <a href="read_ed_veg.html">read_ed_veg</a>).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>path_prefix</th>
+              <td>
+                <p>Desired path and prefix (without latitude and longitude)</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Named list (<code>css</code>, <code>pss</code>, <code>site</code>)
+            of full file paths, invisibly
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/ed/docs/reference/write_restart.ED2.html b/models/ed/docs/reference/write_restart.ED2.html
index 7ede955..9cbf89f 100644
--- a/models/ed/docs/reference/write_restart.ED2.html
+++ b/models/ed/docs/reference/write_restart.ED2.html
@@ -2,198 +2,256 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Write ED2 restart file from SDA results — write_restart.ED2 • PEcAn.ED2</title>
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+                  >1.6.0</span
+                >
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+                      <a href="../articles/running_ed_from_R.html"
+                        >Running ED from R</a
+                      >
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write ED2 restart file from SDA results</h1>
-    
-    <div class="hidden name"><code>write_restart.ED2.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write ED2 restart file from SDA results</h1>
 
-    <div class="ref-description">
-    
-    <p>Write ED2 restart file from SDA results</p>
-    
-    </div>
+            <div class="hidden name"><code>write_restart.ED2.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Write ED2 restart file from SDA results</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>write_restart.ED2</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>write_restart.ED2</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
   <span class='no'>new.state</span>, <span class='kw'>RENAME</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>new.params</span>, <span class='no'>inputs</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>outout directory</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>run id</p></td>
-    </tr>
-    <tr>
-      <th>start.time</th>
-      <td><p>Time of current assimilation step</p></td>
-    </tr>
-    <tr>
-      <th>stop.time</th>
-      <td><p>Time of next assimilation step</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>pecan settings list</p></td>
-    </tr>
-    <tr>
-      <th>new.state</th>
-      <td><p>Analysis state matrix returned by <code>sda.enkf</code></p></td>
-    </tr>
-    <tr>
-      <th>RENAME</th>
-      <td><p>flag to either rename output file or not</p></td>
-    </tr>
-    <tr>
-      <th>new.params</th>
-      <td><p>optional, additionals params to pass write.configs that are deterministically related to the parameters updated by the analysis</p></td>
-    </tr>
-    <tr>
-      <th>inputs</th>
-      <td><p>new input paths updated by the SDA workflow, will be passed to write.configs</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>TRUE if successful</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>outout directory</p></td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>run id</p></td>
+            </tr>
+            <tr>
+              <th>start.time</th>
+              <td><p>Time of current assimilation step</p></td>
+            </tr>
+            <tr>
+              <th>stop.time</th>
+              <td><p>Time of next assimilation step</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>pecan settings list</p></td>
+            </tr>
+            <tr>
+              <th>new.state</th>
+              <td>
+                <p>Analysis state matrix returned by <code>sda.enkf</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>RENAME</th>
+              <td><p>flag to either rename output file or not</p></td>
+            </tr>
+            <tr>
+              <th>new.params</th>
+              <td>
+                <p>
+                  optional, additionals params to pass write.configs that are
+                  deterministically related to the parameters updated by the
+                  analysis
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>inputs</th>
+              <td>
+                <p>
+                  new input paths updated by the SDA workflow, will be passed to
+                  write.configs
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>TRUE if successful</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov, Istem Fer
+        </div>
+      </div>
 
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index 5fdc3e9..761284a 100644
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-    <div class="page-header">
-    <h1>Imports from other packages</h1>
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-    
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+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Imports from other packages</h1>
 
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+            <div class="hidden name"><code>zz.imports.Rd</code></div>
+          </div>
 
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-</div>
+          <div class="ref-description">
+            <p>Imports from other packages</p>
+          </div>
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+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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diff --git a/models/fates/docs/LICENSE-text.html b/models/fates/docs/LICENSE-text.html
index f08c9b9..a33e2e7 100644
--- a/models/fates/docs/LICENSE-text.html
+++ b/models/fates/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.FATES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
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+                  >1.6.0</span
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+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
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diff --git a/models/fates/docs/authors.html b/models/fates/docs/authors.html
index 9fcdacf..381401a 100644
--- a/models/fates/docs/authors.html
+++ b/models/fates/docs/authors.html
@@ -2,122 +2,143 @@
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+            <div class="navbar-header">
+              <button
+                type="button"
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+                data-target="#navbar"
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+                <span class="icon-bar"></span>
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.FATES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
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+                  >1.6.0</span
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-<div class="row">
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-
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-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
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-    </ul>
-
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-
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+      <div class="row">
+        <div class="contents col-md-9">
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+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/fates/docs/docsearch.css b/models/fates/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/fates/docs/docsearch.css
+++ b/models/fates/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/fates/docs/docsearch.js b/models/fates/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/fates/docs/docsearch.js
+++ b/models/fates/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/fates/docs/index.html b/models/fates/docs/index.html
index d58afef..a83ceca 100644
--- a/models/fates/docs/index.html
+++ b/models/fates/docs/index.html
@@ -1,113 +1,168 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of FATES model • PEcAn.FATES</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of FATES model">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn package for integration of FATES model • PEcAn.FATES</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of FATES model"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation. This package provides functions to
-    link the FATES model to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    link the FATES model to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.FATES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation. This package provides functions to
-    link the FATES model to PEcAn.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
-
-  </div>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.FATES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation. This package
+          provides functions to link the FATES model to PEcAn.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/fates/docs/pkgdown.css b/models/fates/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/fates/docs/pkgdown.css
+++ b/models/fates/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/fates/docs/pkgdown.js b/models/fates/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/fates/docs/pkgdown.js
+++ b/models/fates/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/fates/docs/reference/index.html b/models/fates/docs/reference/index.html
index cdd9c25..557823e 100644
--- a/models/fates/docs/reference/index.html
+++ b/models/fates/docs/reference/index.html
@@ -2,162 +2,213 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.FATES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.FATES</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Function reference" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.FATES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.FATES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="met2model.FATES.html">met2model.FATES()</a></code> </p>
-        </td>
-        <td><p>met2model for FATES</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.FATES.html">model2netcdf.FATES()</a></code> </p>
-        </td>
-        <td><p>Code to convert FATES netcdf output into into CF standard</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="recurse.create.html">recurse.create()</a></code> </p>
-        </td>
-        <td><p>recurse.create</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.FATES.html">write.config.FATES()</a></code> </p>
-        </td>
-        <td><p>Write FATES configuration files</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.FATES.html"
+                        >met2model.FATES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2model for FATES</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.FATES.html"
+                        >model2netcdf.FATES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Code to convert FATES netcdf output into into CF standard
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="recurse.create.html">recurse.create()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>recurse.create</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.FATES.html"
+                        >write.config.FATES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write FATES configuration files</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/fates/docs/reference/met2model.FATES.html b/models/fates/docs/reference/met2model.FATES.html
index 653fb61..2f08174 100644
--- a/models/fates/docs/reference/met2model.FATES.html
+++ b/models/fates/docs/reference/met2model.FATES.html
@@ -2,172 +2,214 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>met2model for FATES — met2model.FATES • PEcAn.FATES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-<!-- clipboard.js -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="met2model for FATES — met2model.FATES" />
-
-<meta property="og:description" content="met2model wrapper for FATES" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>met2model for FATES — met2model.FATES • PEcAn.FATES</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    <meta property="og:title" content="met2model for FATES — met2model.FATES" />
+
+    <meta property="og:description" content="met2model wrapper for FATES" />
+    <meta name="twitter:card" content="summary" />
+
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.FATES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2model for FATES</h1>
-    
-    <div class="hidden name"><code>met2model.FATES.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2model for FATES</h1>
 
-    <div class="ref-description">
-    
-    <p>met2model wrapper for FATES</p>
-    
-    </div>
+            <div class="hidden name"><code>met2model.FATES.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2model.FATES</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>lst</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>lst</th>
-      <td><p>timezone offset to GMT in hours</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbosefor(year in start_year:end_year)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>met2model wrapper for FATES</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.FATES</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>lst</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lst</th>
+              <td><p>timezone offset to GMT in hours</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  should the function be very verbosefor(year in
+                  start_year:end_year)
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/fates/docs/reference/model2netcdf.FATES.html b/models/fates/docs/reference/model2netcdf.FATES.html
index 343cdd1..8a5b17b 100644
--- a/models/fates/docs/reference/model2netcdf.FATES.html
+++ b/models/fates/docs/reference/model2netcdf.FATES.html
@@ -2,121 +2,164 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Code to convert FATES netcdf output into into CF standard —
+      model2netcdf.FATES • PEcAn.FATES
+    </title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
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+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
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+    <script src="../pkgdown.js"></script>
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+      content="Code to convert FATES netcdf output into into CF standard — model2netcdf.FATES"
+    />
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+      content="Code to convert FATES netcdf output into into CF standard"
+    />
+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.FATES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Code to convert FATES netcdf output into into CF standard</h1>
-    
-    <div class="hidden name"><code>model2netcdf.FATES.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Code to convert FATES netcdf output into into CF standard</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model2netcdf.FATES</span>(<span class='no'>outdir</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of FATES model output</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"># NOT RUN {
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Code to convert FATES netcdf output into into CF standard</h1>
+
+            <div class="hidden name"><code>model2netcdf.FATES.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Code to convert FATES netcdf output into into CF standard</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.FATES</span>(<span class='no'>outdir</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of FATES model output</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"># NOT RUN {
  
 # }
 <span class='co'># NOT RUN {</span>
@@ -125,36 +168,32 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze, Shawn Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Michael Dietze, Shawn Serbin
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/models/fates/docs/reference/recurse.create.html b/models/fates/docs/reference/recurse.create.html
index 3dea97e..38fb9a2 100644
--- a/models/fates/docs/reference/recurse.create.html
+++ b/models/fates/docs/reference/recurse.create.html
@@ -2,151 +2,187 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>recurse.create — recurse.create • PEcAn.FATES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="recurse.create — recurse.create" />
-
-<meta property="og:description" content="recursively follow the file structure in 'ins' and create all the same folders in 'path' as well as symbolic links to all the file. This is done, rather than creating a symbolic link to the whole structure, so individual files can later be unlinked and replaced with different files/links." />
-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>recurse.create — recurse.create • PEcAn.FATES</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="recurse.create — recurse.create" />
+
+    <meta
+      property="og:description"
+      content="recursively follow the file structure in 'ins' and create all the same folders in 'path' as well as symbolic links to all the file. This is done, rather than creating a symbolic link to the whole structure, so individual files can later be unlinked and replaced with different files/links."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.FATES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="../reference/index.html">Reference</a>
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-</div><!--/.navbar -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.FATES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>recurse.create</h1>
-    
-    <div class="hidden name"><code>recurse.create.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>recursively follow the file structure in 'ins' and create all the same folders in 'path' as well as symbolic links to all the file. This is done, rather than creating a symbolic link to the whole structure, so individual files can later be unlinked and replaced with different files/links.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>recurse.create</span>(<span class='no'>path</span>, <span class='no'>ins</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>path</th>
-      <td><p>new location to create folders and links</p></td>
-    </tr>
-    <tr>
-      <th>ins</th>
-      <td><p>reference location of inputs</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>recurse.create</h1>
+
+            <div class="hidden name"><code>recurse.create.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              recursively follow the file structure in 'ins' and create all the
+              same folders in 'path' as well as symbolic links to all the file.
+              This is done, rather than creating a symbolic link to the whole
+              structure, so individual files can later be unlinked and replaced
+              with different files/links.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>recurse.create</span>(<span class='no'>path</span>, <span class='no'>ins</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>path</th>
+              <td><p>new location to create folders and links</p></td>
+            </tr>
+            <tr>
+              <th>ins</th>
+              <td><p>reference location of inputs</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/models/fates/docs/reference/write.config.FATES.html b/models/fates/docs/reference/write.config.FATES.html
index db2ce97..00ac74a 100644
--- a/models/fates/docs/reference/write.config.FATES.html
+++ b/models/fates/docs/reference/write.config.FATES.html
@@ -2,165 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Write FATES configuration files — write.config.FATES • PEcAn.FATES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Write FATES configuration files — write.config.FATES" />
-
-<meta property="og:description" content="Writes config files for use with FATES." />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Write FATES configuration files — write.config.FATES • PEcAn.FATES
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write FATES configuration files — write.config.FATES"
+    />
+
+    <meta
+      property="og:description"
+      content="Writes config files for use with FATES."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <a class="navbar-link" href="../index.html">PEcAn.FATES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.FATES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write FATES configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.FATES.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes config files for use with FATES.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.FATES</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>trait.values</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>none</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write FATES configuration files</h1>
+
+            <div class="hidden name"><code>write.config.FATES.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes config files for use with FATES.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.FATES</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>trait.values</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>none</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze, Shawn Serbin
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze, Shawn Serbin
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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diff --git a/models/gday/docs/LICENSE-text.html b/models/gday/docs/LICENSE-text.html
index dafa6e6..9be6e2e 100644
--- a/models/gday/docs/LICENSE-text.html
+++ b/models/gday/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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+
+    <!-- jquery -->
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-        <a class="navbar-link" href="index.html">PEcAn.GDAY</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
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-  <a href="reference/index.html">Reference</a>
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-      
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-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.GDAY</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -125,27 +154,22 @@ <h1>License</h1>
 ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/models/gday/docs/authors.html b/models/gday/docs/authors.html
index dcee5fa..5fac87d 100644
--- a/models/gday/docs/authors.html
+++ b/models/gday/docs/authors.html
@@ -2,126 +2,146 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
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-
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
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+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
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+    <![endif]-->
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-      
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.GDAY</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+                <li>
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+              </ul>
+
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Martin De Kauwe</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Tony Gardella</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
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-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Martin De Kauwe</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Tony Gardella</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/gday/docs/docsearch.css b/models/gday/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/gday/docs/docsearch.css
+++ b/models/gday/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/gday/docs/docsearch.js b/models/gday/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/gday/docs/docsearch.js
+++ b/models/gday/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/gday/docs/index.html b/models/gday/docs/index.html
index fdfa364..a123889 100644
--- a/models/gday/docs/index.html
+++ b/models/gday/docs/index.html
@@ -1,103 +1,158 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the GDAY model • PEcAn.GDAY</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the GDAY model">
-<meta property="og:description" content="This module provides functions to link the GDAY model to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn package for integration of the GDAY model • PEcAn.GDAY</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the GDAY model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to link the GDAY model to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.GDAY</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    This module provides functions to link the GDAY model to PEcAn.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.GDAY</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          This module provides functions to link the GDAY model to PEcAn.
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/gday/docs/pkgdown.css b/models/gday/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/gday/docs/pkgdown.css
+++ b/models/gday/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/gday/docs/pkgdown.js b/models/gday/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/gday/docs/pkgdown.js
+++ b/models/gday/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/gday/docs/reference/index.html b/models/gday/docs/reference/index.html
index a21dd64..ab516bc 100644
--- a/models/gday/docs/reference/index.html
+++ b/models/gday/docs/reference/index.html
@@ -2,156 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.GDAY</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.GDAY</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Function reference" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.GDAY</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.GDAY</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="met2model.GDAY.html">met2model.GDAY()</a></code> </p>
-        </td>
-        <td><p>met2model.GDAY</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.GDAY.html">model2netcdf.GDAY()</a></code> </p>
-        </td>
-        <td><p>Function to convert GDAY model output to standard netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.GDAY.html">write.config.GDAY()</a></code> </p>
-        </td>
-        <td><p>Write GDAY configuration files</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.GDAY.html">met2model.GDAY()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2model.GDAY</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.GDAY.html"
+                        >model2netcdf.GDAY()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function to convert GDAY model output to standard netCDF
+                    format
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.GDAY.html"
+                        >write.config.GDAY()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write GDAY configuration files</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/gday/docs/reference/met2model.GDAY.html b/models/gday/docs/reference/met2model.GDAY.html
index 038a701..998f0d2 100644
--- a/models/gday/docs/reference/met2model.GDAY.html
+++ b/models/gday/docs/reference/met2model.GDAY.html
@@ -2,195 +2,243 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>met2model.GDAY — met2model.GDAY • PEcAn.GDAY</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="met2model.GDAY — met2model.GDAY" />
-
-<meta property="og:description" content="Function to convert NetCDF met files in PEcAn-CF format into GDAY met driver files.
-This function is an R wrapper to the python script &quot;generate_forcing_data.py&quot; 
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>met2model.GDAY — met2model.GDAY • PEcAn.GDAY</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="met2model.GDAY — met2model.GDAY" />
+
+    <meta
+      property="og:description"
+      content='Function to convert NetCDF met files in PEcAn-CF format into GDAY met driver files.
+This function is an R wrapper to the python script "generate_forcing_data.py" 
 in the inst/ folder. The python script supports arguments to generate sub-daily (30 min) 
 weather data as well as soil temperature from 6 day running mean. These arguments are 
-hard-coded in this function to generate daily GDAY files without soil temperature." />
-<meta name="twitter:card" content="summary" />
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+hard-coded in this function to generate daily GDAY files without soil temperature.'
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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-        <a class="navbar-link" href="../index.html">PEcAn.GDAY</a>
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+              </ul>
+
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2model.GDAY</h1>
-    
-    <div class="hidden name"><code>met2model.GDAY.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to convert NetCDF met files in PEcAn-CF format into GDAY met driver files.
-This function is an R wrapper to the python script "generate_forcing_data.py" 
-in the inst/ folder. The python script supports arguments to generate sub-daily (30 min) 
-weather data as well as soil temperature from 6 day running mean. These arguments are 
-hard-coded in this function to generate daily GDAY files without soil temperature.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>met2model.GDAY</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2model.GDAY</h1>
+
+            <div class="hidden name"><code>met2model.GDAY.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to convert NetCDF met files in PEcAn-CF format into GDAY
+              met driver files. This function is an R wrapper to the python
+              script "generate_forcing_data.py" in the inst/ folder. The python
+              script supports arguments to generate sub-daily (30 min) weather
+              data as well as soil temperature from 6 day running mean. These
+              arguments are hard-coded in this function to generate daily GDAY
+              files without soil temperature.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.GDAY</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will
-only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use
-the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>generates GDAY formatted met file as a side affect, returns file metadata
-that will be inserted into database</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>met2model for GDAY</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            generates GDAY formatted met file as a side affect, returns file
+            metadata that will be inserted into database
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>met2model for GDAY</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Martin De Kauwe, Tony Gardella
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Martin De Kauwe, Tony Gardella
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/models/gday/docs/reference/model2netcdf.GDAY.html b/models/gday/docs/reference/model2netcdf.GDAY.html
index 258ab8e..df66a29 100644
--- a/models/gday/docs/reference/model2netcdf.GDAY.html
+++ b/models/gday/docs/reference/model2netcdf.GDAY.html
@@ -2,169 +2,206 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
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-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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+      Function to convert GDAY model output to standard netCDF format —
+      model2netcdf.GDAY • PEcAn.GDAY
+    </title>
+
+    <!-- jquery -->
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+      crossorigin="anonymous"
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+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Function to convert GDAY model output to standard netCDF format — model2netcdf.GDAY"
+    />
+
+    <meta property="og:description" content="Convert GDAY output to netCDF" />
+    <meta name="twitter:card" content="summary" />
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to convert GDAY model output to standard netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.GDAY.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert GDAY output to netCDF</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model2netcdf.GDAY</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of GDAY model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Converts all output contained in a folder to netCDF.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function to convert GDAY model output to standard netCDF format
+            </h1>
+
+            <div class="hidden name"><code>model2netcdf.GDAY.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert GDAY output to netCDF</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.GDAY</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of GDAY model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Converts all output contained in a folder to netCDF.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Martin De Kauwe
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Martin De Kauwe
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/gday/docs/reference/write.config.GDAY.html b/models/gday/docs/reference/write.config.GDAY.html
index 1147b62..9856121 100644
--- a/models/gday/docs/reference/write.config.GDAY.html
+++ b/models/gday/docs/reference/write.config.GDAY.html
@@ -2,172 +2,210 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Write GDAY configuration files — write.config.GDAY • PEcAn.GDAY
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write GDAY configuration files — write.config.GDAY"
+    />
+
+    <meta property="og:description" content="Writes a config file for GDAY" />
+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.GDAY</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
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-        
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-  </div><!--/.container -->
-</div><!--/.navbar -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.GDAY</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write GDAY configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.GDAY.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a config file for GDAY</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.GDAY</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file for GDAY for given run</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write GDAY configuration files</h1>
+
+            <div class="hidden name"><code>write.config.GDAY.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a config file for GDAY</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.GDAY</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file for GDAY for given run</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Requires a pft xml object, a list of trait values for a single model
+            run, and the name of the file to create
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Martin De Kauwe
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Martin De Kauwe
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/jules/docs/LICENSE-text.html b/models/jules/docs/LICENSE-text.html
index 92ffc82..c3ef07c 100644
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@@ -2,97 +2,126 @@
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+
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+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.JULES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/jules/docs/authors.html b/models/jules/docs/authors.html
index c999486..cae272a 100644
--- a/models/jules/docs/authors.html
+++ b/models/jules/docs/authors.html
@@ -2,122 +2,143 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.JULES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.JULES</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.JULES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.JULES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/jules/docs/docsearch.css b/models/jules/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/jules/docs/docsearch.css
+++ b/models/jules/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/jules/docs/docsearch.js b/models/jules/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/jules/docs/docsearch.js
+++ b/models/jules/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/jules/docs/index.html b/models/jules/docs/index.html
index 5bbaba3..20df154 100644
--- a/models/jules/docs/index.html
+++ b/models/jules/docs/index.html
@@ -1,130 +1,210 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the JULES model • PEcAn.JULES</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the JULES model">
-<meta property="og:description" content="This module provides functions to link the (JULES) to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn package for integration of the JULES model • PEcAn.JULES
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the JULES model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to link the (JULES) to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.JULES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.JULES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    <div id="installing-jules" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#installing-jules" class="anchor"></a>Installing JULES</h1></div>
-<p>1) Download JULES source code <a href="https://jules.jchmr.org/software-and-documentation/previous-releases/jules-v4.2" class="uri">https://jules.jchmr.org/software-and-documentation/previous-releases/jules-v4.2</a></p>
-<p>2) Download FCM</p>
-<pre><code>wget https://github.com/metomi/fcm/archive/2015.05.0.tar.gz
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div id="installing-jules" class="section level1">
+            <div class="page-header">
+              <h1 class="hasAnchor">
+                <a href="#installing-jules" class="anchor"></a>Installing JULES
+              </h1>
+            </div>
+            <p>
+              1) Download JULES source code
+              <a
+                href="https://jules.jchmr.org/software-and-documentation/previous-releases/jules-v4.2"
+                class="uri"
+                >https://jules.jchmr.org/software-and-documentation/previous-releases/jules-v4.2</a
+              >
+            </p>
+            <p>2) Download FCM</p>
+            <pre><code>wget https://github.com/metomi/fcm/archive/2015.05.0.tar.gz
 tar -xvzf 2015.05.0.tar.gz</code></pre>
-<p>3) Configure netCDF</p>
-<pre><code>cd jules-vn4.2/etc/fcm-make/
+            <p>3) Configure netCDF</p>
+            <pre><code>cd jules-vn4.2/etc/fcm-make/
 vi make.cfg</code></pre>
-<p>modify the following settings and save</p>
-<pre><code># NetCDF settings
+            <p>modify the following settings and save</p>
+            <pre><code># NetCDF settings
 $JULES_NETCDF{?} = actual
 $JULES_NETCDF_PATH{?} = /usr</code></pre>
-<p>4) Compile</p>
-<pre><code>cd ../..
+            <p>4) Compile</p>
+            <pre><code>cd ../..
 ../fcm-2015.05.0/bin/fcm make -f etc/fcm-make/make.cfg --new</code></pre>
-<p>5) Run test example</p>
-<pre><code>cd examples/point_loobos
+            <p>5) Run test example</p>
+            <pre><code>cd examples/point_loobos
 ../../build/bin/jules.exe</code></pre>
-<p>6) Add local executable to BETY database</p>
-<ul>
-<li>Create new File record for the relevant machine with File name = jules.exe and File path = /path/to/jules/build/bin</li>
-<li>Got to Model and search for the version of JULES you are running (currently 4.2)</li>
-<li>Edit Record &gt; View Related Files and search for the File record you just created in order to link the new model executable to the existing Model record</li>
-<li>Go to PEcAn web interface to verify correct JULES version shows up in pull down menu</li>
-</ul>
-</div>
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
-
-  </div>
-</div>
+            <p>6) Add local executable to BETY database</p>
+            <ul>
+              <li>
+                Create new File record for the relevant machine with File name =
+                jules.exe and File path = /path/to/jules/build/bin
+              </li>
+              <li>
+                Got to Model and search for the version of JULES you are running
+                (currently 4.2)
+              </li>
+              <li>
+                Edit Record &gt; View Related Files and search for the File
+                record you just created in order to link the new model
+                executable to the existing Model record
+              </li>
+              <li>
+                Go to PEcAn web interface to verify correct JULES version shows
+                up in pull down menu
+              </li>
+            </ul>
+          </div>
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/jules/docs/pkgdown.css b/models/jules/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/jules/docs/pkgdown.css
+++ b/models/jules/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/jules/docs/pkgdown.js b/models/jules/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/jules/docs/pkgdown.js
+++ b/models/jules/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/jules/docs/reference/detect.timestep.html b/models/jules/docs/reference/detect.timestep.html
index fe587ee..2ac4eb6 100644
--- a/models/jules/docs/reference/detect.timestep.html
+++ b/models/jules/docs/reference/detect.timestep.html
@@ -2,143 +2,178 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Detect timestep of JULES met files — detect.timestep • PEcAn.JULES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Detect timestep of JULES met files — detect.timestep" />
-
-<meta property="og:description" content="Detect timestep of JULES met files" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Detect timestep of JULES met files — detect.timestep • PEcAn.JULES
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+
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-    <h1>Detect timestep of JULES met files</h1>
-    
-    <div class="hidden name"><code>detect.timestep.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Detect timestep of JULES met files</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>detect.timestep</span>(<span class='no'>met.dir</span>, <span class='no'>met.regexp</span>, <span class='no'>start_date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>start_date</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Detect timestep of JULES met files</h1>
+
+            <div class="hidden name"><code>detect.timestep.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Detect timestep of JULES met files</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>detect.timestep</span>(<span class='no'>met.dir</span>, <span class='no'>met.regexp</span>, <span class='no'>start_date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>start_date</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
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diff --git a/models/jules/docs/reference/index.html b/models/jules/docs/reference/index.html
index 066a089..f0950cf 100644
--- a/models/jules/docs/reference/index.html
+++ b/models/jules/docs/reference/index.html
@@ -2,156 +2,199 @@
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 <html>
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-  <meta charset="utf-8">
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+    />
+
+    <!-- clipboard.js -->
+    <script
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+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+          <div class="container">
+            <div class="navbar-header">
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+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.JULES</a>
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+                  class="label label-default"
+                  data-toggle="tooltip"
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="detect.timestep.html">detect.timestep()</a></code> </p>
-        </td>
-        <td><p>Detect timestep of JULES met files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.JULES.html">model2netcdf.JULES()</a></code> </p>
-        </td>
-        <td><p>Code to convert JULES output into netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.JULES.html">write.config.JULES()</a></code> </p>
-        </td>
-        <td><p>Write JULES configuration files</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="detect.timestep.html"
+                        >detect.timestep()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Detect timestep of JULES met files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.JULES.html"
+                        >model2netcdf.JULES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Code to convert JULES output into netCDF format</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.JULES.html"
+                        >write.config.JULES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write JULES configuration files</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/jules/docs/reference/model2netcdf.JULES.html b/models/jules/docs/reference/model2netcdf.JULES.html
index 4247472..b23a4ae 100644
--- a/models/jules/docs/reference/model2netcdf.JULES.html
+++ b/models/jules/docs/reference/model2netcdf.JULES.html
@@ -2,147 +2,183 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Code to convert JULES output into netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.JULES.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert MODEL output into the PEcAn standard</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model2netcdf.JULES</span>(<span class='no'>outdir</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of model output</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Code to convert JULES output into netCDF format</h1>
+
+            <div class="hidden name"><code>model2netcdf.JULES.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert MODEL output into the PEcAn standard</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.JULES</span>(<span class='no'>outdir</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of model output</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
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diff --git a/models/jules/docs/reference/write.config.JULES.html b/models/jules/docs/reference/write.config.JULES.html
index 527b70e..e0d053b 100644
--- a/models/jules/docs/reference/write.config.JULES.html
+++ b/models/jules/docs/reference/write.config.JULES.html
@@ -2,178 +2,219 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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+      Write JULES configuration files — write.config.JULES • PEcAn.JULES
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+                <a class="navbar-link" href="../index.html">PEcAn.JULES</a>
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+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write JULES configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.JULES.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a JULES config file.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.JULES</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file for JULES for given run</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write JULES configuration files</h1>
+
+            <div class="hidden name"><code>write.config.JULES.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a JULES config file.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.JULES</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file for JULES for given run</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Requires a pft xml object, a list of trait values for a single model
+            run, and the name of the file to create
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>write.config.JULES</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
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-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze, Rob Kooper
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Mike Dietze, Rob Kooper
+        </div>
+      </div>
+
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
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 </html>
-
diff --git a/models/linkages/docs/LICENSE-text.html b/models/linkages/docs/LICENSE-text.html
index ebb16af..0fed8e6 100644
--- a/models/linkages/docs/LICENSE-text.html
+++ b/models/linkages/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+    <title>License • PEcAn.LINKAGES</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.LINKAGES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
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-  <a href="reference/index.html">Reference</a>
-</li>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.LINKAGES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/linkages/docs/authors.html b/models/linkages/docs/authors.html
index 74667f5..b6224c1 100644
--- a/models/linkages/docs/authors.html
+++ b/models/linkages/docs/authors.html
@@ -2,126 +2,146 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.LINKAGES</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
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+
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.LINKAGES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.LINKAGES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Ann Raiho</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Ann Raiho</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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       </footer>
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   </body>
 </html>
-
diff --git a/models/linkages/docs/docsearch.css b/models/linkages/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/linkages/docs/docsearch.css
+++ b/models/linkages/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/linkages/docs/docsearch.js b/models/linkages/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/linkages/docs/docsearch.js
+++ b/models/linkages/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/linkages/docs/index.html b/models/linkages/docs/index.html
index bd6bb3d..16eaff8 100644
--- a/models/linkages/docs/index.html
+++ b/models/linkages/docs/index.html
@@ -1,126 +1,216 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the LINKAGES model • PEcAn.LINKAGES</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the LINKAGES model">
-<meta property="og:description" content="This module provides functions to link the (LINKAGES) to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn package for integration of the LINKAGES model • PEcAn.LINKAGES
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the LINKAGES model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to link the (LINKAGES) to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.LINKAGES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    <div id="a-generic-template-for-adding-a-new-model-to-pecan" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#a-generic-template-for-adding-a-new-model-to-pecan" class="anchor"></a>A generic template for adding a new model to PEcAn</h1></div>
-<p>Adding a new model to PEcAn in a few easy steps:</p>
-<ol>
-<li>add modeltype to BETY</li>
-<li>add a model and PFT to BETY for use with modeltype</li>
-<li>implement 3 functions as described below</li>
-<li>execute pecan with new model</li>
-</ol>
-<p>There are 3 functions that will need to be implemented, each of these functions will need to have MODEL be replaced with the actual modeltype as it is defined in the BETY database.</p>
-<ul>
-<li><code>write.config.MODEL.R</code></li>
-</ul>
-<p>This will write the configuratin file as well as the job launcher used by PEcAn. There is an example of the job execution script in the template folder. The configuration file can also be a template that is found based on the revision number of the model. This should use the computed results specified in defaults and trait.values to write a configuration file based on the PFT and traits found.</p>
-<ul>
-<li><code>met2model.MODEL.R</code></li>
-</ul>
-<p>This will convert the standard Met CF file to the model specific file format. This will allow PEcAn to create metereological files for the specific site and model. This will only be called if no meterological data is found for that specific site and model combination.</p>
-<ul>
-<li><code>model2netcdf.MODEL.R</code></li>
-</ul>
-<p>This will convert the model specific output to NACP Intercomparison format. After this function is finished PEcAn will use the generated output and not use the model specific outputs. The outputs should be named YYYY.nc</p>
-</div>
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.LINKAGES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div
+            id="a-generic-template-for-adding-a-new-model-to-pecan"
+            class="section level1"
+          >
+            <div class="page-header">
+              <h1 class="hasAnchor">
+                <a
+                  href="#a-generic-template-for-adding-a-new-model-to-pecan"
+                  class="anchor"
+                ></a
+                >A generic template for adding a new model to PEcAn
+              </h1>
+            </div>
+            <p>Adding a new model to PEcAn in a few easy steps:</p>
+            <ol>
+              <li>add modeltype to BETY</li>
+              <li>add a model and PFT to BETY for use with modeltype</li>
+              <li>implement 3 functions as described below</li>
+              <li>execute pecan with new model</li>
+            </ol>
+            <p>
+              There are 3 functions that will need to be implemented, each of
+              these functions will need to have MODEL be replaced with the
+              actual modeltype as it is defined in the BETY database.
+            </p>
+            <ul>
+              <li><code>write.config.MODEL.R</code></li>
+            </ul>
+            <p>
+              This will write the configuratin file as well as the job launcher
+              used by PEcAn. There is an example of the job execution script in
+              the template folder. The configuration file can also be a template
+              that is found based on the revision number of the model. This
+              should use the computed results specified in defaults and
+              trait.values to write a configuration file based on the PFT and
+              traits found.
+            </p>
+            <ul>
+              <li><code>met2model.MODEL.R</code></li>
+            </ul>
+            <p>
+              This will convert the standard Met CF file to the model specific
+              file format. This will allow PEcAn to create metereological files
+              for the specific site and model. This will only be called if no
+              meterological data is found for that specific site and model
+              combination.
+            </p>
+            <ul>
+              <li><code>model2netcdf.MODEL.R</code></li>
+            </ul>
+            <p>
+              This will convert the model specific output to NACP
+              Intercomparison format. After this function is finished PEcAn will
+              use the generated output and not use the model specific outputs.
+              The outputs should be named YYYY.nc
+            </p>
+          </div>
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/linkages/docs/pkgdown.css b/models/linkages/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/linkages/docs/pkgdown.css
+++ b/models/linkages/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/linkages/docs/pkgdown.js b/models/linkages/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/linkages/docs/pkgdown.js
+++ b/models/linkages/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/linkages/docs/reference/index.html b/models/linkages/docs/reference/index.html
index 06d62c5..9b2e53b 100644
--- a/models/linkages/docs/reference/index.html
+++ b/models/linkages/docs/reference/index.html
@@ -2,174 +2,237 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.LINKAGES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.LINKAGES</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Function reference" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="met2model.LINKAGES.html">met2model.LINKAGES()</a></code> </p>
-        </td>
-        <td><p>Write LINKAGES met files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.LINKAGES.html">model2netcdf.LINKAGES()</a></code> </p>
-        </td>
-        <td><p>Code to convert LINKAGES's output into netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_restart.LINKAGES.html">read_restart.LINKAGES()</a></code> </p>
-        </td>
-        <td><p>read_restart.LINKAGES</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="split_inputs.LINKAGES.html">split_inputs.LINKAGES()</a></code> </p>
-        </td>
-        <td><p>split_inputs.LINKAGES</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.LINKAGES.html">write.config.LINKAGES()</a></code> </p>
-        </td>
-        <td><p>Write LINKAGES configuration files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_restart.LINKAGES.html">write_restart.LINKAGES()</a></code> </p>
-        </td>
-        <td><p>write_restart.LINKAGES</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.LINKAGES.html"
+                        >met2model.LINKAGES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write LINKAGES met files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.LINKAGES.html"
+                        >model2netcdf.LINKAGES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Code to convert LINKAGES's output into netCDF format</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read_restart.LINKAGES.html"
+                        >read_restart.LINKAGES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>read_restart.LINKAGES</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="split_inputs.LINKAGES.html"
+                        >split_inputs.LINKAGES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>split_inputs.LINKAGES</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.LINKAGES.html"
+                        >write.config.LINKAGES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write LINKAGES configuration files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write_restart.LINKAGES.html"
+                        >write_restart.LINKAGES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>write_restart.LINKAGES</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/linkages/docs/reference/met2model.LINKAGES.html b/models/linkages/docs/reference/met2model.LINKAGES.html
index 5d94700..6841f3c 100644
--- a/models/linkages/docs/reference/met2model.LINKAGES.html
+++ b/models/linkages/docs/reference/met2model.LINKAGES.html
@@ -2,164 +2,203 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Write LINKAGES met files — met2model.LINKAGES • PEcAn.LINKAGES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<script src="../pkgdown.js"></script>
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-<meta property="og:title" content="Write LINKAGES met files — met2model.LINKAGES" />
-
-<meta property="og:description" content="Converts a met CF file to a model specific met file. The input
-files are calld &amp;lt;in.path&amp;gt;/&amp;lt;in.prefix&amp;gt;.YYYY.cf" />
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Write LINKAGES met files — met2model.LINKAGES • PEcAn.LINKAGES
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Write LINKAGES met files — met2model.LINKAGES"
+    />
+
+    <meta
+      property="og:description"
+      content="Converts a met CF file to a model specific met file. The input
+files are calld &amp;lt;in.path&amp;gt;/&amp;lt;in.prefix&amp;gt;.YYYY.cf"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-        <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
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-    <div id="navbar" class="navbar-collapse collapse">
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+              >
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write LINKAGES met files</h1>
-    
-    <div class="hidden name"><code>met2model.LINKAGES.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write LINKAGES met files</h1>
 
-    <div class="ref-description">
-    
-    <p>Converts a met CF file to a model specific met file. The input
-files are calld &lt;in.path&gt;/&lt;in.prefix&gt;.YYYY.cf</p>
-    
-    </div>
+            <div class="hidden name"><code>met2model.LINKAGES.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Converts a met CF file to a model specific met file. The input
+              files are calld &lt;in.path&gt;/&lt;in.prefix&gt;.YYYY.cf
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2model.LINKAGES</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.LINKAGES</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>path on disk where CF file lives</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix for each file</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location where model specific output is written.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>OK if everything was succesful.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>path on disk where CF file lives</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix for each file</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location where model specific output is written.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>OK if everything was succesful.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho, Betsy Cowdery
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho, Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
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diff --git a/models/linkages/docs/reference/model2netcdf.LINKAGES.html b/models/linkages/docs/reference/model2netcdf.LINKAGES.html
index 09794b5..ae37ec2 100644
--- a/models/linkages/docs/reference/model2netcdf.LINKAGES.html
+++ b/models/linkages/docs/reference/model2netcdf.LINKAGES.html
@@ -2,164 +2,203 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Code to convert LINKAGES's output into netCDF format — model2netcdf.LINKAGES" />
-
-<meta property="og:description" content="Convert MODEL output into the NACP Intercomparison format (ALMA using netCDF)" />
-<meta name="twitter:card" content="summary" />
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-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Code to convert LINKAGES's output into netCDF format —
+      model2netcdf.LINKAGES • PEcAn.LINKAGES
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Code to convert LINKAGES's output into netCDF format — model2netcdf.LINKAGES"
+    />
+
+    <meta
+      property="og:description"
+      content="Convert MODEL output into the NACP Intercomparison format (ALMA using netCDF)"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+                type="button"
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+              >
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+              </button>
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+                <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
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+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+            </div>
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Code to convert LINKAGES's output into netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.LINKAGES.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Code to convert LINKAGES's output into netCDF format</h1>
 
-    <div class="ref-description">
-    
-    <p>Convert MODEL output into the NACP Intercomparison format (ALMA using netCDF)</p>
-    
-    </div>
+            <div class="hidden name"><code>model2netcdf.LINKAGES.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>model2netcdf.LINKAGES</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>end_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>pft_names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Ann Raiho, Betsy Cowdery
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Convert MODEL output into the NACP Intercomparison format (ALMA
+              using netCDF)
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.LINKAGES</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+  <span class='kw'>end_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>pft_names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Ann Raiho, Betsy Cowdery
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/linkages/docs/reference/read_restart.LINKAGES.html b/models/linkages/docs/reference/read_restart.LINKAGES.html
index 3c04772..a519b48 100644
--- a/models/linkages/docs/reference/read_restart.LINKAGES.html
+++ b/models/linkages/docs/reference/read_restart.LINKAGES.html
@@ -2,170 +2,204 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>read_restart.LINKAGES — read_restart.LINKAGES • PEcAn.LINKAGES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="read_restart.LINKAGES — read_restart.LINKAGES" />
-
-<meta property="og:description" content="Read Restart for LINKAGES" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      read_restart.LINKAGES — read_restart.LINKAGES • PEcAn.LINKAGES
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="read_restart.LINKAGES — read_restart.LINKAGES"
+    />
+
+    <meta property="og:description" content="Read Restart for LINKAGES" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>read_restart.LINKAGES</h1>
-    
-    <div class="hidden name"><code>read_restart.LINKAGES.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>read_restart.LINKAGES</h1>
 
-    <div class="ref-description">
-    
-    <p>Read Restart for LINKAGES</p>
-    
-    </div>
+            <div class="hidden name"><code>read_restart.LINKAGES.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Read Restart for LINKAGES</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>read_restart.LINKAGES</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>read_restart.LINKAGES</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
   <span class='kw'>var.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>params</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>output directory</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>run ID</p></td>
-    </tr>
-    <tr>
-      <th>stop.time</th>
-      <td><p>year that is being read</p></td>
-    </tr>
-    <tr>
-      <th>var.names</th>
-      <td><p>var.names to be extracted</p></td>
-    </tr>
-    <tr>
-      <th>multi.settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>X.vec      vector of forecasts</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>output directory</p></td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>run ID</p></td>
+            </tr>
+            <tr>
+              <th>stop.time</th>
+              <td><p>year that is being read</p></td>
+            </tr>
+            <tr>
+              <th>var.names</th>
+              <td><p>var.names to be extracted</p></td>
+            </tr>
+            <tr>
+              <th>multi.settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>X.vec vector of forecasts</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho <a href='mailto:araiho@nd.edu'>araiho@nd.edu</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho <a href="mailto:araiho@nd.edu">araiho@nd.edu</a>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/linkages/docs/reference/split_inputs.LINKAGES.html b/models/linkages/docs/reference/split_inputs.LINKAGES.html
index 728c440..5a8ed3b 100644
--- a/models/linkages/docs/reference/split_inputs.LINKAGES.html
+++ b/models/linkages/docs/reference/split_inputs.LINKAGES.html
@@ -2,143 +2,171 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>split_inputs.LINKAGES — split_inputs.LINKAGES • PEcAn.LINKAGES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="split_inputs.LINKAGES — split_inputs.LINKAGES" />
-
-<meta property="og:description" content="Splits climate met for LINKAGES" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      split_inputs.LINKAGES — split_inputs.LINKAGES • PEcAn.LINKAGES
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="split_inputs.LINKAGES — split_inputs.LINKAGES"
+    />
+
+    <meta property="og:description" content="Splits climate met for LINKAGES" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
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-        
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-      
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-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>split_inputs.LINKAGES</h1>
-    
-    <div class="hidden name"><code>split_inputs.LINKAGES.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>split_inputs.LINKAGES</h1>
 
-    <div class="ref-description">
-    
-    <p>Splits climate met for LINKAGES</p>
-    
-    </div>
+            <div class="hidden name"><code>split_inputs.LINKAGES.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>split_inputs.LINKAGES</span>(<span class='no'>settings</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>inputs</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <div class="ref-description">
+            <p>Splits climate met for LINKAGES</p>
+          </div>
 
-    <p>files split up climate files</p>
-    
+          <pre
+            class="usage"
+          ><span class='fu'>split_inputs.LINKAGES</span>(<span class='no'>settings</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>inputs</span>)</pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>files split up climate files</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/linkages/docs/reference/write.config.LINKAGES.html b/models/linkages/docs/reference/write.config.LINKAGES.html
index 176cd19..db4929a 100644
--- a/models/linkages/docs/reference/write.config.LINKAGES.html
+++ b/models/linkages/docs/reference/write.config.LINKAGES.html
@@ -2,173 +2,212 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Write LINKAGES configuration files — write.config.LINKAGES • PEcAn.LINKAGES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Write LINKAGES configuration files — write.config.LINKAGES" />
-
-<meta property="og:description" content="Writes a LINKAGES config file." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Write LINKAGES configuration files — write.config.LINKAGES •
+      PEcAn.LINKAGES
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write LINKAGES configuration files — write.config.LINKAGES"
+    />
+
+    <meta property="og:description" content="Writes a LINKAGES config file." />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-        
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-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write LINKAGES configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.LINKAGES.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write LINKAGES configuration files</h1>
 
-    <div class="ref-description">
-    
-    <p>Writes a LINKAGES config file.</p>
-    
-    </div>
+            <div class="hidden name"><code>write.config.LINKAGES.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a LINKAGES config file.</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>write.config.LINKAGES</span>(<span class='kw'>defaults</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.LINKAGES</span>(<span class='kw'>defaults</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>,
   <span class='kw'>restart</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>spinup</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>inputs</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>IC</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file for LINKAGES for given run</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file for LINKAGES for given run</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Requires a pft xml object, a list of trait values for a single model
+            run, and the name of the file to create
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho, Betsy Cowdery
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho, Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/linkages/docs/reference/write_restart.LINKAGES.html b/models/linkages/docs/reference/write_restart.LINKAGES.html
index 7cb5e6d..1eddfd8 100644
--- a/models/linkages/docs/reference/write_restart.LINKAGES.html
+++ b/models/linkages/docs/reference/write_restart.LINKAGES.html
@@ -2,178 +2,217 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>write_restart.LINKAGES — write_restart.LINKAGES • PEcAn.LINKAGES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<script src="../pkgdown.js"></script>
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      write_restart.LINKAGES — write_restart.LINKAGES • PEcAn.LINKAGES
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="write_restart.LINKAGES — write_restart.LINKAGES"
+    />
+
+    <meta
+      property="og:description"
+      content="Write restart files for LINKAGES"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+                data-target="#navbar"
+              >
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.LINKAGES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+
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+                  <a href="../reference/index.html">Reference</a>
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+
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>write_restart.LINKAGES</h1>
-    
-    <div class="hidden name"><code>write_restart.LINKAGES.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>write_restart.LINKAGES</h1>
 
-    <div class="ref-description">
-    
-    <p>Write restart files for LINKAGES</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>write_restart.LINKAGES.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Write restart files for LINKAGES</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>write_restart.LINKAGES</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>write_restart.LINKAGES</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
   <span class='no'>new.state</span>, <span class='kw'>RENAME</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>new.params</span>, <span class='no'>inputs</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>output directory</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>run ID</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>new.state</th>
-      <td><p>analysis vector</p></td>
-    </tr>
-    <tr>
-      <th>RENAME</th>
-      <td><p>flag to either rename output file or not</p></td>
-    </tr>
-    <tr>
-      <th>time</th>
-      <td><p>year that is being read</p></td>
-    </tr>
-    <tr>
-      <th>trait.values</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>NONE</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>output directory</p></td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>run ID</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>new.state</th>
+              <td><p>analysis vector</p></td>
+            </tr>
+            <tr>
+              <th>RENAME</th>
+              <td><p>flag to either rename output file or not</p></td>
+            </tr>
+            <tr>
+              <th>time</th>
+              <td><p>year that is being read</p></td>
+            </tr>
+            <tr>
+              <th>trait.values</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>NONE</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho <a href='mailto:araiho@nd.edu'>araiho@nd.edu</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho <a href="mailto:araiho@nd.edu">araiho@nd.edu</a>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-
diff --git a/models/lpjguess/docs/LICENSE-text.html b/models/lpjguess/docs/LICENSE-text.html
index aee098e..fb83d30 100644
--- a/models/lpjguess/docs/LICENSE-text.html
+++ b/models/lpjguess/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+    <title>License • PEcAn.LPJGUESS</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
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+    <![endif]-->
   </head>
 
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.LPJGUESS</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.LPJGUESS</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
-
diff --git a/models/lpjguess/docs/authors.html b/models/lpjguess/docs/authors.html
index 537703a..838216e 100644
--- a/models/lpjguess/docs/authors.html
+++ b/models/lpjguess/docs/authors.html
@@ -2,126 +2,146 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.LPJGUESS</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.LPJGUESS</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.LPJGUESS</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Istem Fer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Tony Gardella</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Istem Fer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Tony Gardella</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/lpjguess/docs/docsearch.css b/models/lpjguess/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/lpjguess/docs/docsearch.css
+++ b/models/lpjguess/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/lpjguess/docs/docsearch.js b/models/lpjguess/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/lpjguess/docs/docsearch.js
+++ b/models/lpjguess/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/lpjguess/docs/index.html b/models/lpjguess/docs/index.html
index e5e1cc9..e546d17 100644
--- a/models/lpjguess/docs/index.html
+++ b/models/lpjguess/docs/index.html
@@ -1,103 +1,160 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the LPJ-GUESS model • PEcAn.LPJGUESS</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the LPJ-GUESS model">
-<meta property="og:description" content="This module provides functions to link LPJ-GUESS to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn package for integration of the LPJ-GUESS model • PEcAn.LPJGUESS
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the LPJ-GUESS model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to link LPJ-GUESS to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.LPJGUESS</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    This module provides functions to link LPJ-GUESS to PEcAn.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.LPJGUESS</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          This module provides functions to link LPJ-GUESS to PEcAn.
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/lpjguess/docs/pkgdown.css b/models/lpjguess/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/lpjguess/docs/pkgdown.css
+++ b/models/lpjguess/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/lpjguess/docs/pkgdown.js b/models/lpjguess/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/lpjguess/docs/pkgdown.js
+++ b/models/lpjguess/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/lpjguess/docs/reference/index.html b/models/lpjguess/docs/reference/index.html
index dffcdc4..a543ce7 100644
--- a/models/lpjguess/docs/reference/index.html
+++ b/models/lpjguess/docs/reference/index.html
@@ -2,168 +2,228 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.LPJGUESS</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.LPJGUESS</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Function reference" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.LPJGUESS</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.LPJGUESS</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="met2model.LPJGUESS.html">met2model.LPJGUESS()</a></code> </p>
-        </td>
-        <td><p>met2model.LPJGUESS</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.LPJGUESS.html">model2netcdf.LPJGUESS()</a></code> </p>
-        </td>
-        <td><p>Function to convert LPJ-GUESS model output to standard netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="readStateBinary.html">readStateBinary()</a></code> </p>
-        </td>
-        <td><p>readStateBinary.LPJGUESS</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.LPJGUESS.html">write.config.LPJGUESS()</a></code> </p>
-        </td>
-        <td><p>Write LPJ-GUESS configuration files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.insfile.LPJGUESS.html">write.insfile.LPJGUESS()</a></code> </p>
-        </td>
-        <td><p>Write LPJ-GUESS instruction script</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.LPJGUESS.html"
+                        >met2model.LPJGUESS()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2model.LPJGUESS</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.LPJGUESS.html"
+                        >model2netcdf.LPJGUESS()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function to convert LPJ-GUESS model output to standard
+                    netCDF format
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="readStateBinary.html"
+                        >readStateBinary()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>readStateBinary.LPJGUESS</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.LPJGUESS.html"
+                        >write.config.LPJGUESS()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write LPJ-GUESS configuration files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.insfile.LPJGUESS.html"
+                        >write.insfile.LPJGUESS()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write LPJ-GUESS instruction script</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/models/lpjguess/docs/reference/met2model.LPJGUESS.html b/models/lpjguess/docs/reference/met2model.LPJGUESS.html
index 94962f9..96714c5 100644
--- a/models/lpjguess/docs/reference/met2model.LPJGUESS.html
+++ b/models/lpjguess/docs/reference/met2model.LPJGUESS.html
@@ -2,172 +2,212 @@
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-  <meta charset="utf-8">
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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-
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+    <meta charset="utf-8" />
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="met2model.LPJGUESS — met2model.LPJGUESS"
+    />
+
+    <meta property="og:description" content="met2model wrapper for LPJ-GUESS" />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.LPJGUESS</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="../reference/index.html">Reference</a>
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-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.LPJGUESS</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2model.LPJGUESS</h1>
-    
-    <div class="hidden name"><code>met2model.LPJGUESS.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2model.LPJGUESS</h1>
 
-    <div class="ref-description">
-    
-    <p>met2model wrapper for LPJ-GUESS</p>
-    
-    </div>
+            <div class="hidden name"><code>met2model.LPJGUESS.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2model.LPJGUESS</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>met2model wrapper for LPJ-GUESS</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.LPJGUESS</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/lpjguess/docs/reference/model2netcdf.LPJGUESS.html b/models/lpjguess/docs/reference/model2netcdf.LPJGUESS.html
index 9262ec9..d869a4f 100644
--- a/models/lpjguess/docs/reference/model2netcdf.LPJGUESS.html
+++ b/models/lpjguess/docs/reference/model2netcdf.LPJGUESS.html
@@ -2,163 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Function to convert LPJ-GUESS model output to standard netCDF format — model2netcdf.LPJGUESS" />
-
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-<meta name="twitter:card" content="summary" />
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Function to convert LPJ-GUESS model output to standard netCDF format —
+      model2netcdf.LPJGUESS • PEcAn.LPJGUESS
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    <script src="../pkgdown.js"></script>
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+      content="Function to convert LPJ-GUESS model output to standard netCDF format — model2netcdf.LPJGUESS"
+    />
+
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+      content="Convert LPJ-GUESS output to netCDF"
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+    <meta name="twitter:card" content="summary" />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to convert LPJ-GUESS model output to standard netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.LPJGUESS.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert LPJ-GUESS output to netCDF</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model2netcdf.LPJGUESS</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of LPJ-GUESS model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function to convert LPJ-GUESS model output to standard netCDF
+              format
+            </h1>
+
+            <div class="hidden name"><code>model2netcdf.LPJGUESS.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert LPJ-GUESS output to netCDF</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.LPJGUESS</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of LPJ-GUESS model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/models/lpjguess/docs/reference/readStateBinary.html b/models/lpjguess/docs/reference/readStateBinary.html
index 0ace18d..1c01a9a 100644
--- a/models/lpjguess/docs/reference/readStateBinary.html
+++ b/models/lpjguess/docs/reference/readStateBinary.html
@@ -2,157 +2,197 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
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+    />
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+    />
+    <meta name="twitter:card" content="summary" />
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+          <div class="container">
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+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.LPJGUESS</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>readStateBinary.LPJGUESS</h1>
-    
-    <div class="hidden name"><code>readStateBinary.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>read binary state file of LPJ-GUESS</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>readStateBinary</span>(<span class='no'>out.path</span>, <span class='no'>npft</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>out.path</th>
-      <td><p>location on disk where model run outputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>npft</th>
-      <td><p>number of pfts specified in instruction file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Patchpft_list state variables common to all individuals of a particular PFT</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>readStateBinary.LPJGUESS</h1>
+
+            <div class="hidden name"><code>readStateBinary.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>read binary state file of LPJ-GUESS</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>readStateBinary</span>(<span class='no'>out.path</span>, <span class='no'>npft</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>out.path</th>
+              <td>
+                <p>location on disk where model run outputs are stored</p>
+              </td>
+            </tr>
+            <tr>
+              <th>npft</th>
+              <td><p>number of pfts specified in instruction file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Patchpft_list state variables common to all individuals of a
+            particular PFT
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/lpjguess/docs/reference/write.config.LPJGUESS.html b/models/lpjguess/docs/reference/write.config.LPJGUESS.html
index 3bfb83b..87cc18e 100644
--- a/models/lpjguess/docs/reference/write.config.LPJGUESS.html
+++ b/models/lpjguess/docs/reference/write.config.LPJGUESS.html
@@ -2,172 +2,211 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write LPJ-GUESS configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.LPJGUESS.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a LPJ-GUESS config file.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.LPJGUESS</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file for LPJ-GUESS for given run</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write LPJ-GUESS configuration files</h1>
+
+            <div class="hidden name"><code>write.config.LPJGUESS.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a LPJ-GUESS config file.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.LPJGUESS</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file for LPJ-GUESS for given run</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Requires a pft xml object, a list of trait values for a single model
+            run, and the name of the file to create
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer, Tony Gardella
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer, Tony Gardella
+        </div>
+      </div>
 
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diff --git a/models/lpjguess/docs/reference/write.insfile.LPJGUESS.html b/models/lpjguess/docs/reference/write.insfile.LPJGUESS.html
index 6060da2..b8c1b7f 100644
--- a/models/lpjguess/docs/reference/write.insfile.LPJGUESS.html
+++ b/models/lpjguess/docs/reference/write.insfile.LPJGUESS.html
@@ -2,169 +2,209 @@
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+      PEcAn.LPJGUESS
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+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+    ></script>
+
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+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write LPJ-GUESS instruction script</h1>
-    
-    <div class="hidden name"><code>write.insfile.LPJGUESS.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Write LPJ-GUESS instruction script</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.insfile.LPJGUESS</span>(<span class='no'>settings</span>, <span class='no'>trait.values</span>, <span class='no'>rundir</span>, <span class='no'>outdir</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings list</p></td>
-    </tr>
-    <tr>
-      <th>trait.values</th>
-      <td><p>trait.values</p></td>
-    </tr>
-    <tr>
-      <th>rundir</th>
-      <td><p>rundir</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>outdir</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>PEcAn run ID</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>settings Updated list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write LPJ-GUESS instruction script</h1>
+
+            <div class="hidden name">
+              <code>write.insfile.LPJGUESS.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Write LPJ-GUESS instruction script</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.insfile.LPJGUESS</span>(<span class='no'>settings</span>, <span class='no'>trait.values</span>, <span class='no'>rundir</span>, <span class='no'>outdir</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings list</p></td>
+            </tr>
+            <tr>
+              <th>trait.values</th>
+              <td><p>trait.values</p></td>
+            </tr>
+            <tr>
+              <th>rundir</th>
+              <td><p>rundir</p></td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>outdir</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>PEcAn run ID</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>settings Updated list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
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diff --git a/models/maat/docs/LICENSE-text.html b/models/maat/docs/LICENSE-text.html
index e2fa9ea..4a309cb 100644
--- a/models/maat/docs/LICENSE-text.html
+++ b/models/maat/docs/LICENSE-text.html
@@ -2,112 +2,153 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-
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-
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+
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+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
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+    <script src="pkgdown.js"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.MAAT</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
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-    Articles
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-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/create_amerifluxLBL_drivers_for_maat.html">PEcAn: Generating met drivers for the MAAT model using AmerifluxLBL tower observations</a>
-    </li>
-    <li>
-      <a href="articles/running_maat_in_pecan.html">Running MAAT in PEcAn</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
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-  </div><!--/.container -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.MAAT</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a
+                        href="articles/create_amerifluxLBL_drivers_for_maat.html"
+                        >PEcAn: Generating met drivers for the MAAT model using
+                        AmerifluxLBL tower observations</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/running_maat_in_pecan.html"
+                        >Running MAAT in PEcAn</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -141,27 +182,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by Shawn Serbin, Anthony Walker.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by Shawn Serbin, Anthony Walker.</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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+        </div>
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-   </div>
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 </html>
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diff --git a/models/maat/docs/articles/create_amerifluxLBL_drivers_for_maat.html b/models/maat/docs/articles/create_amerifluxLBL_drivers_for_maat.html
index 6ea560c..2d79875 100644
--- a/models/maat/docs/articles/create_amerifluxLBL_drivers_for_maat.html
+++ b/models/maat/docs/articles/create_amerifluxLBL_drivers_for_maat.html
@@ -1,134 +1,298 @@
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+      observations • PEcAn.MAAT
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+                        AmerifluxLBL tower observations</a
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+            <h1>
+              PEcAn: Generating met drivers for the MAAT model using
+              AmerifluxLBL tower observations
+            </h1>
+            <h4 class="author">Shawn Serbin</h4>
 
-      
-      </header><div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header toc-ignore">
-      <h1>PEcAn: Generating met drivers for the MAAT model using AmerifluxLBL tower observations</h1>
-                        <h4 class="author">Shawn Serbin</h4>
-            
             <h4 class="date">2018-08-28</h4>
-      
-      
-      <div class="hidden name"><code>create_amerifluxLBL_drivers_for_maat.Rmd</code></div>
 
-    </div>
+            <div class="hidden name">
+              <code>create_amerifluxLBL_drivers_for_maat.Rmd</code>
+            </div>
+          </div>
 
-    
-    
-<div id="overview" class="section level1">
-<h1 class="hasAnchor">
-<a href="#overview" class="anchor"></a>Overview</h1>
-<p>This is a demonstration of the PEcAn utilities for downloading met data, converting it to the PEcAn-CF format (which is based on the Climate Forecasting conventions and similar to MsTMIP), gapfilling the CF driver data, and converting to model-specific drivers for the MAAT model. These variables are defined in the <a href="https://pecanproject.github.io/pecan-documentation/available-meteorological-drivers.html">PEcAn documentation</a>.</p>
-<p>In this example we will download 6 years of met data from the <a href="http://ameriflux.lbl.gov/sites/siteinfo/US-WCr">Willow Creek Eddy Covariance tower site (US-WCr)</a>. It has an Ameriflux <code>SITE_ID</code> of <code>US-WCr</code></p>
-<p>The PEcAn.data.atmosphere source code is in <a href="https://github.com/PecanProject/pecan/tree/develop/modules/data.atmosphere"><code>modules/data.atmosphere</code></a> and the documentation can be found with either <code>package?PEcAn.data.atmosphere</code> or in the <a href="https://pecanproject.github.io/pecan//modules/data.atmosphere/inst/web/index.html">data.atmosphere package documentation</a>.</p>
-<p>First make sure you have the nescessary PEcAn package for processing met data</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"modules/data.atmosphere"</span>)</code></pre></div>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(knitr)
+          <div id="overview" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#overview" class="anchor"></a>Overview
+            </h1>
+            <p>
+              This is a demonstration of the PEcAn utilities for downloading met
+              data, converting it to the PEcAn-CF format (which is based on the
+              Climate Forecasting conventions and similar to MsTMIP), gapfilling
+              the CF driver data, and converting to model-specific drivers for
+              the MAAT model. These variables are defined in the
+              <a
+                href="https://pecanproject.github.io/pecan-documentation/available-meteorological-drivers.html"
+                >PEcAn documentation</a
+              >.
+            </p>
+            <p>
+              In this example we will download 6 years of met data from the
+              <a href="http://ameriflux.lbl.gov/sites/siteinfo/US-WCr"
+                >Willow Creek Eddy Covariance tower site (US-WCr)</a
+              >. It has an Ameriflux <code>SITE_ID</code> of <code>US-WCr</code>
+            </p>
+            <p>
+              The PEcAn.data.atmosphere source code is in
+              <a
+                href="https://github.com/PecanProject/pecan/tree/develop/modules/data.atmosphere"
+                ><code>modules/data.atmosphere</code></a
+              >
+              and the documentation can be found with either
+              <code>package?PEcAn.data.atmosphere</code> or in the
+              <a
+                href="https://pecanproject.github.io/pecan//modules/data.atmosphere/inst/web/index.html"
+                >data.atmosphere package documentation</a
+              >.
+            </p>
+            <p>
+              First make sure you have the nescessary PEcAn package for
+              processing met data
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"modules/data.atmosphere"</span>)</code></pre>
+            </div>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(knitr)
 <span class="kw">library</span>(ggplot2)
 <span class="kw">library</span>(ggthemes)
-<span class="kw">library</span>(PEcAn.data.atmosphere)</code></pre></div>
-<div id="connect-to-bety-database-and-retrieve-appropriate-format-for-amerifluxlbl-datasets-todo-update-to-work-with-r-opensci-traits-bety" class="section level2">
-<h2 class="hasAnchor">
-<a href="#connect-to-bety-database-and-retrieve-appropriate-format-for-amerifluxlbl-datasets-todo-update-to-work-with-r-opensci-traits-bety" class="anchor"></a>Connect to BETY database and retrieve appropriate format for AmerifluxLBL datasets [TODO: Update to work with R-OpenSci traits BETY]</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">bety &lt;-<span class="st"> </span><span class="kw">list</span>(<span class="dt">user=</span><span class="st">'bety'</span>, <span class="dt">password=</span><span class="st">'bety'</span>, <span class="dt">host=</span><span class="st">'localhost'</span>,
+<span class="kw">library</span>(PEcAn.data.atmosphere)</code></pre>
+            </div>
+            <div
+              id="connect-to-bety-database-and-retrieve-appropriate-format-for-amerifluxlbl-datasets-todo-update-to-work-with-r-opensci-traits-bety"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#connect-to-bety-database-and-retrieve-appropriate-format-for-amerifluxlbl-datasets-todo-update-to-work-with-r-opensci-traits-bety"
+                  class="anchor"
+                ></a
+                >Connect to BETY database and retrieve appropriate format for
+                AmerifluxLBL datasets [TODO: Update to work with R-OpenSci
+                traits BETY]
+              </h2>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">bety &lt;-<span class="st"> </span><span class="kw">list</span>(<span class="dt">user=</span><span class="st">'bety'</span>, <span class="dt">password=</span><span class="st">'bety'</span>, <span class="dt">host=</span><span class="st">'localhost'</span>,
              <span class="dt">dbname=</span><span class="st">'bety'</span>, <span class="dt">driver=</span><span class="st">'PostgreSQL'</span>,<span class="dt">write=</span><span class="ot">TRUE</span>)
 con &lt;-<span class="st"> </span>PEcAn.DB<span class="op">::</span><span class="kw">db.open</span>(bety)
 bety<span class="op">$</span>con &lt;-<span class="st"> </span>con
 format.id &lt;-<span class="st"> </span><span class="dv">5000000002</span>
 format &lt;-<span class="st"> </span>PEcAn.DB<span class="op">::</span><span class="kw">query.format.vars</span>(<span class="dt">format.id=</span>format.id,<span class="dt">bety =</span> bety)
-format<span class="op">$</span>time_zone &lt;-<span class="st"> "America/Chicago"</span></code></pre></div>
-</div>
-<div id="download-amerifluxlbl-data-for-selected-site-and-dates-us-wcr-2000-to-2005" class="section level2">
-<h2 class="hasAnchor">
-<a href="#download-amerifluxlbl-data-for-selected-site-and-dates-us-wcr-2000-to-2005" class="anchor"></a>Download AmerifluxLBL data for selected site and dates (US-WCr, 2000 to 2005)</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/PEcAn.data.atmosphere/topics/download.AmerifluxLBL">download.AmerifluxLBL</a></span>(<span class="dt">sitename =</span> <span class="st">"US-WCr"</span>, <span class="dt">outfolder =</span> <span class="st">"~/scratch/met2model_testing"</span>, 
-                   <span class="dt">start_date =</span> <span class="st">"2000-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2005-12-31"</span>, <span class="dt">overwrite =</span> <span class="ot">TRUE</span>, <span class="dt">verbose =</span> <span class="ot">TRUE</span>)</code></pre></div>
-</div>
-<div id="convert-downloaded-amerifluxlbl-data-to-cf-format" class="section level2">
-<h2 class="hasAnchor">
-<a href="#convert-downloaded-amerifluxlbl-data-to-cf-format" class="anchor"></a>Convert downloaded AmerifluxLBL data to CF format</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/PEcAn.data.atmosphere/topics/met2CF.AmerifluxLBL">met2CF.AmerifluxLBL</a></span>(<span class="dt">in.path =</span> <span class="st">"~/scratch/met2model_testing/"</span>, <span class="dt">in.prefix =</span> <span class="st">"AMF_US-WCr"</span>, <span class="dt">outfolder =</span> <span class="st">"~/scratch/met2model_testing/CF/"</span>, 
-                 <span class="dt">start_date =</span> <span class="st">"2000-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2005-12-31"</span>,<span class="dt">format=</span>format)</code></pre></div>
-</div>
-<div id="gapfill-cf-met-drivers" class="section level2">
-<h2 class="hasAnchor">
-<a href="#gapfill-cf-met-drivers" class="anchor"></a>Gapfill CF met drivers</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/PEcAn.data.atmosphere/topics/metgapfill">metgapfill</a></span>(<span class="dt">in.path =</span> <span class="st">"~/scratch/met2model_testing/CF/"</span>, <span class="dt">in.prefix =</span> <span class="st">"AMF_US-WCr_BASE_HH_14-5"</span>, 
-           <span class="dt">outfolder =</span> <span class="st">"~/scratch/met2model_testing/CF/gapfill/"</span>, <span class="dt">start_date =</span> <span class="st">"2000-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2005-12-31"</span>)</code></pre></div>
-</div>
-<div id="create-maat-model-specific-met-drivers" class="section level2">
-<h2 class="hasAnchor">
-<a href="#create-maat-model-specific-met-drivers" class="anchor"></a>Create MAAT model-specific met drivers</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">in.path &lt;-<span class="st"> "~/scratch/met2model_testing/CF/gapfill/"</span>
+format<span class="op">$</span>time_zone &lt;-<span class="st"> "America/Chicago"</span></code></pre>
+              </div>
+            </div>
+            <div
+              id="download-amerifluxlbl-data-for-selected-site-and-dates-us-wcr-2000-to-2005"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#download-amerifluxlbl-data-for-selected-site-and-dates-us-wcr-2000-to-2005"
+                  class="anchor"
+                ></a
+                >Download AmerifluxLBL data for selected site and dates (US-WCr,
+                2000 to 2005)
+              </h2>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/PEcAn.data.atmosphere/topics/download.AmerifluxLBL">download.AmerifluxLBL</a></span>(<span class="dt">sitename =</span> <span class="st">"US-WCr"</span>, <span class="dt">outfolder =</span> <span class="st">"~/scratch/met2model_testing"</span>, 
+                   <span class="dt">start_date =</span> <span class="st">"2000-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2005-12-31"</span>, <span class="dt">overwrite =</span> <span class="ot">TRUE</span>, <span class="dt">verbose =</span> <span class="ot">TRUE</span>)</code></pre>
+              </div>
+            </div>
+            <div
+              id="convert-downloaded-amerifluxlbl-data-to-cf-format"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#convert-downloaded-amerifluxlbl-data-to-cf-format"
+                  class="anchor"
+                ></a
+                >Convert downloaded AmerifluxLBL data to CF format
+              </h2>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/PEcAn.data.atmosphere/topics/met2CF.AmerifluxLBL">met2CF.AmerifluxLBL</a></span>(<span class="dt">in.path =</span> <span class="st">"~/scratch/met2model_testing/"</span>, <span class="dt">in.prefix =</span> <span class="st">"AMF_US-WCr"</span>, <span class="dt">outfolder =</span> <span class="st">"~/scratch/met2model_testing/CF/"</span>, 
+                 <span class="dt">start_date =</span> <span class="st">"2000-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2005-12-31"</span>,<span class="dt">format=</span>format)</code></pre>
+              </div>
+            </div>
+            <div id="gapfill-cf-met-drivers" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#gapfill-cf-met-drivers" class="anchor"></a>Gapfill CF
+                met drivers
+              </h2>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/PEcAn.data.atmosphere/topics/metgapfill">metgapfill</a></span>(<span class="dt">in.path =</span> <span class="st">"~/scratch/met2model_testing/CF/"</span>, <span class="dt">in.prefix =</span> <span class="st">"AMF_US-WCr_BASE_HH_14-5"</span>, 
+           <span class="dt">outfolder =</span> <span class="st">"~/scratch/met2model_testing/CF/gapfill/"</span>, <span class="dt">start_date =</span> <span class="st">"2000-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2005-12-31"</span>)</code></pre>
+              </div>
+            </div>
+            <div
+              id="create-maat-model-specific-met-drivers"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#create-maat-model-specific-met-drivers"
+                  class="anchor"
+                ></a
+                >Create MAAT model-specific met drivers
+              </h2>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">in.path &lt;-<span class="st"> "~/scratch/met2model_testing/CF/gapfill/"</span>
 in.prefix &lt;-<span class="st"> "AMF_US-WCr_BASE_HH_14-5"</span>
 outfolder &lt;-<span class="st"> "~/scratch/met2model_testing/CF/gapfill/maat_drivers/"</span>
 start_date &lt;-<span class="st"> "2000-01-01"</span>
@@ -137,44 +301,67 @@ <h2 class="hasAnchor">
 verbose &lt;-<span class="st"> </span><span class="ot">TRUE</span>
 leap_year =<span class="st"> </span><span class="ot">TRUE</span>
 PEcAn.MAAT<span class="op">::</span><span class="kw">met2model.MAAT</span>(in.path, in.prefix, outfolder, start_date, end_date,
-                           <span class="dt">overwrite =</span> overwrite, <span class="dt">verbose =</span> verbose)</code></pre></div>
-</div>
-</div>
-  </div>
+                           <span class="dt">overwrite =</span> overwrite, <span class="dt">verbose =</span> verbose)</code></pre>
+              </div>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li>
-<a href="#overview">Overview</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#connect-to-bety-database-and-retrieve-appropriate-format-for-amerifluxlbl-datasets-todo-update-to-work-with-r-opensci-traits-bety">Connect to BETY database and retrieve appropriate format for AmerifluxLBL datasets [TODO: Update to work with R-OpenSci traits BETY]</a></li>
-      <li><a href="#download-amerifluxlbl-data-for-selected-site-and-dates-us-wcr-2000-to-2005">Download AmerifluxLBL data for selected site and dates (US-WCr, 2000 to 2005)</a></li>
-      <li><a href="#convert-downloaded-amerifluxlbl-data-to-cf-format">Convert downloaded AmerifluxLBL data to CF format</a></li>
-      <li><a href="#gapfill-cf-met-drivers">Gapfill CF met drivers</a></li>
-      <li><a href="#create-maat-model-specific-met-drivers">Create MAAT model-specific met drivers</a></li>
-      </ul>
-</li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#overview">Overview</a>
+                <ul class="nav nav-pills nav-stacked">
+                  <li>
+                    <a
+                      href="#connect-to-bety-database-and-retrieve-appropriate-format-for-amerifluxlbl-datasets-todo-update-to-work-with-r-opensci-traits-bety"
+                      >Connect to BETY database and retrieve appropriate format
+                      for AmerifluxLBL datasets [TODO: Update to work with
+                      R-OpenSci traits BETY]</a
+                    >
+                  </li>
+                  <li>
+                    <a
+                      href="#download-amerifluxlbl-data-for-selected-site-and-dates-us-wcr-2000-to-2005"
+                      >Download AmerifluxLBL data for selected site and dates
+                      (US-WCr, 2000 to 2005)</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#convert-downloaded-amerifluxlbl-data-to-cf-format"
+                      >Convert downloaded AmerifluxLBL data to CF format</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#gapfill-cf-met-drivers">Gapfill CF met drivers</a>
+                  </li>
+                  <li>
+                    <a href="#create-maat-model-specific-met-drivers"
+                      >Create MAAT model-specific met drivers</a
+                    >
+                  </li>
+                </ul>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
-</div>
-
-
-      <footer><div class="copyright">
-  <p>Developed by Shawn Serbin, Anthony Walker.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by Shawn Serbin, Anthony Walker.</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
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+    </div>
   </body>
 </html>
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index eda79d1..3f7f8ca 100644
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+                >
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+                <a href="running_maat_in_pecan.html">Running MAAT in PEcAn</a>
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diff --git a/models/maat/docs/articles/running_maat_in_pecan.html b/models/maat/docs/articles/running_maat_in_pecan.html
index 5a14494..811fe57 100644
--- a/models/maat/docs/articles/running_maat_in_pecan.html
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+                        >PEcAn: Generating met drivers for the MAAT model using
+                        AmerifluxLBL tower observations</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/running_maat_in_pecan.html"
+                        >Running MAAT in PEcAn</a
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+            <h1>Running MAAT in PEcAn</h1>
+            <h4 class="author">Shawn Serbin</h4>
 
-      
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-  <div class="col-md-9 contents">
-    <div class="page-header toc-ignore">
-      <h1>Running MAAT in PEcAn</h1>
-                        <h4 class="author">Shawn Serbin</h4>
-            
             <h4 class="date">2018-08-28</h4>
-      
-      
-      <div class="hidden name"><code>running_maat_in_pecan.Rmd</code></div>
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-    
-    
-<div id="overview" class="section level1">
-<h1 class="hasAnchor">
-<a href="#overview" class="anchor"></a>Overview</h1>
-<p>A simple example to show how to setup and run MAAT simulations within the PEcAn framework. Running the MAAT model within PEcAn provides access to additional tools such as the PEcAn met process functions that enable the creation of model-specific met driver files using various sources such as reanalysis products including CRU-NCEP and NARR, as well as site-level tower observations from AmerifluxLBL and FLUXNET. In addition, the PEcAn framework provides the ability to define custom plant functional types (PFTs) for MAAT simulation and conduct multi-ensemble simulations using observationally-constrained MAAT parameter distributions based on a hierarchical Bayesian meta-analysis approach linked to the BETYdb trait database (betydb.org).</p>
-<p>Presently the full MAAT process representation, functionality and tools are not yet fully enabled in the PEcAn framework but adding in more the MAAT functionality is planned in future updates to the PEcAn wrapper code.</p>
-<div id="maat-installation-and-usage" class="section level2">
-<h2 class="hasAnchor">
-<a href="#maat-installation-and-usage" class="anchor"></a>MAAT Installation and usage</h2>
-<p><strong>MAAT model source:</strong> <a href="https://github.com/walkeranthonyp/MAAT" class="uri">https://github.com/walkeranthonyp/MAAT</a> <br> Follow the instructions found here: <a href="https://github.com/walkeranthonyp/MAAT/blob/master/README.html" class="uri">https://github.com/walkeranthonyp/MAAT/blob/master/README.md</a> <br></p>
-</div>
-<div id="installing-the-r-packages" class="section level2">
-<h2 class="hasAnchor">
-<a href="#installing-the-r-packages" class="anchor"></a>Installing the R packages</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"base/logger"</span>)
+            <div class="hidden name">
+              <code>running_maat_in_pecan.Rmd</code>
+            </div>
+          </div>
+
+          <div id="overview" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#overview" class="anchor"></a>Overview
+            </h1>
+            <p>
+              A simple example to show how to setup and run MAAT simulations
+              within the PEcAn framework. Running the MAAT model within PEcAn
+              provides access to additional tools such as the PEcAn met process
+              functions that enable the creation of model-specific met driver
+              files using various sources such as reanalysis products including
+              CRU-NCEP and NARR, as well as site-level tower observations from
+              AmerifluxLBL and FLUXNET. In addition, the PEcAn framework
+              provides the ability to define custom plant functional types
+              (PFTs) for MAAT simulation and conduct multi-ensemble simulations
+              using observationally-constrained MAAT parameter distributions
+              based on a hierarchical Bayesian meta-analysis approach linked to
+              the BETYdb trait database (betydb.org).
+            </p>
+            <p>
+              Presently the full MAAT process representation, functionality and
+              tools are not yet fully enabled in the PEcAn framework but adding
+              in more the MAAT functionality is planned in future updates to the
+              PEcAn wrapper code.
+            </p>
+            <div id="maat-installation-and-usage" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#maat-installation-and-usage" class="anchor"></a>MAAT
+                Installation and usage
+              </h2>
+              <p>
+                <strong>MAAT model source:</strong>
+                <a href="https://github.com/walkeranthonyp/MAAT" class="uri"
+                  >https://github.com/walkeranthonyp/MAAT</a
+                >
+                <br />
+                Follow the instructions found here:
+                <a
+                  href="https://github.com/walkeranthonyp/MAAT/blob/master/README.html"
+                  class="uri"
+                  >https://github.com/walkeranthonyp/MAAT/blob/master/README.md</a
+                >
+                <br />
+              </p>
+            </div>
+            <div id="installing-the-r-packages" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#installing-the-r-packages" class="anchor"></a
+                >Installing the R packages
+              </h2>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"base/logger"</span>)
 devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir=</span> <span class="st">"base/remote"</span>)
 devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"base/utils"</span>)
 devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"base/settings"</span>)
 devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"modules/data.atmosphere"</span>)
 devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir =</span> <span class="st">"models/maat"</span>)
 
-<span class="kw">library</span>(PEcAn.MAAT)</code></pre></div>
-</div>
-<div id="maat-xml-configuration" class="section level2">
-<h2 class="hasAnchor">
-<a href="#maat-xml-configuration" class="anchor"></a>MAAT XML configuration</h2>
-<div id="e-g--running-without-met-drivers-and-using-user-specified-met-conditions" class="section level3">
-<h3 class="hasAnchor">
-<a href="#e-g--running-without-met-drivers-and-using-user-specified-met-conditions" class="anchor"></a>E.g. Running without met drivers and using user-specified met conditions</h3>
-<div class="sourceCode"><pre class="sourceCode xml"><code class="sourceCode xml"><span class="kw">&lt;config&gt;</span>
+<span class="kw">library</span>(PEcAn.MAAT)</code></pre>
+              </div>
+            </div>
+            <div id="maat-xml-configuration" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#maat-xml-configuration" class="anchor"></a>MAAT XML
+                configuration
+              </h2>
+              <div
+                id="e-g--running-without-met-drivers-and-using-user-specified-met-conditions"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#e-g--running-without-met-drivers-and-using-user-specified-met-conditions"
+                    class="anchor"
+                  ></a
+                  >E.g. Running without met drivers and using user-specified met
+                  conditions
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode xml"
+                  ><code class="sourceCode xml"><span class="kw">&lt;config&gt;</span>
   <span class="kw">&lt;mod_obj&gt;</span>leaf<span class="kw">&lt;/mod_obj&gt;</span>
   <span class="kw">&lt;leaf&gt;</span>
     <span class="kw">&lt;fnames&gt;</span>
@@ -135,12 +249,18 @@ <h3 class="hasAnchor">
       <span class="kw">&lt;wind&gt;</span>1<span class="kw">&lt;/wind&gt;</span>
      <span class="kw">&lt;/env&gt;</span>
   <span class="kw">&lt;/leaf&gt;</span>
-<span class="kw">&lt;/config&gt;</span></code></pre></div>
-</div>
-<div id="e-g--running-with-met-drivers" class="section level3">
-<h3 class="hasAnchor">
-<a href="#e-g--running-with-met-drivers" class="anchor"></a>E.g. Running with met drivers</h3>
-<div class="sourceCode"><pre class="sourceCode xml"><code class="sourceCode xml"><span class="kw">&lt;config&gt;</span>
+<span class="kw">&lt;/config&gt;</span></code></pre>
+                </div>
+              </div>
+              <div id="e-g--running-with-met-drivers" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#e-g--running-with-met-drivers" class="anchor"></a
+                  >E.g. Running with met drivers
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode xml"
+                  ><code class="sourceCode xml"><span class="kw">&lt;config&gt;</span>
   <span class="kw">&lt;mod_obj&gt;</span>leaf<span class="kw">&lt;/mod_obj&gt;</span>
   <span class="kw">&lt;leaf&gt;</span>
     <span class="kw">&lt;fnames&gt;</span>
@@ -151,17 +271,45 @@ <h3 class="hasAnchor">
       <span class="kw">&lt;etrans&gt;</span>'f_j_farquharwong1984'<span class="kw">&lt;/etrans&gt;</span>
      <span class="kw">&lt;/fnames&gt;</span>
   <span class="kw">&lt;/leaf&gt;</span>
-<span class="kw">&lt;/config&gt;</span></code></pre></div>
-</div>
-</div>
-<div id="full-pecan-xml-configuration-with-maat-options" class="section level2">
-<h2 class="hasAnchor">
-<a href="#full-pecan-xml-configuration-with-maat-options" class="anchor"></a>Full PEcAn XML configuration with MAAT options</h2>
-<div id="e-g--pecan-xml-file-with-maat-configuration-options-" class="section level3">
-<h3 class="hasAnchor">
-<a href="#e-g--pecan-xml-file-with-maat-configuration-options-" class="anchor"></a>E.g. pecan.xml file with MAAT configuration options.</h3>
-<p>In this example the MAAT model is configured for a temperate deciduous forest based on the temperate.deciduous PFT in the BETYdb database (<a href="https://www.betydb.org/pfts/2000000044" class="uri">https://www.betydb.org/pfts/2000000044</a>).</p>
-<div class="sourceCode"><pre class="sourceCode xml"><code class="sourceCode xml"><span class="kw">&lt;?xml</span> version="1.0"<span class="kw">?&gt;</span>
+<span class="kw">&lt;/config&gt;</span></code></pre>
+                </div>
+              </div>
+            </div>
+            <div
+              id="full-pecan-xml-configuration-with-maat-options"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#full-pecan-xml-configuration-with-maat-options"
+                  class="anchor"
+                ></a
+                >Full PEcAn XML configuration with MAAT options
+              </h2>
+              <div
+                id="e-g--pecan-xml-file-with-maat-configuration-options-"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#e-g--pecan-xml-file-with-maat-configuration-options-"
+                    class="anchor"
+                  ></a
+                  >E.g. pecan.xml file with MAAT configuration options.
+                </h3>
+                <p>
+                  In this example the MAAT model is configured for a temperate
+                  deciduous forest based on the temperate.deciduous PFT in the
+                  BETYdb database (<a
+                    href="https://www.betydb.org/pfts/2000000044"
+                    class="uri"
+                    >https://www.betydb.org/pfts/2000000044</a
+                  >).
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode xml"
+                  ><code class="sourceCode xml"><span class="kw">&lt;?xml</span> version="1.0"<span class="kw">?&gt;</span>
 <span class="kw">&lt;pecan&gt;</span>
   <span class="kw">&lt;outdir&gt;</span>~/scratch/maat_pecan_test_run/<span class="kw">&lt;/outdir&gt;</span>
   
@@ -256,14 +404,28 @@ <h3 class="hasAnchor">
     <span class="kw">&lt;name&gt;</span>localhost<span class="kw">&lt;/name&gt;</span>
   <span class="kw">&lt;/host&gt;</span>
   
-<span class="kw">&lt;/pecan&gt;</span></code></pre></div>
-</div>
-</div>
-<div id="simple-maat-run-in-pecan" class="section level2">
-<h2 class="hasAnchor">
-<a href="#simple-maat-run-in-pecan" class="anchor"></a>Simple MAAT run in PEcAn</h2>
-<p>In this example we will run ten MAAT model ensembles in serial based on parameter values derived from the temperate.deciduous PFT in the BETYdb database (<a href="https://www.betydb.org/pfts/2000000044" class="uri">https://www.betydb.org/pfts/2000000044</a>) and the PEcAn meta analysis step</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAn.all)
+<span class="kw">&lt;/pecan&gt;</span></code></pre>
+                </div>
+              </div>
+            </div>
+            <div id="simple-maat-run-in-pecan" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#simple-maat-run-in-pecan" class="anchor"></a>Simple
+                MAAT run in PEcAn
+              </h2>
+              <p>
+                In this example we will run ten MAAT model ensembles in serial
+                based on parameter values derived from the temperate.deciduous
+                PFT in the BETYdb database (<a
+                  href="https://www.betydb.org/pfts/2000000044"
+                  class="uri"
+                  >https://www.betydb.org/pfts/2000000044</a
+                >) and the PEcAn meta analysis step
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">library</span>(PEcAn.all)
 <span class="kw">library</span>(PEcAn.utils)
 <span class="kw">library</span>(RCurl)
 
@@ -381,48 +543,77 @@ <h2 class="hasAnchor">
 <span class="kw">lines</span>(x_axis,PEcAn.utils<span class="op">::</span><span class="kw">misc.convert</span>(timeseries_stats[<span class="dv">2</span>,],<span class="st">"kg C m-2 s-1"</span>,<span class="st">"umol C m-2 s-1"</span>),<span class="dt">lwd=</span><span class="dv">1</span>, <span class="dt">lty=</span><span class="dv">1</span>, <span class="dt">col=</span><span class="st">"light grey"</span>)
 
 <span class="co"># close plot</span>
-<span class="kw">dev.off</span>()</code></pre></div>
-<p>Example output MAAT assimilation rate from the five PEcAn model esemble simulations. The green shaded area represents the ensemble spread and the grey line shows the mean simulation.</p>
-<div class="figure">
-<img src="graphics/example_assimilation_rate.png" alt="Example output MAAT assimilation rate from the five PEcAn model esemble simulations"><p class="caption">Example output MAAT assimilation rate from the five PEcAn model esemble simulations</p>
-</div>
-</div>
-</div>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li>
-<a href="#overview">Overview</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#maat-installation-and-usage">MAAT Installation and usage</a></li>
-      <li><a href="#installing-the-r-packages">Installing the R packages</a></li>
-      <li><a href="#maat-xml-configuration">MAAT XML configuration</a></li>
-      <li><a href="#full-pecan-xml-configuration-with-maat-options">Full PEcAn XML configuration with MAAT options</a></li>
-      <li><a href="#simple-maat-run-in-pecan">Simple MAAT run in PEcAn</a></li>
-      </ul>
-</li>
-      </ul>
-</div>
+<span class="kw">dev.off</span>()</code></pre>
+              </div>
+              <p>
+                Example output MAAT assimilation rate from the five PEcAn model
+                esemble simulations. The green shaded area represents the
+                ensemble spread and the grey line shows the mean simulation.
+              </p>
+              <div class="figure">
+                <img
+                  src="graphics/example_assimilation_rate.png"
+                  alt="Example output MAAT assimilation rate from the five PEcAn model esemble simulations"
+                />
+                <p class="caption">
+                  Example output MAAT assimilation rate from the five PEcAn
+                  model esemble simulations
+                </p>
+              </div>
+            </div>
+          </div>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#overview">Overview</a>
+                <ul class="nav nav-pills nav-stacked">
+                  <li>
+                    <a href="#maat-installation-and-usage"
+                      >MAAT Installation and usage</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#installing-the-r-packages"
+                      >Installing the R packages</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#maat-xml-configuration">MAAT XML configuration</a>
+                  </li>
+                  <li>
+                    <a href="#full-pecan-xml-configuration-with-maat-options"
+                      >Full PEcAn XML configuration with MAAT options</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#simple-maat-run-in-pecan"
+                      >Simple MAAT run in PEcAn</a
+                    >
+                  </li>
+                </ul>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by Shawn Serbin, Anthony Walker.</p>
+        </div>
 
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 </html>
diff --git a/models/maat/docs/authors.html b/models/maat/docs/authors.html
index 2477ebb..bf12333 100644
--- a/models/maat/docs/authors.html
+++ b/models/maat/docs/authors.html
@@ -2,141 +2,173 @@
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 <html>
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+    ></script>
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.MAAT</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/create_amerifluxLBL_drivers_for_maat.html">PEcAn: Generating met drivers for the MAAT model using AmerifluxLBL tower observations</a>
-    </li>
-    <li>
-      <a href="articles/running_maat_in_pecan.html">Running MAAT in PEcAn</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.MAAT</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a
+                        href="articles/create_amerifluxLBL_drivers_for_maat.html"
+                        >PEcAn: Generating met drivers for the MAAT model using
+                        AmerifluxLBL tower observations</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/running_maat_in_pecan.html"
+                        >Running MAAT in PEcAn</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Shawn Serbin</strong>. Author, maintainer. 
-        </p>
-      </li>
-      <li>
-        <p><strong>Anthony Walker</strong>. Author. 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Shawn Serbin</strong>. Author, maintainer.</p>
+            </li>
+            <li>
+              <p><strong>Anthony Walker</strong>. Author.</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by Shawn Serbin, Anthony Walker.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by Shawn Serbin, Anthony Walker.</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/maat/docs/docsearch.css b/models/maat/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/maat/docs/docsearch.css
+++ b/models/maat/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/maat/docs/docsearch.js b/models/maat/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/maat/docs/docsearch.js
+++ b/models/maat/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/maat/docs/index.html b/models/maat/docs/index.html
index 3348a73..01f2d8e 100644
--- a/models/maat/docs/index.html
+++ b/models/maat/docs/index.html
@@ -1,149 +1,294 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the MAAT model • PEcAn.MAAT</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the MAAT model">
-<meta property="og:description" content="This module provides functions to wrap the MAAT model into the PEcAn workflows.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn package for integration of the MAAT model • PEcAn.MAAT</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the MAAT model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to wrap the MAAT model into the PEcAn workflows."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.MAAT</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.MAAT</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/create_amerifluxLBL_drivers_for_maat.html">PEcAn: Generating met drivers for the MAAT model using AmerifluxLBL tower observations</a>
-    </li>
-    <li>
-      <a href="articles/running_maat_in_pecan.html">Running MAAT in PEcAn</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    <div id="the-multi-assumption-architecture-and-testbed-maat-modelling-system-pecan-module" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#the-multi-assumption-architecture-and-testbed-maat-modelling-system-pecan-module" class="anchor"></a>The Multi-Assumption Architecture and Testbed (MAAT) modelling system PEcAn module</h1></div>
-<p><strong>PEcAn module corresponding author</strong> <br> Shawn Serbin <br> Environmental and Climate Sciences Department <br> Brookhaven National Laboratory <br><a href="mailto:sserbin@bnl.gov">sserbin@bnl.gov</a> <br></p>
-<p><strong>MAAT model description and technical article:</strong> <a href="https://www.geosci-model-dev.net/11/3159/2018/gmd-11-3159-2018.html" class="uri">https://www.geosci-model-dev.net/11/3159/2018/gmd-11-3159-2018.html</a> <br><strong>MAAT model author:</strong> Anthony Walker (<a href="mailto:walkerap@ornl.gov">walkerap@ornl.gov</a>) <br></p>
-<div id="maat-installation-and-usage" class="section level2">
-<h2 class="hasAnchor">
-<a href="#maat-installation-and-usage" class="anchor"></a>MAAT Installation and usage</h2>
-<p><strong>MAAT model source:</strong> <a href="https://github.com/walkeranthonyp/MAAT" class="uri">https://github.com/walkeranthonyp/MAAT</a> <br> Follow the instructions found here: <a href="https://github.com/walkeranthonyp/MAAT/blob/master/README.html" class="uri">https://github.com/walkeranthonyp/MAAT/blob/master/README.md</a> <br></p>
-</div>
-<div id="maat-module-installation" class="section level2">
-<h2 class="hasAnchor">
-<a href="#maat-module-installation" class="anchor"></a>MAAT module installation</h2>
-<p>R dependencies: PEcAn packages - PEcAn.logger, PEcAn.remote, PEcAn.settings, PEcAn.utils. Additional dependencies: lubridate, ncdf4, udunits2, XML, and those within each package <br></p>
-<p>–ncdf4 requires netCDF installed at the system level</p>
-<p>Easiest way to install is via <code>install_github</code> from the <code>devtools</code> package. <br></p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools)
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a
+                        href="articles/create_amerifluxLBL_drivers_for_maat.html"
+                        >PEcAn: Generating met drivers for the MAAT model using
+                        AmerifluxLBL tower observations</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/running_maat_in_pecan.html"
+                        >Running MAAT in PEcAn</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div
+            id="the-multi-assumption-architecture-and-testbed-maat-modelling-system-pecan-module"
+            class="section level1"
+          >
+            <div class="page-header">
+              <h1 class="hasAnchor">
+                <a
+                  href="#the-multi-assumption-architecture-and-testbed-maat-modelling-system-pecan-module"
+                  class="anchor"
+                ></a
+                >The Multi-Assumption Architecture and Testbed (MAAT) modelling
+                system PEcAn module
+              </h1>
+            </div>
+            <p>
+              <strong>PEcAn module corresponding author</strong> <br />
+              Shawn Serbin <br />
+              Environmental and Climate Sciences Department <br />
+              Brookhaven National Laboratory <br /><a
+                href="mailto:sserbin@bnl.gov"
+                >sserbin@bnl.gov</a
+              >
+              <br />
+            </p>
+            <p>
+              <strong>MAAT model description and technical article:</strong>
+              <a
+                href="https://www.geosci-model-dev.net/11/3159/2018/gmd-11-3159-2018.html"
+                class="uri"
+                >https://www.geosci-model-dev.net/11/3159/2018/gmd-11-3159-2018.html</a
+              >
+              <br /><strong>MAAT model author:</strong> Anthony Walker (<a
+                href="mailto:walkerap@ornl.gov"
+                >walkerap@ornl.gov</a
+              >) <br />
+            </p>
+            <div id="maat-installation-and-usage" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#maat-installation-and-usage" class="anchor"></a>MAAT
+                Installation and usage
+              </h2>
+              <p>
+                <strong>MAAT model source:</strong>
+                <a href="https://github.com/walkeranthonyp/MAAT" class="uri"
+                  >https://github.com/walkeranthonyp/MAAT</a
+                >
+                <br />
+                Follow the instructions found here:
+                <a
+                  href="https://github.com/walkeranthonyp/MAAT/blob/master/README.html"
+                  class="uri"
+                  >https://github.com/walkeranthonyp/MAAT/blob/master/README.md</a
+                >
+                <br />
+              </p>
+            </div>
+            <div id="maat-module-installation" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#maat-module-installation" class="anchor"></a>MAAT
+                module installation
+              </h2>
+              <p>
+                R dependencies: PEcAn packages - PEcAn.logger, PEcAn.remote,
+                PEcAn.settings, PEcAn.utils. Additional dependencies: lubridate,
+                ncdf4, udunits2, XML, and those within each package <br />
+              </p>
+              <p>–ncdf4 requires netCDF installed at the system level</p>
+              <p>
+                Easiest way to install is via <code>install_github</code> from
+                the <code>devtools</code> package. <br />
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">library</span>(devtools)
 <span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir=</span><span class="st">"base/logger"</span>)
 <span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir=</span><span class="st">"base/remote"</span>)
 <span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir=</span><span class="st">"base/settings"</span>)
 <span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir=</span><span class="st">"base/utils"</span>)
-<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir=</span><span class="st">"models/maat"</span>)</code></pre></div>
-<p>If you want a specific branch, do <code><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github(..., ref="&lt;branch&gt;")</a></code>.</p>
-<p>From there, you should be able to load the package in your typical R session.</p>
-</div>
-<div id="maat-pecan-run-examples" class="section level2">
-<h2 class="hasAnchor">
-<a href="#maat-pecan-run-examples" class="anchor"></a>MAAT-PEcAn run examples</h2>
-<p>See <a href="vignettes/">vignettes</a></p>
-</div>
-</div>
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li>Shawn Serbin <br><small class="roles"> Author, maintainer </small>  </li>
-<li>Anthony Walker <br><small class="roles"> Author </small>  </li>
-</ul>
-</div>
-
-  </div>
-</div>
-
+<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>, <span class="dt">ref =</span> <span class="st">"develop"</span>, <span class="dt">subdir=</span><span class="st">"models/maat"</span>)</code></pre>
+              </div>
+              <p>
+                If you want a specific branch, do
+                <code
+                  ><a
+                    href="http://www.rdocumentation.org/packages/devtools/topics/install_github"
+                    >install_github(..., ref="&lt;branch&gt;")</a
+                  ></code
+                >.
+              </p>
+              <p>
+                From there, you should be able to load the package in your
+                typical R session.
+              </p>
+            </div>
+            <div id="maat-pecan-run-examples" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#maat-pecan-run-examples" class="anchor"></a>MAAT-PEcAn
+                run examples
+              </h2>
+              <p>See <a href="vignettes/">vignettes</a></p>
+            </div>
+          </div>
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by Shawn Serbin, Anthony Walker.</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li>
+                Shawn Serbin <br /><small class="roles">
+                  Author, maintainer
+                </small>
+              </li>
+              <li>
+                Anthony Walker <br /><small class="roles"> Author </small>
+              </li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by Shawn Serbin, Anthony Walker.</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/maat/docs/pkgdown.css b/models/maat/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/maat/docs/pkgdown.css
+++ b/models/maat/docs/pkgdown.css
@@ -13,7 +13,8 @@
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@@ -68,7 +69,7 @@ img {
 
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@@ -133,19 +135,41 @@ a.anchor {
 
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-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
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-.ref-index td {vertical-align: top;}
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+  text-align: right;
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+.ref-arguments th,
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+}
 
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@@ -162,7 +186,8 @@ pre {
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@@ -183,7 +208,8 @@ pre .img img {
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-code a, pre a {
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@@ -191,15 +217,35 @@ a.sourceLine:hover {
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-.fl      {color: #1514b5;}
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-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
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diff --git a/models/maat/docs/pkgdown.js b/models/maat/docs/pkgdown.js
index de9bd72..ddf7401 100644
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@@ -1,18 +1,21 @@
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-
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-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
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@@ -47,40 +49,38 @@
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     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
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-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
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-    element.setAttribute('data-original-title', msg);
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+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
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+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
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+  if (Clipboard.isSupported()) {
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+      var copyButton =
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+})(window.jQuery || window.$);
diff --git a/models/maat/docs/reference/convert.samples.MAAT.html b/models/maat/docs/reference/convert.samples.MAAT.html
index 28d4008..8ded46e 100644
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+                      >
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+                    <li>
+                      <a href="../articles/running_maat_in_pecan.html"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert samples for MAAT</h1>
-    
-    <div class="hidden name"><code>convert.samples.MAAT.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>convert parameters and parameter names from PEcAn database default units/names with MAAT</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>convert.samples.MAAT</span>(<span class='no'>trait.samples</span>, <span class='no'>runid</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>a matrix or dataframe of samples from the trait distribution</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>optional parameter for debugging</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>matrix or dataframe with values transformed</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Performs model specific unit conversions on a a list of trait values,
-such as those provided to write.config</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert samples for MAAT</h1>
+
+            <div class="hidden name"><code>convert.samples.MAAT.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              convert parameters and parameter names from PEcAn database default
+              units/names with MAAT
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>convert.samples.MAAT</span>(<span class='no'>trait.samples</span>, <span class='no'>runid</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.samples</th>
+              <td>
+                <p>
+                  a matrix or dataframe of samples from the trait distribution
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>optional parameter for debugging</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>matrix or dataframe with values transformed</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Performs model specific unit conversions on a a list of trait
+            values, such as those provided to write.config
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, Anthony Walker
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, Anthony Walker
+        </div>
+      </div>
 
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+                        >PEcAn: Generating met drivers for the MAAT model using
+                        AmerifluxLBL tower observations</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/running_maat_in_pecan.html"
+                        >Running MAAT in PEcAn</a
+                      >
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-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="convert.samples.MAAT.html">convert.samples.MAAT()</a></code> </p>
-        </td>
-        <td><p>Convert samples for MAAT</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2model.MAAT.html">met2model.MAAT()</a></code> </p>
-        </td>
-        <td><p>Create MAAT met driver files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.MAAT.html">model2netcdf.MAAT()</a></code> </p>
-        </td>
-        <td><p>Function to convert MAAT model output to standard netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.MAAT.html">write.config.MAAT()</a></code> </p>
-        </td>
-        <td><p>Write MAAT model configuration files</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="convert.samples.MAAT.html"
+                        >convert.samples.MAAT()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Convert samples for MAAT</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.MAAT.html">met2model.MAAT()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create MAAT met driver files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.MAAT.html"
+                        >model2netcdf.MAAT()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function to convert MAAT model output to standard netCDF
+                    format
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.MAAT.html"
+                        >write.config.MAAT()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write MAAT model configuration files</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by Shawn Serbin, Anthony Walker.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by Shawn Serbin, Anthony Walker.</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/maat/docs/reference/met2model.MAAT.html b/models/maat/docs/reference/met2model.MAAT.html
index c1f3464..a3338ef 100644
--- a/models/maat/docs/reference/met2model.MAAT.html
+++ b/models/maat/docs/reference/met2model.MAAT.html
@@ -2,192 +2,253 @@
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+
+    <!-- Font Awesome icons -->
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+    ></script>
+
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-        <a class="navbar-link" href="../index.html">PEcAn.MAAT</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/create_amerifluxLBL_drivers_for_maat.html">PEcAn: Generating met drivers for the MAAT model using AmerifluxLBL tower observations</a>
-    </li>
-    <li>
-      <a href="../articles/running_maat_in_pecan.html">Running MAAT in PEcAn</a>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
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+                <a class="navbar-link" href="../index.html">PEcAn.MAAT</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+                    class="dropdown-toggle"
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+                    role="button"
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a
+                        href="../articles/create_amerifluxLBL_drivers_for_maat.html"
+                        >PEcAn: Generating met drivers for the MAAT model using
+                        AmerifluxLBL tower observations</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/running_maat_in_pecan.html"
+                        >Running MAAT in PEcAn</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create MAAT met driver files</h1>
-    
-    <div class="hidden name"><code>met2model.MAAT.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create MAAT met driver files</h1>
 
-    <div class="ref-description">
-    
-    <p>met2model wrapper for MAAT</p>
-    
-    </div>
+            <div class="hidden name"><code>met2model.MAAT.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2model.MAAT</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>leap_year</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs (CF met drivers) are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where MAAT met outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    <tr>
-      <th>leap_year</th>
-      <td><p>Enforce Leap-years? If set to TRUE, will require leap years to have 366 days. 
-If set to false, will require all years to have 365 days. Default = TRUE.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Shawn P. Serbin
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>met2model wrapper for MAAT</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Shawn Serbin, Anthony Walker.</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.MAAT</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>leap_year</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td>
+                <p>location on disk where inputs (CF met drivers) are stored</p>
+              </td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td>
+                <p>location on disk where MAAT met outputs will be stored</p>
+              </td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+            <tr>
+              <th>leap_year</th>
+              <td>
+                <p>
+                  Enforce Leap-years? If set to TRUE, will require leap years to
+                  have 366 days. If set to false, will require all years to have
+                  365 days. Default = TRUE.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Shawn P. Serbin
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by Shawn Serbin, Anthony Walker.</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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-
+    </div>
   </body>
 </html>
-
diff --git a/models/maat/docs/reference/model2netcdf.MAAT.html b/models/maat/docs/reference/model2netcdf.MAAT.html
index 40c17e0..062e99b 100644
--- a/models/maat/docs/reference/model2netcdf.MAAT.html
+++ b/models/maat/docs/reference/model2netcdf.MAAT.html
@@ -2,162 +2,224 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<!-- Bootstrap -->
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to convert MAAT model output to standard netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.MAAT.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function to convert MAAT model output to standard netCDF format
+            </h1>
 
-    <div class="ref-description">
-    
-    <p>Convert MAAT output to netCDF</p>
-    
-    </div>
+            <div class="hidden name"><code>model2netcdf.MAAT.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert MAAT output to netCDF</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>model2netcdf.MAAT</span>(<span class='no'>rundir</span>, <span class='no'>outdir</span>, <span class='kw'>sitelat</span> <span class='kw'>=</span> -<span class='fl'>999</span>, <span class='kw'>sitelon</span> <span class='kw'>=</span> -<span class='fl'>999</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.MAAT</span>(<span class='no'>rundir</span>, <span class='no'>outdir</span>, <span class='kw'>sitelat</span> <span class='kw'>=</span> -<span class='fl'>999</span>, <span class='kw'>sitelon</span> <span class='kw'>=</span> -<span class='fl'>999</span>,
   <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>end_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>rundir</th>
-      <td><p>Location of MAAT model run (i.e. MAAT project) directory with all required model run inputs.
-This is needed to identify model runs with and without met drivers and control the model output conversion process</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of MAAT model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Converts all output contained in a folder to netCDF.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>rundir</th>
+              <td>
+                <p>
+                  Location of MAAT model run (i.e. MAAT project) directory with
+                  all required model run inputs. This is needed to identify
+                  model runs with and without met drivers and control the model
+                  output conversion process
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of MAAT model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Converts all output contained in a folder to netCDF.</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>run_dir</span> <span class='kw'>&lt;-</span> <span class='st'>"~/scratch/run/"</span>
 <span class='kw'>if</span> (! <span class='fu'>file.exists</span>(<span class='no'>run_dir</span>)) <span class='fu'>dir.create</span>(<span class='no'>run_dir</span>,<span class='kw'>recursive</span><span class='kw'>=</span><span class='fl'>TRUE</span>)
 <span class='no'>output_dir</span> <span class='kw'>&lt;-</span> <span class='st'>"~/scratch/out/"</span>
@@ -178,38 +240,34 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Shawn Serbin, Anthony Walker
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Shawn Serbin, Anthony Walker.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
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-  
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diff --git a/models/maat/docs/reference/write.config.MAAT.html b/models/maat/docs/reference/write.config.MAAT.html
index 3bcb603..9929ff3 100644
--- a/models/maat/docs/reference/write.config.MAAT.html
+++ b/models/maat/docs/reference/write.config.MAAT.html
@@ -2,187 +2,237 @@
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+                data-target="#navbar"
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.MAAT</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
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+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a
+                        href="../articles/create_amerifluxLBL_drivers_for_maat.html"
+                        >PEcAn: Generating met drivers for the MAAT model using
+                        AmerifluxLBL tower observations</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/running_maat_in_pecan.html"
+                        >Running MAAT in PEcAn</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write MAAT model configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.MAAT.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a MAAT config file.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.MAAT</span>(<span class='kw'>defaults</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file for MAAT for given run</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write MAAT model configuration files</h1>
+
+            <div class="hidden name"><code>write.config.MAAT.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a MAAT config file.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.MAAT</span>(<span class='kw'>defaults</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file for MAAT for given run</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Requires a pft xml object, a list of trait values for a single model
+            run, and the name of the file to create
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, Anthony Walker, Rob Kooper, Chris Black
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, Anthony Walker, Rob Kooper, Chris Black
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by Shawn Serbin, Anthony Walker.</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by Shawn Serbin, Anthony Walker.</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index 1c910c8..2b1b301 100644
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+++ b/models/maespa/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.MAESPA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+            </div>
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-      <h1>License</h1>
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+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
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-
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+</pre
+          >
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/models/maespa/docs/authors.html b/models/maespa/docs/authors.html
index 52200b0..46885ad 100644
--- a/models/maespa/docs/authors.html
+++ b/models/maespa/docs/authors.html
@@ -2,122 +2,143 @@
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.MAESPA</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.MAESPA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Tony Gardella</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Tony Gardella</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/maespa/docs/docsearch.css b/models/maespa/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/maespa/docs/docsearch.css
+++ b/models/maespa/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/maespa/docs/docsearch.js b/models/maespa/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/maespa/docs/docsearch.js
+++ b/models/maespa/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/maespa/docs/index.html b/models/maespa/docs/index.html
index 5885872..0326b67 100644
--- a/models/maespa/docs/index.html
+++ b/models/maespa/docs/index.html
@@ -1,113 +1,171 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for ecological forecasts and reanalysis using MAESPA • PEcAn.MAESPA</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and reanalysis using MAESPA">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis using MAESPA
+      • PEcAn.MAESPA
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and reanalysis using MAESPA"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation.This package allows for MAESPA to be
-    run through the PEcAN workflow.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    run through the PEcAN workflow."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.MAESPA</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.This package allows for MAESPA to be
-    run through the PEcAN workflow.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
-
-  </div>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.MAESPA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.This package allows
+          for MAESPA to be run through the PEcAN workflow.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/maespa/docs/pkgdown.css b/models/maespa/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/maespa/docs/pkgdown.css
+++ b/models/maespa/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
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+html,
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@@ -68,7 +69,7 @@ img {
 
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+  display: inline-block;
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@@ -89,10 +90,12 @@ a.anchor {
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 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
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@@ -107,7 +110,6 @@ a.anchor {
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-
 /* Sidebar --------------------------*/
 
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@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
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-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
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   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
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 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
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+}
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+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/maespa/docs/pkgdown.js b/models/maespa/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/maespa/docs/pkgdown.js
+++ b/models/maespa/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
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@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/maespa/docs/reference/index.html b/models/maespa/docs/reference/index.html
index 11d2352..90dd581 100644
--- a/models/maespa/docs/reference/index.html
+++ b/models/maespa/docs/reference/index.html
@@ -2,156 +2,201 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.MAESPA</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.MAESPA</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
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+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Function reference" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.MAESPA</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.MAESPA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="met2model.MAESPA.html">met2model.MAESPA()</a></code> </p>
-        </td>
-        <td><p>met2model.MAESPA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.MAESPA.html">model2netcdf.MAESPA()</a></code> </p>
-        </td>
-        <td><p>Code to convert MAESPA's output into netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.MAESPA.html">write.config.MAESPA()</a></code> </p>
-        </td>
-        <td><p>Write MAESPA configuration files</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.MAESPA.html"
+                        >met2model.MAESPA()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2model.MAESPA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.MAESPA.html"
+                        >model2netcdf.MAESPA()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Code to convert MAESPA's output into netCDF format</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.MAESPA.html"
+                        >write.config.MAESPA()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write MAESPA configuration files</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/maespa/docs/reference/met2model.MAESPA.html b/models/maespa/docs/reference/met2model.MAESPA.html
index 9ebad1d..7e4887e 100644
--- a/models/maespa/docs/reference/met2model.MAESPA.html
+++ b/models/maespa/docs/reference/met2model.MAESPA.html
@@ -2,172 +2,209 @@
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-<!-- clipboard.js -->
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+                <a class="navbar-link" href="../index.html">PEcAn.MAESPA</a>
+                <span
+                  class="label label-default"
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+                  >1.6.0</span
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2model.MAESPA</h1>
-    
-    <div class="hidden name"><code>met2model.MAESPA.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2model.MAESPA</h1>
 
-    <div class="ref-description">
-    
-    <p>met2model wrapper for MAESPA</p>
-    
-    </div>
+            <div class="hidden name"><code>met2model.MAESPA.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2model.MAESPA</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Tony Gardella
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>met2model wrapper for MAESPA</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.MAESPA</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Tony Gardella
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/models/maespa/docs/reference/model2netcdf.MAESPA.html b/models/maespa/docs/reference/model2netcdf.MAESPA.html
index f295677..6963225 100644
--- a/models/maespa/docs/reference/model2netcdf.MAESPA.html
+++ b/models/maespa/docs/reference/model2netcdf.MAESPA.html
@@ -2,168 +2,207 @@
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+      Code to convert MAESPA's output into netCDF format — model2netcdf.MAESPA •
+      PEcAn.MAESPA
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      content="Code to convert MAESPA's output into netCDF format — model2netcdf.MAESPA"
+    />
+
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+      property="og:description"
+      content="Convert MAESPA output into the NACP Intercomparison format (ALMA using netCDF)"
+    />
+    <meta name="twitter:card" content="summary" />
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+                  class="label label-default"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Code to convert MAESPA's output into netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.MAESPA.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Code to convert MAESPA's output into netCDF format</h1>
 
-    <div class="ref-description">
-    
-    <p>Convert MAESPA output into the NACP Intercomparison format (ALMA using netCDF)</p>
-    
-    </div>
+            <div class="hidden name"><code>model2netcdf.MAESPA.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>model2netcdf.MAESPA</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='no'>stem_density</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of MAESPA output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>stem_density</th>
-      <td><p>Number of trees/plotsize. Values in trees.dat</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Tony Gardella
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Convert MAESPA output into the NACP Intercomparison format (ALMA
+              using netCDF)
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.MAESPA</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='no'>stem_density</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of MAESPA output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>stem_density</th>
+              <td><p>Number of trees/plotsize. Values in trees.dat</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Tony Gardella
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/maespa/docs/reference/write.config.MAESPA.html b/models/maespa/docs/reference/write.config.MAESPA.html
index fd75907..0071291 100644
--- a/models/maespa/docs/reference/write.config.MAESPA.html
+++ b/models/maespa/docs/reference/write.config.MAESPA.html
@@ -2,172 +2,210 @@
 <!DOCTYPE html>
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-<!-- Bootstrap -->
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-
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+      Write MAESPA configuration files — write.config.MAESPA • PEcAn.MAESPA
+    </title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
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+      crossorigin="anonymous"
+    ></script>
+
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+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
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+                data-target="#navbar"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.MAESPA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write MAESPA configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.MAESPA.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a config file for Maespa</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.MAESPA</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file for MAESPA for given run</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write MAESPA configuration files</h1>
+
+            <div class="hidden name"><code>write.config.MAESPA.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a config file for Maespa</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.MAESPA</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file for MAESPA for given run</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Requires a pft xml object, a list of trait values for a single model
+            run, and the name of the file to create
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Tony Gardella
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Tony Gardella
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/preles/docs/LICENSE-text.html b/models/preles/docs/LICENSE-text.html
index 87578bc..2411757 100644
--- a/models/preles/docs/LICENSE-text.html
+++ b/models/preles/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
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+    />
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.PRELES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.PRELES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/preles/docs/authors.html b/models/preles/docs/authors.html
index af05801..3a91f31 100644
--- a/models/preles/docs/authors.html
+++ b/models/preles/docs/authors.html
@@ -2,126 +2,146 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.PRELES</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.PRELES</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.PRELES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.PRELES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Tony Gardella</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Tony Gardella</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/preles/docs/docsearch.css b/models/preles/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/preles/docs/docsearch.css
+++ b/models/preles/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/preles/docs/docsearch.js b/models/preles/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/preles/docs/docsearch.js
+++ b/models/preles/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/preles/docs/index.html b/models/preles/docs/index.html
index c66d988..097c8c2 100644
--- a/models/preles/docs/index.html
+++ b/models/preles/docs/index.html
@@ -1,115 +1,172 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the PRELES model • PEcAn.PRELES</title>
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-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the PRELES model">
-<meta property="og:description" content="This module provides functions to run the PREdict Light use
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn package for integration of the PRELES model • PEcAn.PRELES
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    <!-- sticky kit -->
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+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the PRELES model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to run the PREdict Light use
     efficiency Evapotranspiration and Soil moisture (PRELES) model on the PEcAn
     project. The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool designed to simplify the management of model
     parameterization,execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    efficacy of scientific investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.PRELES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.PRELES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    This module provides functions to run the PREdict Light use
-    efficiency Evapotranspiration and Soil moisture (PRELES) model on the PEcAn
-    project. The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool designed to simplify the management of model
-    parameterization,execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
-  </div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          This module provides functions to run the PREdict Light use efficiency
+          Evapotranspiration and Soil moisture (PRELES) model on the PEcAn
+          project. The Predictive Ecosystem Carbon Analyzer (PEcAn) is a
+          scientific workflow management tool designed to simplify the
+          management of model parameterization,execution, and analysis. The goal
+          of PECAn is to streamline the interaction between data and models, and
+          to improve the efficacy of scientific investigation.
+        </div>
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-  </div>
-</div>
-
-
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/preles/docs/pkgdown.css b/models/preles/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/preles/docs/pkgdown.css
+++ b/models/preles/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
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+  display: inline-block;
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   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/preles/docs/pkgdown.js b/models/preles/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/preles/docs/pkgdown.js
+++ b/models/preles/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/preles/docs/reference/index.html b/models/preles/docs/reference/index.html
index 75cbe82..a09fbc8 100644
--- a/models/preles/docs/reference/index.html
+++ b/models/preles/docs/reference/index.html
@@ -2,150 +2,192 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<title>Function reference • PEcAn.PRELES</title>
-
-<!-- jquery -->
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-<!-- pkgdown -->
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-<script src="../pkgdown.js"></script>
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-
-
-<meta property="og:title" content="Function reference" />
-
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Function reference • PEcAn.PRELES</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-      <h1>Reference</h1>
-    </div>
-
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-
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-      
-      <col class="alias" />
-      <col class="title" />
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-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="runPRELES.jobsh.html">runPRELES.jobsh()</a></code> </p>
-        </td>
-        <td><p>Function to process ncdf file, run PRELES model, and convert output .nc file in CF standard</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.PRELES.html">write.config.PRELES()</a></code> </p>
-        </td>
-        <td><p>Write PRELES configuration files</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="runPRELES.jobsh.html"
+                        >runPRELES.jobsh()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function to process ncdf file, run PRELES model, and convert
+                    output .nc file in CF standard
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.PRELES.html"
+                        >write.config.PRELES()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write PRELES configuration files</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+          <p>Developed by .</p>
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diff --git a/models/preles/docs/reference/runPRELES.jobsh.html b/models/preles/docs/reference/runPRELES.jobsh.html
index 8bddb47..7455c0d 100644
--- a/models/preles/docs/reference/runPRELES.jobsh.html
+++ b/models/preles/docs/reference/runPRELES.jobsh.html
@@ -2,164 +2,206 @@
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+      Function to process ncdf file, run PRELES model, and convert output .nc
+      file in CF standard — runPRELES.jobsh • PEcAn.PRELES
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to process ncdf file, run PRELES model, and convert output .nc file in CF standard</h1>
-    
-    <div class="hidden name"><code>runPRELES.jobsh.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to process ncdf file, run PRELES model, and convert output .nc file in CF standard</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>runPRELES.jobsh</span>(<span class='no'>met.file</span>, <span class='no'>outdir</span>, <span class='no'>parameters</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start.date</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function to process ncdf file, run PRELES model, and convert
+              output .nc file in CF standard
+            </h1>
+
+            <div class="hidden name"><code>runPRELES.jobsh.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to process ncdf file, run PRELES model, and convert
+              output .nc file in CF standard
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>runPRELES.jobsh</span>(<span class='no'>met.file</span>, <span class='no'>outdir</span>, <span class='no'>parameters</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start.date</span>,
   <span class='no'>end.date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of PRELES model output</p></td>
-    </tr>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Tony Gardella, Michael Dietze
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of PRELES model output</p></td>
+            </tr>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Tony Gardella, Michael Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
-
diff --git a/models/preles/docs/reference/write.config.PRELES.html b/models/preles/docs/reference/write.config.PRELES.html
index 03443a5..12bc68f 100644
--- a/models/preles/docs/reference/write.config.PRELES.html
+++ b/models/preles/docs/reference/write.config.PRELES.html
@@ -2,165 +2,199 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Write PRELES configuration files — write.config.PRELES • PEcAn.PRELES
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write PRELES configuration files — write.config.PRELES"
+    />
+
+    <meta property="og:description" content="Writes a PRELES config file." />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.PRELES</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
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-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
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-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.PRELES</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write PRELES configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.PRELES.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a PRELES config file.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.PRELES</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file for PRELES for given run</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write PRELES configuration files</h1>
+
+            <div class="hidden name"><code>write.config.PRELES.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a PRELES config file.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.PRELES</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file for PRELES for given run</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Tony Gardella, Micheal Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Tony Gardella, Micheal Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/models/sipnet/docs/LICENSE-text.html b/models/sipnet/docs/LICENSE-text.html
index ceee9a6..b8682a0 100644
--- a/models/sipnet/docs/LICENSE-text.html
+++ b/models/sipnet/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.SIPNET</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                    <span class="fa fa-home fa-lg"></span>
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+              </ul>
+
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+          <!--/.container -->
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+        <!--/.navbar -->
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-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/authors.html b/models/sipnet/docs/authors.html
index a9c4c87..cfb79fd 100644
--- a/models/sipnet/docs/authors.html
+++ b/models/sipnet/docs/authors.html
@@ -2,122 +2,143 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.SIPNET</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.SIPNET</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.SIPNET</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.SIPNET</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/docsearch.css b/models/sipnet/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/sipnet/docs/docsearch.css
+++ b/models/sipnet/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/sipnet/docs/docsearch.js b/models/sipnet/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/sipnet/docs/docsearch.js
+++ b/models/sipnet/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/sipnet/docs/index.html b/models/sipnet/docs/index.html
index c1147d3..4c9a442 100644
--- a/models/sipnet/docs/index.html
+++ b/models/sipnet/docs/index.html
@@ -1,111 +1,169 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for ecological forecasts and reanalysis • PEcAn.SIPNET</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
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-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis •
+      PEcAn.SIPNET
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.">
-<meta name="twitter:card" content="summary">
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    efficacy of scientific investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
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-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.SIPNET</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
-  </div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.SIPNET</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-  </div>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/sipnet/docs/pkgdown.css b/models/sipnet/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/sipnet/docs/pkgdown.css
+++ b/models/sipnet/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/sipnet/docs/pkgdown.js b/models/sipnet/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/sipnet/docs/pkgdown.js
+++ b/models/sipnet/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/sipnet/docs/reference/get.model.output.SIPNET.html b/models/sipnet/docs/reference/get.model.output.SIPNET.html
index 14e6e5d..991a0ba 100644
--- a/models/sipnet/docs/reference/get.model.output.SIPNET.html
+++ b/models/sipnet/docs/reference/get.model.output.SIPNET.html
@@ -2,133 +2,165 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Retrieve model output from local or remote server — get.model.output.SIPNET • PEcAn.SIPNET</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Retrieve model output from local or remote server — get.model.output.SIPNET" />
-
-<meta property="og:description" content="Function to retrieve model output from local or remote server" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Retrieve model output from local or remote server —
+      get.model.output.SIPNET • PEcAn.SIPNET
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Retrieve model output from local or remote server — get.model.output.SIPNET"
+    />
+
+    <meta
+      property="og:description"
+      content="Function to retrieve model output from local or remote server"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
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-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Retrieve model output from local or remote server</h1>
-    
-    <div class="hidden name"><code>get.model.output.SIPNET.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to retrieve model output from local or remote server</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.model.output.SIPNET</span>(<span class='no'>settings</span>)</pre>
-        
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Retrieve model output from local or remote server</h1>
+
+            <div class="hidden name">
+              <code>get.model.output.SIPNET.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Function to retrieve model output from local or remote server</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.model.output.SIPNET</span>(<span class='no'>settings</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/reference/index.html b/models/sipnet/docs/reference/index.html
index 587b958..0a6f3cf 100644
--- a/models/sipnet/docs/reference/index.html
+++ b/models/sipnet/docs/reference/index.html
@@ -2,192 +2,280 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-<title>Function reference • PEcAn.SIPNET</title>
+    <title>Function reference • PEcAn.SIPNET</title>
 
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
 
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
 
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
 
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
 
+    <meta property="og:title" content="Function reference" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
-<meta property="og:title" content="Function reference" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
-      </header>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
 
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="get.model.output.SIPNET.html">get.model.output.SIPNET()</a></code> </p>
-        </td>
-        <td><p>Retrieve model output from local or remote server</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2model.SIPNET.html">met2model.SIPNET()</a></code> </p>
-        </td>
-        <td><p>met2model.SIPNET</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.SIPNET.html">model2netcdf.SIPNET()</a></code> </p>
-        </td>
-        <td><p>Function to convert SIPNET model output to standard netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_restart.SIPNET.html">read_restart.SIPNET()</a></code> </p>
-        </td>
-        <td><p>Read restart function for SDA with SIPNET</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="remove.config.SIPNET.html">remove.config.SIPNET()</a></code> </p>
-        </td>
-        <td><p>Clear out previous SIPNET config and parameter files.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sample.IC.SIPNET.html">sample.IC.SIPNET()</a></code> </p>
-        </td>
-        <td><p>sample.IC.SIPNET</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="split_inputs.SIPNET.html">split_inputs.SIPNET()</a></code> </p>
-        </td>
-        <td><p>split_inputs.SIPNET</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.SIPNET.html">write.config.SIPNET()</a></code> </p>
-        </td>
-        <td><p>Writes a configuration files for SIPNET model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_restart.SIPNET.html">write_restart.SIPNET()</a></code> </p>
-        </td>
-        <td><p>write_restart.SIPNET</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.model.output.SIPNET.html"
+                        >get.model.output.SIPNET()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Retrieve model output from local or remote server</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.SIPNET.html"
+                        >met2model.SIPNET()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2model.SIPNET</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.SIPNET.html"
+                        >model2netcdf.SIPNET()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function to convert SIPNET model output to standard netCDF
+                    format
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read_restart.SIPNET.html"
+                        >read_restart.SIPNET()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read restart function for SDA with SIPNET</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="remove.config.SIPNET.html"
+                        >remove.config.SIPNET()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Clear out previous SIPNET config and parameter files.</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="sample.IC.SIPNET.html"
+                        >sample.IC.SIPNET()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>sample.IC.SIPNET</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="split_inputs.SIPNET.html"
+                        >split_inputs.SIPNET()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>split_inputs.SIPNET</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.SIPNET.html"
+                        >write.config.SIPNET()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Writes a configuration files for SIPNET model</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write_restart.SIPNET.html"
+                        >write_restart.SIPNET()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>write_restart.SIPNET</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-      </footer>
-   </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
-  
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/reference/met2model.SIPNET.html b/models/sipnet/docs/reference/met2model.SIPNET.html
index aa52960..bd62e91 100644
--- a/models/sipnet/docs/reference/met2model.SIPNET.html
+++ b/models/sipnet/docs/reference/met2model.SIPNET.html
@@ -2,181 +2,233 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>met2model.SIPNET — met2model.SIPNET • PEcAn.SIPNET</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="met2model.SIPNET — met2model.SIPNET" />
-
-<meta property="og:description" content="met2model wrapper for SIPNET" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>met2model.SIPNET — met2model.SIPNET • PEcAn.SIPNET</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    <meta property="og:description" content="met2model wrapper for SIPNET" />
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+                <span
+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2model.SIPNET</h1>
-    
-    <div class="hidden name"><code>met2model.SIPNET.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2model.SIPNET</h1>
 
-    <div class="ref-description">
-    
-    <p>met2model wrapper for SIPNET</p>
-    
-    </div>
+            <div class="hidden name"><code>met2model.SIPNET.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2model.SIPNET</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>year.fragment</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files OR the full file name if year.fragment = TRUE</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    <tr>
-      <th>year.fragment</th>
-      <td><p>the function should ignore whether or not the data is stored as a set of complete years (such as for forecasts).</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>a data file to use for input - default behavior is to use all MET.year.nc files within the start and end year 
-range in the directory in.path.  If not null, overrides default behavior.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Luke Dramko, Michael Dietze, Alexey Shiklomanov, Rob Kooper
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>met2model wrapper for SIPNET</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.SIPNET</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>year.fragment</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td>
+                <p>
+                  prefix of input and output files OR the full file name if
+                  year.fragment = TRUE
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+            <tr>
+              <th>year.fragment</th>
+              <td>
+                <p>
+                  the function should ignore whether or not the data is stored
+                  as a set of complete years (such as for forecasts).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td>
+                <p>
+                  a data file to use for input - default behavior is to use all
+                  MET.year.nc files within the start and end year range in the
+                  directory in.path. If not null, overrides default behavior.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Luke Dramko, Michael Dietze, Alexey Shiklomanov, Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/reference/model2netcdf.SIPNET.html b/models/sipnet/docs/reference/model2netcdf.SIPNET.html
index 8d9c480..8f6ffaf 100644
--- a/models/sipnet/docs/reference/model2netcdf.SIPNET.html
+++ b/models/sipnet/docs/reference/model2netcdf.SIPNET.html
@@ -2,178 +2,215 @@
 <!DOCTYPE html>
 <html>
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+      Function to convert SIPNET model output to standard netCDF format —
+      model2netcdf.SIPNET • PEcAn.SIPNET
+    </title>
+
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+    ></script>
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Function to convert SIPNET model output to standard netCDF format — model2netcdf.SIPNET"
+    />
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+    <meta name="twitter:card" content="summary" />
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to convert SIPNET model output to standard netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.SIPNET.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function to convert SIPNET model output to standard netCDF format
+            </h1>
 
-    <div class="ref-description">
-    
-    <p>Convert SIPNET output to netCDF</p>
-    
-    </div>
+            <div class="hidden name"><code>model2netcdf.SIPNET.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert SIPNET output to netCDF</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>model2netcdf.SIPNET</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.SIPNET</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='no'>delete.raw</span>, <span class='no'>revision</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of SIPNET model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>revision</th>
-      <td><p>model revision</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>Flag for overwriting nc files or not</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Converts all output contained in a folder to netCDF.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of SIPNET model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>revision</th>
+              <td><p>model revision</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>Flag for overwriting nc files or not</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Converts all output contained in a folder to netCDF.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/reference/read_restart.SIPNET.html b/models/sipnet/docs/reference/read_restart.SIPNET.html
index 19e444f..b916a45 100644
--- a/models/sipnet/docs/reference/read_restart.SIPNET.html
+++ b/models/sipnet/docs/reference/read_restart.SIPNET.html
@@ -2,173 +2,208 @@
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 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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+      Read restart function for SDA with SIPNET — read_restart.SIPNET •
+      PEcAn.SIPNET
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Read restart function for SDA with SIPNET — read_restart.SIPNET"
+    />
+
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+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
   </head>
 
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-        <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
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-        
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-      
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read restart function for SDA with SIPNET</h1>
-    
-    <div class="hidden name"><code>read_restart.SIPNET.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Read Restart for SIPNET</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_restart.SIPNET</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>, <span class='no'>var.names</span>, <span class='no'>params</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Output directory</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>Run ID</p></td>
-    </tr>
-    <tr>
-      <th>stop.time</th>
-      <td><p>Year that is being read</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>var.names</th>
-      <td><p>Variable names to be extracted</p></td>
-    </tr>
-    <tr>
-      <th>params</th>
-      <td><p>Any parameters required for state calculations</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>X.vec      vector of forecasts</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read restart function for SDA with SIPNET</h1>
+
+            <div class="hidden name"><code>read_restart.SIPNET.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Read Restart for SIPNET</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_restart.SIPNET</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>, <span class='no'>var.names</span>, <span class='no'>params</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Output directory</p></td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>Run ID</p></td>
+            </tr>
+            <tr>
+              <th>stop.time</th>
+              <td><p>Year that is being read</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>var.names</th>
+              <td><p>Variable names to be extracted</p></td>
+            </tr>
+            <tr>
+              <th>params</th>
+              <td><p>Any parameters required for state calculations</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>X.vec vector of forecasts</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho <a href='mailto:araiho@nd.edu'>araiho@nd.edu</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho <a href="mailto:araiho@nd.edu">araiho@nd.edu</a>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/reference/remove.config.SIPNET.html b/models/sipnet/docs/reference/remove.config.SIPNET.html
index 7551bc6..28fa53f 100644
--- a/models/sipnet/docs/reference/remove.config.SIPNET.html
+++ b/models/sipnet/docs/reference/remove.config.SIPNET.html
@@ -2,157 +2,197 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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+      remove.config.SIPNET • PEcAn.SIPNET
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+    />
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+    ></script>
+
+    <!-- sticky kit -->
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+
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+      content="Clear out previous SIPNET config and parameter files. — remove.config.SIPNET"
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+    <![endif]-->
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+                type="button"
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Clear out previous SIPNET config and parameter files.</h1>
-    
-    <div class="hidden name"><code>remove.config.SIPNET.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Clear out previous SIPNET config and parameter files.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>remove.config.SIPNET</span>(<span class='no'>main.outdir</span>, <span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>main.outdir</th>
-      <td><p>Primary PEcAn output directory (will be depreciated)</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings file</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing, removes config files as side effect</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Clear out previous SIPNET config and parameter files.</h1>
+
+            <div class="hidden name"><code>remove.config.SIPNET.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Clear out previous SIPNET config and parameter files.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>remove.config.SIPNET</span>(<span class='no'>main.outdir</span>, <span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>main.outdir</th>
+              <td>
+                <p>Primary PEcAn output directory (will be depreciated)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings file</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing, removes config files as side effect</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/reference/sample.IC.SIPNET.html b/models/sipnet/docs/reference/sample.IC.SIPNET.html
index 3846525..39a616d 100644
--- a/models/sipnet/docs/reference/sample.IC.SIPNET.html
+++ b/models/sipnet/docs/reference/sample.IC.SIPNET.html
@@ -2,157 +2,189 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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+
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+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    />
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+    <![endif]-->
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   <body>
     <div class="container template-reference-topic">
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+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+                </li>
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+
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>sample.IC.SIPNET</h1>
-    
-    <div class="hidden name"><code>sample.IC.SIPNET.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>samples intial conditions for SIPNET</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sample.IC.SIPNET</span>(<span class='no'>ne</span>, <span class='no'>state</span>, <span class='kw'>year</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ne</th>
-      <td><p>number of ensembles</p></td>
-    </tr>
-    <tr>
-      <th>state</th>
-      <td><p>state variables you want to pull</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>IC matrix of initial conditions</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>sample.IC.SIPNET</h1>
+
+            <div class="hidden name"><code>sample.IC.SIPNET.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>samples intial conditions for SIPNET</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sample.IC.SIPNET</span>(<span class='no'>ne</span>, <span class='no'>state</span>, <span class='kw'>year</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ne</th>
+              <td><p>number of ensembles</p></td>
+            </tr>
+            <tr>
+              <th>state</th>
+              <td><p>state variables you want to pull</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>IC matrix of initial conditions</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze and Ann Raiho
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze and Ann Raiho
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/reference/split_inputs.SIPNET.html b/models/sipnet/docs/reference/split_inputs.SIPNET.html
index 40585be..da66bcb 100644
--- a/models/sipnet/docs/reference/split_inputs.SIPNET.html
+++ b/models/sipnet/docs/reference/split_inputs.SIPNET.html
@@ -2,158 +2,195 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>split_inputs.SIPNET — split_inputs.SIPNET • PEcAn.SIPNET</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-<div class="row">
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-    <h1>split_inputs.SIPNET</h1>
-    
-    <div class="hidden name"><code>split_inputs.SIPNET.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>split_inputs.SIPNET</h1>
 
-    <div class="ref-description">
-    
-    <p>Splits climate met for SIPNET</p>
-    
-    </div>
+            <div class="hidden name"><code>split_inputs.SIPNET.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Splits climate met for SIPNET</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>split_inputs.SIPNET</span>(<span class='no'>settings</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>inputs</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>split_inputs.SIPNET</span>(<span class='no'>settings</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>inputs</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>outpath</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outpath</th>
-      <td><p>if specified, write output to a new directory. Default NULL writes back to the directory being read</p></td>
-    </tr>
-    <tr>
-      <th>ens</th>
-      <td><p>ensemble number. default = 1</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>file split up climate file</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outpath</th>
+              <td>
+                <p>
+                  if specified, write output to a new directory. Default NULL
+                  writes back to the directory being read
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ens</th>
+              <td><p>ensemble number. default = 1</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>file split up climate file</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze and Ann Raiho
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze and Ann Raiho
+        </div>
+      </div>
 
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diff --git a/models/sipnet/docs/reference/write.config.SIPNET.html b/models/sipnet/docs/reference/write.config.SIPNET.html
index 5fa219f..1b090cd 100644
--- a/models/sipnet/docs/reference/write.config.SIPNET.html
+++ b/models/sipnet/docs/reference/write.config.SIPNET.html
@@ -2,138 +2,168 @@
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+      PEcAn.SIPNET
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-<div class="row">
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-    <div class="page-header">
-    <h1>Writes a configuration files for SIPNET model</h1>
-    
-    <div class="hidden name"><code>write.config.SIPNET.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Writes a configuration files for SIPNET model</h1>
 
-    <div class="ref-description">
-    
-    <p>Writes a configuration files for your model</p>
-    
-    </div>
+            <div class="hidden name"><code>write.config.SIPNET.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>write.config.SIPNET</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>,
-  <span class='kw'>inputs</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>IC</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>restart</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>spinup</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-        
+          <div class="ref-description">
+            <p>Writes a configuration files for your model</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.SIPNET</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>,
+  <span class='kw'>inputs</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>IC</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>restart</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>spinup</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/sipnet/docs/reference/write_restart.SIPNET.html b/models/sipnet/docs/reference/write_restart.SIPNET.html
index 3aca0ea..5ad0669 100644
--- a/models/sipnet/docs/reference/write_restart.SIPNET.html
+++ b/models/sipnet/docs/reference/write_restart.SIPNET.html
@@ -2,178 +2,210 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>write_restart.SIPNET — write_restart.SIPNET • PEcAn.SIPNET</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
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-<script src="../pkgdown.js"></script>
-
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-
-<meta property="og:title" content="write_restart.SIPNET — write_restart.SIPNET" />
-
-<meta property="og:description" content="Write restart files for SIPNET" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>write_restart.SIPNET — write_restart.SIPNET • PEcAn.SIPNET</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="write_restart.SIPNET — write_restart.SIPNET"
+    />
+
+    <meta property="og:description" content="Write restart files for SIPNET" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.SIPNET</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>write_restart.SIPNET</h1>
-    
-    <div class="hidden name"><code>write_restart.SIPNET.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>write_restart.SIPNET</h1>
 
-    <div class="ref-description">
-    
-    <p>Write restart files for SIPNET</p>
-    
-    </div>
+            <div class="hidden name"><code>write_restart.SIPNET.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Write restart files for SIPNET</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>write_restart.SIPNET</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>write_restart.SIPNET</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
   <span class='no'>new.state</span>, <span class='kw'>RENAME</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>new.params</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>inputs</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>output directory</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>run ID</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>new.state</th>
-      <td><p>analysis state vector</p></td>
-    </tr>
-    <tr>
-      <th>RENAME</th>
-      <td><p>flag to either rename output file or not</p></td>
-    </tr>
-    <tr>
-      <th>time</th>
-      <td><p>year that is being read</p></td>
-    </tr>
-    <tr>
-      <th>met</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>NONE</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>output directory</p></td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>run ID</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>new.state</th>
+              <td><p>analysis state vector</p></td>
+            </tr>
+            <tr>
+              <th>RENAME</th>
+              <td><p>flag to either rename output file or not</p></td>
+            </tr>
+            <tr>
+              <th>time</th>
+              <td><p>year that is being read</p></td>
+            </tr>
+            <tr>
+              <th>met</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>NONE</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho <a href='mailto:araiho@nd.edu'>araiho@nd.edu</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho <a href="mailto:araiho@nd.edu">araiho@nd.edu</a>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/template/docs/LICENSE-text.html b/models/template/docs/LICENSE-text.html
index 803474f..afdab5c 100644
--- a/models/template/docs/LICENSE-text.html
+++ b/models/template/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>License • PEcAn.ModelName</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
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+
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+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="index.html">PEcAn.ModelName</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    <span class="fa fa-home fa-lg"></span>
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-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.ModelName</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/template/docs/authors.html b/models/template/docs/authors.html
index 717e0da..697b606 100644
--- a/models/template/docs/authors.html
+++ b/models/template/docs/authors.html
@@ -2,122 +2,143 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.ModelName</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.ModelName</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.ModelName</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.ModelName</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Jane Doe</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Jane Doe</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/template/docs/docsearch.css b/models/template/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/models/template/docs/docsearch.css
+++ b/models/template/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/models/template/docs/docsearch.js b/models/template/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/models/template/docs/docsearch.js
+++ b/models/template/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/models/template/docs/index.html b/models/template/docs/index.html
index c1fbb05..553601d 100644
--- a/models/template/docs/index.html
+++ b/models/template/docs/index.html
@@ -1,150 +1,258 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn package for integration of the ModelName model • PEcAn.ModelName</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn package for integration of the ModelName model">
-<meta property="og:description" content="This module provides functions to link the (ModelName) to PEcAn.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn package for integration of the ModelName model • PEcAn.ModelName
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn package for integration of the ModelName model"
+    />
+    <meta
+      property="og:description"
+      content="This module provides functions to link the (ModelName) to PEcAn."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.ModelName</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    <div id="a-generic-template-for-adding-a-new-model-to-pecan" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#a-generic-template-for-adding-a-new-model-to-pecan" class="anchor"></a>A generic template for adding a new model to PEcAn</h1></div>
-<p>Adding a new model to PEcAn in a few easy steps:</p>
-<ol>
-<li>add modeltype to BETY</li>
-<li>add a model and PFT to BETY for use with modeltype</li>
-<li>implement 3 functions as described below</li>
-<li>Add tests to <code>tests/testthat</code>
-</li>
-<li>Update README, documentation</li>
-<li>execute pecan with new model</li>
-</ol>
-<div id="three-functions" class="section level3">
-<h3 class="hasAnchor">
-<a href="#three-functions" class="anchor"></a>Three Functions</h3>
-<p>There are 3 functions that will need to be implemented, each of these functions will need to have MODEL be replaced with the actual modeltype as it is defined in the BETY database.</p>
-<ul>
-<li><code>write.config.MODEL.R</code></li>
-</ul>
-<p>This will write the configuratin file as well as the job launcher used by PEcAn. There is an example of the job execution script in the template folder. The configuration file can also be a template that is found based on the revision number of the model. This should use the computed results specified in defaults and trait.values to write a configuration file based on the PFT and traits found.</p>
-<ul>
-<li><code>met2model.MODEL.R</code></li>
-</ul>
-<p>This will convert the standard Met CF file to the model specific file format. This will allow PEcAn to create metereological files for the specific site and model. This will only be called if no meterological data is found for that specific site and model combination.</p>
-<ul>
-<li><code>model2netcdf.MODEL.R</code></li>
-</ul>
-<p>This will convert the model specific output to NACP Intercomparison format. After this function is finished PEcAn will use the generated output and not use the model specific outputs. The outputs should be named YYYY.nc</p>
-</div>
-<div id="additional-changes" class="section level3">
-<h3 class="hasAnchor">
-<a href="#additional-changes" class="anchor"></a>Additional Changes</h3>
-<ul>
-<li><code>README.md</code></li>
-</ul>
-<p>This file should contain basic background information about the model. At a minimum, this should include the scientific motivation and scope, name(s) of maintainer(s), links to project homepage, and a list of a few key publications. relevant publications.</p>
-<ul>
-<li><code>/tests/testthat/</code></li>
-</ul>
-<p>Each package should have tests that cover the key functions of the package, at a minimum, the three functions above.</p>
-<ul>
-<li>documentation</li>
-</ul>
-<p>Update the <code>NAMESPACE</code>, <code>DESCRIPTION</code> and <code>man/*.Rd</code> files by running</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">devtools</span>(<span class="st">"models/&lt;modelname&gt;/"</span>)</code></pre></div>
-</div>
-</div>
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.ModelName</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div
+            id="a-generic-template-for-adding-a-new-model-to-pecan"
+            class="section level1"
+          >
+            <div class="page-header">
+              <h1 class="hasAnchor">
+                <a
+                  href="#a-generic-template-for-adding-a-new-model-to-pecan"
+                  class="anchor"
+                ></a
+                >A generic template for adding a new model to PEcAn
+              </h1>
+            </div>
+            <p>Adding a new model to PEcAn in a few easy steps:</p>
+            <ol>
+              <li>add modeltype to BETY</li>
+              <li>add a model and PFT to BETY for use with modeltype</li>
+              <li>implement 3 functions as described below</li>
+              <li>Add tests to <code>tests/testthat</code></li>
+              <li>Update README, documentation</li>
+              <li>execute pecan with new model</li>
+            </ol>
+            <div id="three-functions" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#three-functions" class="anchor"></a>Three Functions
+              </h3>
+              <p>
+                There are 3 functions that will need to be implemented, each of
+                these functions will need to have MODEL be replaced with the
+                actual modeltype as it is defined in the BETY database.
+              </p>
+              <ul>
+                <li><code>write.config.MODEL.R</code></li>
+              </ul>
+              <p>
+                This will write the configuratin file as well as the job
+                launcher used by PEcAn. There is an example of the job execution
+                script in the template folder. The configuration file can also
+                be a template that is found based on the revision number of the
+                model. This should use the computed results specified in
+                defaults and trait.values to write a configuration file based on
+                the PFT and traits found.
+              </p>
+              <ul>
+                <li><code>met2model.MODEL.R</code></li>
+              </ul>
+              <p>
+                This will convert the standard Met CF file to the model specific
+                file format. This will allow PEcAn to create metereological
+                files for the specific site and model. This will only be called
+                if no meterological data is found for that specific site and
+                model combination.
+              </p>
+              <ul>
+                <li><code>model2netcdf.MODEL.R</code></li>
+              </ul>
+              <p>
+                This will convert the model specific output to NACP
+                Intercomparison format. After this function is finished PEcAn
+                will use the generated output and not use the model specific
+                outputs. The outputs should be named YYYY.nc
+              </p>
+            </div>
+            <div id="additional-changes" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#additional-changes" class="anchor"></a>Additional
+                Changes
+              </h3>
+              <ul>
+                <li><code>README.md</code></li>
+              </ul>
+              <p>
+                This file should contain basic background information about the
+                model. At a minimum, this should include the scientific
+                motivation and scope, name(s) of maintainer(s), links to project
+                homepage, and a list of a few key publications. relevant
+                publications.
+              </p>
+              <ul>
+                <li><code>/tests/testthat/</code></li>
+              </ul>
+              <p>
+                Each package should have tests that cover the key functions of
+                the package, at a minimum, the three functions above.
+              </p>
+              <ul>
+                <li>documentation</li>
+              </ul>
+              <p>
+                Update the <code>NAMESPACE</code>, <code>DESCRIPTION</code> and
+                <code>man/*.Rd</code> files by running
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">devtools</span>(<span class="st">"models/&lt;modelname&gt;/"</span>)</code></pre>
+              </div>
+            </div>
+          </div>
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/models/template/docs/pkgdown.css b/models/template/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/models/template/docs/pkgdown.css
+++ b/models/template/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/models/template/docs/pkgdown.js b/models/template/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/models/template/docs/pkgdown.js
+++ b/models/template/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/models/template/docs/reference/index.html b/models/template/docs/reference/index.html
index 606a690..5a6d442 100644
--- a/models/template/docs/reference/index.html
+++ b/models/template/docs/reference/index.html
@@ -2,168 +2,225 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Function reference • PEcAn.ModelName</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
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+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
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+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <![endif]-->
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+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
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+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="met2model.MODEL.html">met2model.MODEL()</a></code> </p>
-        </td>
-        <td><p>Write MODEL met files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model2netcdf.MODEL.html">model2netcdf.MODEL()</a></code> </p>
-        </td>
-        <td><p>Code to convert MODELS's output into netCDF format</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_restart.ModelName.html">read_restart.ModelName()</a></code> </p>
-        </td>
-        <td><p>Read restart template for SDA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.config.MODEL.html">write.config.MODEL()</a></code> </p>
-        </td>
-        <td><p>Write MODEL configuration files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_restart.ModelName.html">write_restart.ModelName()</a></code> </p>
-        </td>
-        <td><p>Write restart template for SDA</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2model.MODEL.html"
+                        >met2model.MODEL()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write MODEL met files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="model2netcdf.MODEL.html"
+                        >model2netcdf.MODEL()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Code to convert MODELS's output into netCDF format</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read_restart.ModelName.html"
+                        >read_restart.ModelName()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read restart template for SDA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.config.MODEL.html"
+                        >write.config.MODEL()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write MODEL configuration files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write_restart.ModelName.html"
+                        >write_restart.ModelName()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write restart template for SDA</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/models/template/docs/reference/met2model.MODEL.html b/models/template/docs/reference/met2model.MODEL.html
index 9bcd9a0..68c2977 100644
--- a/models/template/docs/reference/met2model.MODEL.html
+++ b/models/template/docs/reference/met2model.MODEL.html
@@ -2,163 +2,200 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-
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-<meta property="og:title" content="Write MODEL met files — met2model.MODEL" />
-
-<meta property="og:description" content="Converts a met CF file to a model specific met file. The input
-files are calld &amp;lt;in.path&amp;gt;/&amp;lt;in.prefix&amp;gt;.YYYY.cf" />
-<meta name="twitter:card" content="summary" />
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Write MODEL met files — met2model.MODEL"
+    />
+
+    <meta
+      property="og:description"
+      content="Converts a met CF file to a model specific met file. The input
+files are calld &amp;lt;in.path&amp;gt;/&amp;lt;in.prefix&amp;gt;.YYYY.cf"
+    />
+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-        <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../reference/index.html">Reference</a>
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-        
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-      
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-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write MODEL met files</h1>
-    
-    <div class="hidden name"><code>met2model.MODEL.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Converts a met CF file to a model specific met file. The input
-files are calld &lt;in.path&gt;/&lt;in.prefix&gt;.YYYY.cf</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>met2model.MODEL</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>path on disk where CF file lives</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix for each file</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location where model specific output is written.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>OK if everything was succesful.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write MODEL met files</h1>
+
+            <div class="hidden name"><code>met2model.MODEL.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Converts a met CF file to a model specific met file. The input
+              files are calld &lt;in.path&gt;/&lt;in.prefix&gt;.YYYY.cf
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>met2model.MODEL</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>path on disk where CF file lives</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix for each file</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location where model specific output is written.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>OK if everything was succesful.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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-  
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+    </div>
   </body>
 </html>
-
diff --git a/models/template/docs/reference/model2netcdf.MODEL.html b/models/template/docs/reference/model2netcdf.MODEL.html
index 79be93e..fc76c4c 100644
--- a/models/template/docs/reference/model2netcdf.MODEL.html
+++ b/models/template/docs/reference/model2netcdf.MODEL.html
@@ -2,163 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Code to convert MODELS's output into netCDF format — model2netcdf.MODEL • PEcAn.ModelName</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
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-<script src="../pkgdown.js"></script>
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-<meta property="og:title" content="Code to convert MODELS's output into netCDF format — model2netcdf.MODEL" />
-
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-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Code to convert MODELS's output into netCDF format — model2netcdf.MODEL •
+      PEcAn.ModelName
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Code to convert MODELS's output into netCDF format — model2netcdf.MODEL"
+    />
+
+    <meta
+      property="og:description"
+      content="Convert MODEL output into the NACP Intercomparison format (ALMA using netCDF)"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Code to convert MODELS's output into netCDF format</h1>
-    
-    <div class="hidden name"><code>model2netcdf.MODEL.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert MODEL output into the NACP Intercomparison format (ALMA using netCDF)</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model2netcdf.MODEL</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Location of model output</p></td>
-    </tr>
-    <tr>
-      <th>sitelat</th>
-      <td><p>Latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>sitelon</th>
-      <td><p>Longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start time of the simulation</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End time of the simulation</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Code to convert MODELS's output into netCDF format</h1>
+
+            <div class="hidden name"><code>model2netcdf.MODEL.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Convert MODEL output into the NACP Intercomparison format (ALMA
+              using netCDF)
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model2netcdf.MODEL</span>(<span class='no'>outdir</span>, <span class='no'>sitelat</span>, <span class='no'>sitelon</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Location of model output</p></td>
+            </tr>
+            <tr>
+              <th>sitelat</th>
+              <td><p>Latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>sitelon</th>
+              <td><p>Longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start time of the simulation</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End time of the simulation</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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diff --git a/models/template/docs/reference/read_restart.ModelName.html b/models/template/docs/reference/read_restart.ModelName.html
index ed25833..bec7f47 100644
--- a/models/template/docs/reference/read_restart.ModelName.html
+++ b/models/template/docs/reference/read_restart.ModelName.html
@@ -2,174 +2,210 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Read restart template for SDA — read_restart.ModelName • PEcAn.ModelName
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
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+
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+    <script src="../pkgdown.js"></script>
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../index.html">
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-</div><!--/.navbar -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read restart template for SDA</h1>
-    
-    <div class="hidden name"><code>read_restart.ModelName.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read restart template for SDA</h1>
 
-    <div class="ref-description">
-    
-    <p>Read restart files from model.</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>read_restart.ModelName.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Read restart files from model.</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>read_restart.ModelName</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>, <span class='no'>var.names</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>read_restart.ModelName</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>, <span class='no'>var.names</span>,
   <span class='no'>params</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Output directory</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>Run ID</p></td>
-    </tr>
-    <tr>
-      <th>stop.time</th>
-      <td><p>Year that is being read</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>var.names</th>
-      <td><p>Variable names to be extracted</p></td>
-    </tr>
-    <tr>
-      <th>params</th>
-      <td><p>Any parameters required for state calculations</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Forecast numeric matrix</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Output directory</p></td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>Run ID</p></td>
+            </tr>
+            <tr>
+              <th>stop.time</th>
+              <td><p>Year that is being read</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>var.names</th>
+              <td><p>Variable names to be extracted</p></td>
+            </tr>
+            <tr>
+              <th>params</th>
+              <td><p>Any parameters required for state calculations</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Forecast numeric matrix</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/template/docs/reference/write.config.MODEL.html b/models/template/docs/reference/write.config.MODEL.html
index 54da665..803e46b 100644
--- a/models/template/docs/reference/write.config.MODEL.html
+++ b/models/template/docs/reference/write.config.MODEL.html
@@ -2,172 +2,210 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Write MODEL configuration files — write.config.MODEL • PEcAn.ModelName</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Write MODEL configuration files — write.config.MODEL" />
-
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-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Write MODEL configuration files — write.config.MODEL • PEcAn.ModelName
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Write MODEL configuration files — write.config.MODEL"
+    />
+
+    <meta property="og:description" content="Writes a MODEL config file." />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
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-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write MODEL configuration files</h1>
-    
-    <div class="hidden name"><code>write.config.MODEL.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes a MODEL config file.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.config.MODEL</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>list of defaults to process</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of settings from pecan settings file</p></td>
-    </tr>
-    <tr>
-      <th>run.id</th>
-      <td><p>id of run</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>vector of samples for a given trait</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>configuration file for MODEL for given run</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Requires a pft xml object, a list of trait values for a single model run,
-and the name of the file to create</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write MODEL configuration files</h1>
+
+            <div class="hidden name"><code>write.config.MODEL.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Writes a MODEL config file.</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.config.MODEL</span>(<span class='no'>defaults</span>, <span class='no'>trait.values</span>, <span class='no'>settings</span>, <span class='no'>run.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>list of defaults to process</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of settings from pecan settings file</p></td>
+            </tr>
+            <tr>
+              <th>run.id</th>
+              <td><p>id of run</p></td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td><p>vector of samples for a given trait</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>configuration file for MODEL for given run</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Requires a pft xml object, a list of trait values for a single model
+            run, and the name of the file to create
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Rob Kooper
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/models/template/docs/reference/write_restart.ModelName.html b/models/template/docs/reference/write_restart.ModelName.html
index 572ba38..7d9f8b6 100644
--- a/models/template/docs/reference/write_restart.ModelName.html
+++ b/models/template/docs/reference/write_restart.ModelName.html
@@ -2,180 +2,227 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Write restart template for SDA — write_restart.ModelName • PEcAn.ModelName</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    <!-- sticky kit -->
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+    <script src="../pkgdown.js"></script>
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+    <![endif]-->
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.ModelName</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write restart template for SDA</h1>
-    
-    <div class="hidden name"><code>write_restart.ModelName.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write restart template for SDA</h1>
 
-    <div class="ref-description">
-    
-    <p>Write restart files for model</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>write_restart.ModelName.Rd</code>
+            </div>
+          </div>
 
-    <pre class="usage"><span class='fu'>write_restart.ModelName</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
-  <span class='no'>new.state</span>, <span class='no'>RENAME</span>, <span class='no'>new.params</span>, <span class='no'>inputs</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>outout directory</p></td>
-    </tr>
-    <tr>
-      <th>runid</th>
-      <td><p>run id</p></td>
-    </tr>
-    <tr>
-      <th>start.time</th>
-      <td><p>Time of current assimilation step</p></td>
-    </tr>
-    <tr>
-      <th>stop.time</th>
-      <td><p>Time of next assimilation step</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>pecan settings list</p></td>
-    </tr>
-    <tr>
-      <th>new.state</th>
-      <td><p>Analysis state matrix returned by <code>sda.enkf</code></p></td>
-    </tr>
-    <tr>
-      <th>RENAME</th>
-      <td><p>flag to either rename output file or not</p></td>
-    </tr>
-    <tr>
-      <th>new.params</th>
-      <td><p>optional, additionals params to pass write.configs that are deterministically related to the parameters updated by the analysis</p></td>
-    </tr>
-    <tr>
-      <th>inputs</th>
-      <td><p>new input paths updated by the SDA workflow, will be passed to write.configs</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Write restart files for model</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>write_restart.ModelName</span>(<span class='no'>outdir</span>, <span class='no'>runid</span>, <span class='no'>start.time</span>, <span class='no'>stop.time</span>, <span class='no'>settings</span>,
+  <span class='no'>new.state</span>, <span class='no'>RENAME</span>, <span class='no'>new.params</span>, <span class='no'>inputs</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>outout directory</p></td>
+            </tr>
+            <tr>
+              <th>runid</th>
+              <td><p>run id</p></td>
+            </tr>
+            <tr>
+              <th>start.time</th>
+              <td><p>Time of current assimilation step</p></td>
+            </tr>
+            <tr>
+              <th>stop.time</th>
+              <td><p>Time of next assimilation step</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>pecan settings list</p></td>
+            </tr>
+            <tr>
+              <th>new.state</th>
+              <td>
+                <p>Analysis state matrix returned by <code>sda.enkf</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>RENAME</th>
+              <td><p>flag to either rename output file or not</p></td>
+            </tr>
+            <tr>
+              <th>new.params</th>
+              <td>
+                <p>
+                  optional, additionals params to pass write.configs that are
+                  deterministically related to the parameters updated by the
+                  analysis
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>inputs</th>
+              <td>
+                <p>
+                  new input paths updated by the SDA workflow, will be passed to
+                  write.configs
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/allometry/docs/LICENSE-text.html b/modules/allometry/docs/LICENSE-text.html
index 68e13dc..fac9f9c 100644
--- a/modules/allometry/docs/LICENSE-text.html
+++ b/modules/allometry/docs/LICENSE-text.html
@@ -2,109 +2,146 @@
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+            <div class="navbar-header">
+              <button
+                type="button"
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+                <a class="navbar-link" href="index.html">PEcAn.allometry</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+                      <a href="articles/AllomVignette.html"
+                        >PEcAn.allometry Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -133,27 +170,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
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-
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-
+</pre
+          >
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+      </div>
 
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diff --git a/modules/allometry/docs/articles/AllomVignette.html b/modules/allometry/docs/articles/AllomVignette.html
index e9164ed..37924bb 100644
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+++ b/modules/allometry/docs/articles/AllomVignette.html
@@ -1,111 +1,180 @@
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+                  >1.6.0</span
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+                        >PEcAn.allometry Vignette</a
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+            <h4 class="author">Mike Dietze</h4>
 
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-      <h1>PEcAn.allometry Vignette</h1>
-                        <h4 class="author">Mike Dietze</h4>
-            
             <h4 class="date">April 23, 2015</h4>
-      
-      
-      <div class="hidden name"><code>AllomVignette.Rmd</code></div>
-
-    </div>
 
-    
-    
-<div id="install-package-from-github" class="section level2">
-<h2 class="hasAnchor">
-<a href="#install-package-from-github" class="anchor"></a>install package from Github</h2>
-<p>Only needs to be done the first time</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools)
+            <div class="hidden name"><code>AllomVignette.Rmd</code></div>
+          </div>
+
+          <div id="install-package-from-github" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#install-package-from-github" class="anchor"></a>install
+              package from Github
+            </h2>
+            <p>Only needs to be done the first time</p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(devtools)
 <span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>,<span class="dt">subdir=</span><span class="st">"base/logger"</span>)
-<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>,<span class="dt">subdir=</span><span class="st">"modules/allometry"</span>)</code></pre></div>
-</div>
-<div id="define-species-groups" class="section level2">
-<h2 class="hasAnchor">
-<a href="#define-species-groups" class="anchor"></a>Define species groups</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAn.allometry)</code></pre></div>
-<pre><code>## Loading required package: MCMCpack</code></pre>
-<pre><code>## Loading required package: coda</code></pre>
-<pre><code>## Loading required package: MASS</code></pre>
-<pre><code>## ##
+<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>,<span class="dt">subdir=</span><span class="st">"modules/allometry"</span>)</code></pre>
+            </div>
+          </div>
+          <div id="define-species-groups" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#define-species-groups" class="anchor"></a>Define species
+              groups
+            </h2>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(PEcAn.allometry)</code></pre>
+            </div>
+            <pre><code>## Loading required package: MCMCpack</code></pre>
+            <pre><code>## Loading required package: coda</code></pre>
+            <pre><code>## Loading required package: MASS</code></pre>
+            <pre><code>## ##
 ## ## Markov Chain Monte Carlo Package (MCMCpack)</code></pre>
-<pre><code>## ## Copyright (C) 2003-2018 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park</code></pre>
-<pre><code>## ##
+            <pre><code>## ## Copyright (C) 2003-2018 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park</code></pre>
+            <pre><code>## ##
 ## ## Support provided by the U.S. National Science Foundation</code></pre>
-<pre><code>## ## (Grants SES-0350646 and SES-0350613)
+            <pre><code>## ## (Grants SES-0350646 and SES-0350613)
 ## ##</code></pre>
-<pre><code>## Loading required package: mvtnorm</code></pre>
-<pre><code>## Loading required package: tools</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">## define the Plant Functional Types you want to fit based on USDA acronyms and USFS species codes (spcd)
+            <pre><code>## Loading required package: mvtnorm</code></pre>
+            <pre><code>## Loading required package: tools</code></pre>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">## define the Plant Functional Types you want to fit based on USDA acronyms and USFS species codes (spcd)
 ## can involve one or many species
 ## multiple PFTs can be fit at once by putting them in a list
 ## Note that the name used in the PFT list defines the name that the code will match against when making predictions for new individuals
@@ -113,15 +182,35 @@ <h2 class="hasAnchor">
 
 ## example of a PFT with multiple species (LH = late hardwood)
 ## note that if you're just using Jenkins the acronym column is optional
-pfts =<span class="st"> </span><span class="kw">list</span>(<span class="dt">LH =</span> <span class="kw">data.frame</span>(<span class="dt">spcd =</span> <span class="kw">c</span>(<span class="dv">531</span>,<span class="dv">318</span>),<span class="dt">acronym=</span><span class="kw">c</span>(<span class="st">"FAGR"</span>,<span class="st">"ACSA3"</span>)))</code></pre></div>
-</div>
-<div id="run-the-bayesian-allometry-model" class="section level2">
-<h2 class="hasAnchor">
-<a href="#run-the-bayesian-allometry-model" class="anchor"></a>Run the Bayesian allometry model</h2>
-<p>Note the side effects of this function are that it will create two files in your working directory for every PFT and component pair, a pdf file of diagnostics and a RData file saving the full output. These files will be named based on the PFT and the component.</p>
-<p>The return from this function will be a summary table of statistics. The function will actually run two variants of the model, a “global” modelthat fits a single equation to all equations and a ‘hierarchical’ model that accounts for the variability among equations. This function also print out DIC statistics on which fit was better (lowest score wins): DIC is the hierarchical model, DICg is the global model.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">allom.stats =<span class="st"> </span><span class="kw"><a href="../reference/AllomAve.html">AllomAve</a></span>(pfts,<span class="dt">ngibbs=</span><span class="dv">500</span>)</code></pre></div>
-<pre><code>## [1] "writing output to"                                        
+pfts =<span class="st"> </span><span class="kw">list</span>(<span class="dt">LH =</span> <span class="kw">data.frame</span>(<span class="dt">spcd =</span> <span class="kw">c</span>(<span class="dv">531</span>,<span class="dv">318</span>),<span class="dt">acronym=</span><span class="kw">c</span>(<span class="st">"FAGR"</span>,<span class="st">"ACSA3"</span>)))</code></pre>
+            </div>
+          </div>
+          <div id="run-the-bayesian-allometry-model" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#run-the-bayesian-allometry-model" class="anchor"></a>Run
+              the Bayesian allometry model
+            </h2>
+            <p>
+              Note the side effects of this function are that it will create two
+              files in your working directory for every PFT and component pair,
+              a pdf file of diagnostics and a RData file saving the full output.
+              These files will be named based on the PFT and the component.
+            </p>
+            <p>
+              The return from this function will be a summary table of
+              statistics. The function will actually run two variants of the
+              model, a “global” modelthat fits a single equation to all
+              equations and a ‘hierarchical’ model that accounts for the
+              variability among equations. This function also print out DIC
+              statistics on which fit was better (lowest score wins): DIC is the
+              hierarchical model, DICg is the global model.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">allom.stats =<span class="st"> </span><span class="kw"><a href="../reference/AllomAve.html">AllomAve</a></span>(pfts,<span class="dt">ngibbs=</span><span class="dv">500</span>)</code></pre>
+            </div>
+            <pre><code>## [1] "writing output to"                                        
 ## [2] "/fs/data3/tonygard/work/pecan/modules/allometry/vignettes"
 ## $spcd
 ## [1] 531 318
@@ -132,14 +221,14 @@ <h2 class="hasAnchor">
 ## 
 ## [[3]]
 ## [1] 6</code></pre>
-<pre><code>## Warning in nu(allom$parm$Component.ID): NAs introduced by coercion</code></pre>
-<pre><code>## [1] "Dropping allom rows: "
+            <pre><code>## Warning in nu(allom$parm$Component.ID): NAs introduced by coercion</code></pre>
+            <pre><code>## [1] "Dropping allom rows: "
 ## 
   |                                                                       
   |                                                                 |   0%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189,9 +278,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -244,9 +333,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -299,14 +388,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |                                                                 |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -356,14 +445,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -413,9 +502,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -468,9 +557,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -523,9 +612,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -578,14 +667,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -635,9 +724,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -690,9 +779,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -745,9 +834,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -800,14 +889,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -857,14 +946,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   3%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -914,9 +1003,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -969,9 +1058,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1024,9 +1113,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1079,9 +1168,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1134,14 +1223,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1191,9 +1280,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1246,14 +1335,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1303,9 +1392,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1358,9 +1447,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1413,14 +1502,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1470,9 +1559,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1525,9 +1614,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1580,9 +1669,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1635,14 +1724,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1692,14 +1781,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   6%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1749,9 +1838,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1804,9 +1893,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1859,9 +1948,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1914,9 +2003,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -1969,14 +2058,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2026,9 +2115,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2081,14 +2170,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2138,9 +2227,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2193,9 +2282,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2248,14 +2337,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   8%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2305,9 +2394,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2360,9 +2449,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2415,9 +2504,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2470,9 +2559,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2525,14 +2614,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |   9%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2582,9 +2671,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2637,9 +2726,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2692,9 +2781,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2747,9 +2836,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2802,14 +2891,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2859,9 +2948,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2914,9 +3003,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -2969,14 +3058,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3026,9 +3115,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3081,14 +3170,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  11%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3138,9 +3227,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3193,9 +3282,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3248,9 +3337,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3303,9 +3392,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3358,14 +3447,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  12%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3415,9 +3504,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3470,9 +3559,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3525,9 +3614,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3580,9 +3669,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3635,14 +3724,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3692,9 +3781,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3747,9 +3836,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3802,14 +3891,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3859,9 +3948,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3914,14 +4003,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  14%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -3971,9 +4060,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4026,9 +4115,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4081,9 +4170,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4136,9 +4225,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4191,14 +4280,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4248,14 +4337,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4305,9 +4394,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4360,9 +4449,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4415,9 +4504,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4470,14 +4559,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4527,9 +4616,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4582,9 +4671,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4637,14 +4726,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4694,9 +4783,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4749,14 +4838,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  17%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4806,9 +4895,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4861,9 +4950,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4916,9 +5005,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -4971,9 +5060,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5026,14 +5115,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5083,14 +5172,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5140,9 +5229,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5195,9 +5284,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5250,9 +5339,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5305,14 +5394,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5362,9 +5451,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5417,9 +5506,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5472,9 +5561,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5527,14 +5616,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5584,14 +5673,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  20%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5641,9 +5730,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5696,9 +5785,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5751,9 +5840,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5806,9 +5895,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5861,14 +5950,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5918,14 +6007,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -5975,9 +6064,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6030,9 +6119,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6085,9 +6174,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6140,14 +6229,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6197,9 +6286,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6252,9 +6341,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6307,9 +6396,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6362,14 +6451,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6419,14 +6508,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  23%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6476,9 +6565,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6531,9 +6620,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6586,9 +6675,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6641,9 +6730,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6696,14 +6785,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6753,9 +6842,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6808,14 +6897,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6865,9 +6954,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6920,9 +7009,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -6975,14 +7064,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7032,9 +7121,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7087,9 +7176,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7142,9 +7231,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7197,14 +7286,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7254,14 +7343,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  26%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7311,9 +7400,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7366,9 +7455,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7421,9 +7510,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7476,9 +7565,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7531,14 +7620,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7588,9 +7677,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7643,14 +7732,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7700,9 +7789,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7755,9 +7844,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7810,14 +7899,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  28%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7867,9 +7956,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7922,9 +8011,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -7977,9 +8066,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8032,9 +8121,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8087,14 +8176,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  29%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8144,9 +8233,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8199,9 +8288,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8254,9 +8343,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8309,9 +8398,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8364,14 +8453,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8421,9 +8510,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8476,14 +8565,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8533,9 +8622,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8588,9 +8677,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8643,14 +8732,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  31%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8700,9 +8789,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8755,9 +8844,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8810,9 +8899,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8865,9 +8954,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8920,14 +9009,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  32%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -8977,9 +9066,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9032,9 +9121,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9087,9 +9176,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9142,9 +9231,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9197,14 +9286,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9254,9 +9343,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9309,9 +9398,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9364,14 +9453,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9421,9 +9510,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9476,14 +9565,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  34%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9533,9 +9622,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9588,9 +9677,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9643,9 +9732,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9698,9 +9787,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9753,14 +9842,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9810,14 +9899,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9867,9 +9956,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9922,9 +10011,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -9977,9 +10066,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10032,14 +10121,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10089,9 +10178,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10144,9 +10233,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10199,14 +10288,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10256,9 +10345,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10311,14 +10400,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  37%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10368,9 +10457,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10423,9 +10512,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10478,9 +10567,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10533,9 +10622,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10588,14 +10677,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10645,14 +10734,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10702,9 +10791,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10757,9 +10846,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10812,9 +10901,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10867,14 +10956,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10924,9 +11013,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -10979,9 +11068,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11034,9 +11123,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11089,14 +11178,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11146,14 +11235,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  40%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11203,9 +11292,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11258,9 +11347,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11313,9 +11402,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11368,9 +11457,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11423,14 +11512,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11480,14 +11569,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11537,9 +11626,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11592,9 +11681,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11647,9 +11736,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11702,14 +11791,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11759,9 +11848,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11814,9 +11903,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11869,9 +11958,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11924,14 +12013,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -11981,14 +12070,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  43%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12038,9 +12127,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12093,9 +12182,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12148,9 +12237,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12203,9 +12292,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12258,14 +12347,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12315,9 +12404,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12370,14 +12459,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12427,9 +12516,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12482,9 +12571,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12537,14 +12626,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12594,9 +12683,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12649,9 +12738,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12704,9 +12793,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12759,14 +12848,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12816,14 +12905,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  46%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12873,9 +12962,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12928,9 +13017,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -12983,9 +13072,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13038,9 +13127,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13093,14 +13182,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13150,9 +13239,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13205,14 +13294,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13262,9 +13351,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13317,9 +13406,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13372,14 +13461,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  48%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13429,9 +13518,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13484,9 +13573,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13539,9 +13628,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13594,9 +13683,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13649,14 +13738,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  49%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13706,9 +13795,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13761,9 +13850,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13816,9 +13905,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13871,9 +13960,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13926,14 +14015,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -13983,9 +14072,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14038,9 +14127,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14093,14 +14182,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14150,9 +14239,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14205,14 +14294,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  51%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14262,9 +14351,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14317,9 +14406,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14372,9 +14461,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14427,9 +14516,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14482,14 +14571,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  52%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14539,9 +14628,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14594,9 +14683,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14649,9 +14738,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14704,9 +14793,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14759,14 +14848,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14816,9 +14905,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14871,9 +14960,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14926,14 +15015,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -14983,9 +15072,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15038,14 +15127,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  54%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15095,9 +15184,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15150,9 +15239,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15205,9 +15294,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15260,9 +15349,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15315,14 +15404,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15372,14 +15461,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15429,9 +15518,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15484,9 +15573,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15539,9 +15628,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15594,14 +15683,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15651,9 +15740,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15706,9 +15795,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15761,14 +15850,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15818,9 +15907,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15873,14 +15962,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  57%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15930,9 +16019,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -15985,9 +16074,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16040,9 +16129,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16095,9 +16184,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16150,14 +16239,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16207,14 +16296,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16264,9 +16353,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16319,9 +16408,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16374,9 +16463,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16429,14 +16518,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16486,9 +16575,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16541,9 +16630,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16596,9 +16685,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16651,14 +16740,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16708,14 +16797,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  60%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16765,9 +16854,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16820,9 +16909,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16875,9 +16964,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16930,9 +17019,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -16985,14 +17074,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17042,14 +17131,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17099,9 +17188,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17154,9 +17243,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17209,9 +17298,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17264,14 +17353,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17321,9 +17410,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17376,9 +17465,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17431,9 +17520,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17486,14 +17575,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17543,14 +17632,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  63%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17600,9 +17689,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17655,9 +17744,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17710,9 +17799,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17765,9 +17854,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17820,14 +17909,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17877,9 +17966,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17932,14 +18021,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -17989,9 +18078,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18044,9 +18133,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18099,14 +18188,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18156,9 +18245,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18211,9 +18300,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18266,9 +18355,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18321,14 +18410,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18378,14 +18467,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  66%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18435,9 +18524,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18490,9 +18579,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18545,9 +18634,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18600,9 +18689,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18655,14 +18744,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18712,9 +18801,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18767,14 +18856,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18824,9 +18913,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18879,9 +18968,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18934,14 +19023,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  68%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -18991,9 +19080,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19046,9 +19135,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19101,9 +19190,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19156,9 +19245,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19211,14 +19300,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  69%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19268,9 +19357,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19323,9 +19412,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19378,9 +19467,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19433,9 +19522,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19488,14 +19577,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19545,9 +19634,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19600,14 +19689,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19657,9 +19746,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19712,9 +19801,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19767,14 +19856,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  71%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19824,9 +19913,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19879,9 +19968,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19934,9 +20023,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -19989,9 +20078,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20044,14 +20133,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  72%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20101,9 +20190,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20156,9 +20245,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20211,9 +20300,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20266,9 +20355,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20321,14 +20410,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20378,9 +20467,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20433,9 +20522,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20488,14 +20577,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20545,9 +20634,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20600,14 +20689,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  74%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20657,9 +20746,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20712,9 +20801,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20767,9 +20856,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20822,9 +20911,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20877,14 +20966,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20934,14 +21023,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -20991,9 +21080,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21046,9 +21135,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21101,9 +21190,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21156,14 +21245,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21213,9 +21302,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21268,9 +21357,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21323,14 +21412,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21380,9 +21469,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21435,14 +21524,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  77%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21492,9 +21581,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21547,9 +21636,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21602,9 +21691,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21657,9 +21746,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21712,14 +21801,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21769,14 +21858,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21826,9 +21915,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21881,9 +21970,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21936,9 +22025,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -21991,14 +22080,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22048,9 +22137,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22103,9 +22192,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22158,9 +22247,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22213,14 +22302,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22270,14 +22359,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  80%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22327,9 +22416,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22382,9 +22471,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22437,9 +22526,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22492,9 +22581,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22547,14 +22636,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22604,14 +22693,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22661,9 +22750,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22716,9 +22805,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22771,9 +22860,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22826,14 +22915,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22883,9 +22972,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22938,9 +23027,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -22993,9 +23082,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23048,14 +23137,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23105,14 +23194,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  83%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23162,9 +23251,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23217,9 +23306,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23272,9 +23361,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23327,9 +23416,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23382,14 +23471,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23439,9 +23528,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23494,14 +23583,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23551,9 +23640,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23606,9 +23695,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23661,14 +23750,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23718,9 +23807,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23773,9 +23862,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23828,9 +23917,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23883,14 +23972,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23940,14 +24029,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  86%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -23997,9 +24086,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24052,9 +24141,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24107,9 +24196,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24162,9 +24251,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24217,14 +24306,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24274,9 +24363,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24329,14 +24418,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24386,9 +24475,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24441,9 +24530,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24496,14 +24585,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  88%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24553,9 +24642,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24608,9 +24697,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24663,9 +24752,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24718,9 +24807,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24773,14 +24862,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  89%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24830,9 +24919,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24885,9 +24974,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24940,9 +25029,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -24995,9 +25084,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25050,14 +25139,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25107,9 +25196,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25162,9 +25251,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25217,14 +25306,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25274,9 +25363,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25329,14 +25418,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  91%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25386,9 +25475,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25441,9 +25530,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25496,9 +25585,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25551,9 +25640,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25606,14 +25695,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  92%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25663,9 +25752,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25718,9 +25807,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25773,9 +25862,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25828,9 +25917,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25883,14 +25972,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25940,9 +26029,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -25995,9 +26084,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26050,14 +26139,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26107,9 +26196,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26162,14 +26251,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  94%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26219,9 +26308,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26274,9 +26363,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26329,9 +26418,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26384,9 +26473,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26439,14 +26528,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26496,14 +26585,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26553,9 +26642,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26608,9 +26697,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26663,9 +26752,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26718,14 +26807,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26775,9 +26864,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26830,9 +26919,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26885,14 +26974,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26942,9 +27031,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -26997,14 +27086,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  97%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27054,9 +27143,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27109,9 +27198,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27164,9 +27253,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27219,9 +27308,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27274,14 +27363,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27331,14 +27420,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27388,9 +27477,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27443,9 +27532,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27498,9 +27587,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27553,14 +27642,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27610,9 +27699,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27665,9 +27754,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27720,9 +27809,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27775,14 +27864,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================|  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27832,14 +27921,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================| 100%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27889,9 +27978,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -27944,16 +28033,16 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
 ## [1] "Dropping allom rows: "
 ## 
   |                                                                       
   |                                                                 |   0%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28003,9 +28092,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28058,9 +28147,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28113,14 +28202,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |                                                                 |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28170,14 +28259,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28227,9 +28316,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28282,9 +28371,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28337,9 +28426,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28392,14 +28481,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28449,9 +28538,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28504,9 +28593,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28559,9 +28648,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28614,14 +28703,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28671,14 +28760,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   3%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28728,9 +28817,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28783,9 +28872,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28838,9 +28927,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28893,9 +28982,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -28948,14 +29037,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29005,9 +29094,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29060,14 +29149,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29117,9 +29206,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29172,9 +29261,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29227,14 +29316,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29284,9 +29373,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29339,9 +29428,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29394,9 +29483,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29449,14 +29538,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29506,14 +29595,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   6%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29563,9 +29652,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29618,9 +29707,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29673,9 +29762,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29728,9 +29817,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29783,14 +29872,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29840,9 +29929,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29895,14 +29984,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -29952,9 +30041,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30007,9 +30096,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30062,14 +30151,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   8%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30119,9 +30208,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30174,9 +30263,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30229,9 +30318,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30284,9 +30373,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30339,14 +30428,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |   9%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30396,9 +30485,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30451,9 +30540,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30506,9 +30595,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30561,9 +30650,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30616,14 +30705,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30673,9 +30762,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30728,9 +30817,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30783,14 +30872,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30840,9 +30929,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30895,14 +30984,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  11%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -30952,9 +31041,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31007,9 +31096,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31062,9 +31151,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31117,9 +31206,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31172,14 +31261,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  12%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31229,9 +31318,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31284,9 +31373,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31339,9 +31428,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31394,9 +31483,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31449,14 +31538,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31506,9 +31595,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31561,9 +31650,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31616,14 +31705,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31673,9 +31762,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31728,14 +31817,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  14%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31785,9 +31874,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31840,9 +31929,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31895,9 +31984,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -31950,9 +32039,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32005,14 +32094,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32062,14 +32151,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32119,9 +32208,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32174,9 +32263,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32229,9 +32318,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32284,14 +32373,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32341,9 +32430,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32396,9 +32485,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32451,14 +32540,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32508,9 +32597,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32563,14 +32652,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  17%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32620,9 +32709,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32675,9 +32764,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32730,9 +32819,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32785,9 +32874,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32840,14 +32929,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32897,14 +32986,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -32954,9 +33043,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33009,9 +33098,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33064,9 +33153,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33119,14 +33208,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33176,9 +33265,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33231,9 +33320,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33286,9 +33375,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33341,14 +33430,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33398,14 +33487,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  20%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33455,9 +33544,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33510,9 +33599,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33565,9 +33654,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33620,9 +33709,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33675,14 +33764,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33732,14 +33821,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33789,9 +33878,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33844,9 +33933,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33899,9 +33988,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -33954,14 +34043,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34011,9 +34100,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34066,9 +34155,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34121,9 +34210,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34176,14 +34265,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34233,14 +34322,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  23%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34290,9 +34379,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34345,9 +34434,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34400,9 +34489,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34455,9 +34544,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34510,14 +34599,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34567,9 +34656,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34622,14 +34711,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34679,9 +34768,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34734,9 +34823,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34789,14 +34878,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34846,9 +34935,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34901,9 +34990,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -34956,9 +35045,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35011,14 +35100,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35068,14 +35157,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  26%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35125,9 +35214,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35180,9 +35269,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35235,9 +35324,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35290,9 +35379,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35345,14 +35434,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35402,9 +35491,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35457,14 +35546,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35514,9 +35603,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35569,9 +35658,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35624,14 +35713,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  28%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35681,9 +35770,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35736,9 +35825,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35791,9 +35880,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35846,9 +35935,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35901,14 +35990,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  29%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -35958,9 +36047,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36013,9 +36102,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36068,9 +36157,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36123,9 +36212,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36178,14 +36267,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36235,9 +36324,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36290,14 +36379,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36347,9 +36436,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36402,9 +36491,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36457,14 +36546,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  31%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36514,9 +36603,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36569,9 +36658,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36624,9 +36713,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36679,9 +36768,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36734,14 +36823,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  32%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36791,9 +36880,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36846,9 +36935,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36901,9 +36990,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -36956,9 +37045,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37011,14 +37100,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37068,9 +37157,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37123,9 +37212,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37178,14 +37267,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37235,9 +37324,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37290,14 +37379,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  34%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37347,9 +37436,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37402,9 +37491,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37457,9 +37546,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37512,9 +37601,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37567,14 +37656,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37624,14 +37713,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37681,9 +37770,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37736,9 +37825,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37791,9 +37880,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37846,14 +37935,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37903,9 +37992,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -37958,9 +38047,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38013,14 +38102,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38070,9 +38159,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38125,14 +38214,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  37%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38182,9 +38271,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38237,9 +38326,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38292,9 +38381,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38347,9 +38436,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38402,14 +38491,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38459,14 +38548,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38516,9 +38605,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38571,9 +38660,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38626,9 +38715,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38681,14 +38770,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38738,9 +38827,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38793,9 +38882,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38848,9 +38937,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38903,14 +38992,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -38960,14 +39049,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  40%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39017,9 +39106,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39072,9 +39161,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39127,9 +39216,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39182,9 +39271,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39237,14 +39326,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39294,14 +39383,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39351,9 +39440,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39406,9 +39495,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39461,9 +39550,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39516,14 +39605,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39573,9 +39662,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39628,9 +39717,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39683,9 +39772,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39738,14 +39827,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39795,14 +39884,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  43%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39852,9 +39941,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39907,9 +39996,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -39962,9 +40051,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40017,9 +40106,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40072,14 +40161,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40129,9 +40218,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40184,14 +40273,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40241,9 +40330,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40296,9 +40385,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40351,14 +40440,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40408,9 +40497,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40463,9 +40552,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40518,9 +40607,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40573,14 +40662,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40630,14 +40719,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  46%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40687,9 +40776,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40742,9 +40831,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40797,9 +40886,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40852,9 +40941,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40907,14 +40996,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -40964,9 +41053,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41019,14 +41108,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41076,9 +41165,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41131,9 +41220,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41186,14 +41275,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  48%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41243,9 +41332,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41298,9 +41387,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41353,9 +41442,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41408,9 +41497,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41463,14 +41552,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  49%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41520,9 +41609,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41575,9 +41664,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41630,9 +41719,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41685,9 +41774,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41740,14 +41829,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41797,9 +41886,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41852,9 +41941,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41907,14 +41996,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -41964,9 +42053,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42019,14 +42108,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  51%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42076,9 +42165,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42131,9 +42220,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42186,9 +42275,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42241,9 +42330,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42296,14 +42385,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  52%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42353,9 +42442,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42408,9 +42497,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42463,9 +42552,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42518,9 +42607,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42573,14 +42662,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42630,9 +42719,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42685,9 +42774,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42740,14 +42829,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42797,9 +42886,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42852,14 +42941,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  54%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42909,9 +42998,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -42964,9 +43053,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43019,9 +43108,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43074,9 +43163,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43129,14 +43218,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43186,14 +43275,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43243,9 +43332,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43298,9 +43387,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43353,9 +43442,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43408,14 +43497,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43465,9 +43554,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43520,9 +43609,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43575,14 +43664,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43632,9 +43721,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43687,14 +43776,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  57%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43744,9 +43833,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43799,9 +43888,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43854,9 +43943,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43909,9 +43998,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -43964,14 +44053,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44021,14 +44110,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44078,9 +44167,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44133,9 +44222,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44188,9 +44277,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44243,14 +44332,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44300,9 +44389,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44355,9 +44444,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44410,9 +44499,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44465,14 +44554,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44522,14 +44611,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  60%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44579,9 +44668,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44634,9 +44723,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44689,9 +44778,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44744,9 +44833,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44799,14 +44888,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44856,14 +44945,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44913,9 +45002,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -44968,9 +45057,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45023,9 +45112,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45078,14 +45167,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45135,9 +45224,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45190,9 +45279,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45245,9 +45334,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45300,14 +45389,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45357,14 +45446,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  63%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45414,9 +45503,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45469,9 +45558,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45524,9 +45613,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45579,9 +45668,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45634,14 +45723,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45691,9 +45780,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45746,14 +45835,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45803,9 +45892,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45858,9 +45947,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45913,14 +46002,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -45970,9 +46059,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46025,9 +46114,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46080,9 +46169,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46135,14 +46224,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46192,14 +46281,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  66%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46249,9 +46338,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46304,9 +46393,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46359,9 +46448,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46414,9 +46503,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46469,14 +46558,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46526,9 +46615,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46581,14 +46670,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46638,9 +46727,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46693,9 +46782,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46748,14 +46837,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  68%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46805,9 +46894,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46860,9 +46949,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46915,9 +47004,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -46970,9 +47059,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47025,14 +47114,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  69%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47082,9 +47171,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47137,9 +47226,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47192,9 +47281,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47247,9 +47336,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47302,14 +47391,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47359,9 +47448,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47414,14 +47503,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47471,9 +47560,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47526,9 +47615,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47581,14 +47670,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  71%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47638,9 +47727,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47693,9 +47782,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47748,9 +47837,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47803,9 +47892,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47858,14 +47947,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  72%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47915,9 +48004,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -47970,9 +48059,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48025,9 +48114,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48080,9 +48169,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48135,14 +48224,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48192,9 +48281,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48247,9 +48336,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48302,14 +48391,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48359,9 +48448,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48414,14 +48503,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  74%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48471,9 +48560,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48526,9 +48615,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48581,9 +48670,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48636,9 +48725,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48691,14 +48780,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48748,14 +48837,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48805,9 +48894,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48860,9 +48949,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48915,9 +49004,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -48970,14 +49059,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49027,9 +49116,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49082,9 +49171,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49137,14 +49226,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49194,9 +49283,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49249,14 +49338,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  77%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49306,9 +49395,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49361,9 +49450,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49416,9 +49505,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49471,9 +49560,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49526,14 +49615,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49583,14 +49672,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49640,9 +49729,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49695,9 +49784,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49750,9 +49839,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49805,14 +49894,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49862,9 +49951,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49917,9 +50006,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -49972,9 +50061,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50027,14 +50116,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50084,14 +50173,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  80%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50141,9 +50230,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50196,9 +50285,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50251,9 +50340,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50306,9 +50395,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50361,14 +50450,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50418,14 +50507,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50475,9 +50564,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50530,9 +50619,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50585,9 +50674,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50640,14 +50729,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50697,9 +50786,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50752,9 +50841,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50807,9 +50896,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50862,14 +50951,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50919,14 +51008,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  83%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -50976,9 +51065,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51031,9 +51120,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51086,9 +51175,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51141,9 +51230,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51196,14 +51285,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51253,9 +51342,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51308,14 +51397,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51365,9 +51454,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51420,9 +51509,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51475,14 +51564,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51532,9 +51621,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51587,9 +51676,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51642,9 +51731,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51697,14 +51786,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51754,14 +51843,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  86%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51811,9 +51900,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51866,9 +51955,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51921,9 +52010,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -51976,9 +52065,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52031,14 +52120,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52088,9 +52177,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52143,14 +52232,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52200,9 +52289,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52255,9 +52344,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52310,14 +52399,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  88%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52367,9 +52456,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52422,9 +52511,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52477,9 +52566,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52532,9 +52621,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52587,14 +52676,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  89%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52644,9 +52733,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52699,9 +52788,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52754,9 +52843,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52809,9 +52898,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52864,14 +52953,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52921,9 +53010,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -52976,9 +53065,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53031,14 +53120,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53088,9 +53177,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53143,14 +53232,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  91%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53200,9 +53289,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53255,9 +53344,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53310,9 +53399,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53365,9 +53454,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53420,14 +53509,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  92%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53477,9 +53566,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53532,9 +53621,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53587,9 +53676,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53642,9 +53731,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53697,14 +53786,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53754,9 +53843,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53809,9 +53898,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53864,14 +53953,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53921,9 +54010,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -53976,14 +54065,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  94%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54033,9 +54122,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54088,9 +54177,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54143,9 +54232,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54198,9 +54287,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54253,14 +54342,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54310,14 +54399,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54367,9 +54456,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54422,9 +54511,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54477,9 +54566,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54532,14 +54621,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54589,9 +54678,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54644,9 +54733,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54699,14 +54788,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54756,9 +54845,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54811,14 +54900,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  97%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54868,9 +54957,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54923,9 +55012,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -54978,9 +55067,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55033,9 +55122,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55088,14 +55177,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55145,14 +55234,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55202,9 +55291,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55257,9 +55346,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55312,9 +55401,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55367,14 +55456,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55424,9 +55513,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55479,9 +55568,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55534,9 +55623,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55589,14 +55678,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================|  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55646,14 +55735,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================| 100%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55703,9 +55792,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55758,16 +55847,16 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
 ## [1] "Dropping allom rows: "
 ## 
   |                                                                       
   |                                                                 |   0%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55817,9 +55906,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55872,9 +55961,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55927,14 +56016,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |                                                                 |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -55984,14 +56073,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56041,9 +56130,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56096,9 +56185,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56151,9 +56240,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56206,14 +56295,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56263,9 +56352,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56318,9 +56407,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56373,9 +56462,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56428,14 +56517,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56485,14 +56574,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   3%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56542,9 +56631,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56597,9 +56686,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56652,9 +56741,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56707,9 +56796,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56762,14 +56851,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56819,9 +56908,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56874,14 +56963,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56931,9 +57020,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -56986,9 +57075,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57041,14 +57130,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57098,9 +57187,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57153,9 +57242,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57208,9 +57297,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57263,14 +57352,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57320,14 +57409,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   6%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57377,9 +57466,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57432,9 +57521,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57487,9 +57576,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57542,9 +57631,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57597,14 +57686,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57654,9 +57743,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57709,14 +57798,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57766,9 +57855,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57821,9 +57910,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57876,14 +57965,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   8%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57933,9 +58022,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -57988,9 +58077,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58043,9 +58132,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58098,9 +58187,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58153,14 +58242,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |   9%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58210,9 +58299,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58265,9 +58354,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58320,9 +58409,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58375,9 +58464,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58430,14 +58519,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58487,9 +58576,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58542,9 +58631,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58597,14 +58686,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58654,9 +58743,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58709,14 +58798,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  11%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58766,9 +58855,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58821,9 +58910,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58876,9 +58965,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58931,9 +59020,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -58986,14 +59075,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  12%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59043,9 +59132,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59098,9 +59187,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59153,9 +59242,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59208,9 +59297,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59263,14 +59352,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59320,9 +59409,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59375,9 +59464,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59430,14 +59519,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59487,9 +59576,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59542,14 +59631,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  14%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59599,9 +59688,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59654,9 +59743,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59709,9 +59798,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59764,9 +59853,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59819,14 +59908,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59876,14 +59965,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59933,9 +60022,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -59988,9 +60077,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60043,9 +60132,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60098,14 +60187,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60155,9 +60244,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60210,9 +60299,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60265,14 +60354,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60322,9 +60411,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60377,14 +60466,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  17%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60434,9 +60523,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60489,9 +60578,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60544,9 +60633,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60599,9 +60688,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60654,14 +60743,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60711,14 +60800,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60768,9 +60857,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60823,9 +60912,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60878,9 +60967,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60933,14 +61022,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -60990,9 +61079,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61045,9 +61134,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61100,9 +61189,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61155,14 +61244,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61212,14 +61301,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  20%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61269,9 +61358,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61324,9 +61413,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61379,9 +61468,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61434,9 +61523,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61489,14 +61578,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61546,14 +61635,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61603,9 +61692,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61658,9 +61747,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61713,9 +61802,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61768,14 +61857,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61825,9 +61914,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61880,9 +61969,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61935,9 +62024,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -61990,14 +62079,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62047,14 +62136,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  23%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62104,9 +62193,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62159,9 +62248,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62214,9 +62303,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62269,9 +62358,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62324,14 +62413,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62381,9 +62470,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62436,14 +62525,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62493,9 +62582,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62548,9 +62637,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62603,14 +62692,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62660,9 +62749,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62715,9 +62804,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62770,9 +62859,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62825,14 +62914,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62882,14 +62971,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  26%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62939,9 +63028,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -62994,9 +63083,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63049,9 +63138,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63104,9 +63193,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63159,14 +63248,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63216,9 +63305,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63271,14 +63360,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63328,9 +63417,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63383,9 +63472,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63438,14 +63527,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  28%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63495,9 +63584,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63550,9 +63639,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63605,9 +63694,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63660,9 +63749,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63715,14 +63804,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  29%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63772,9 +63861,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63827,9 +63916,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63882,9 +63971,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63937,9 +64026,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -63992,14 +64081,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64049,9 +64138,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64104,14 +64193,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64161,9 +64250,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64216,9 +64305,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64271,14 +64360,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  31%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64328,9 +64417,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64383,9 +64472,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64438,9 +64527,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64493,9 +64582,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64548,14 +64637,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  32%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64605,9 +64694,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64660,9 +64749,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64715,9 +64804,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64770,9 +64859,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64825,14 +64914,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64882,9 +64971,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64937,9 +65026,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -64992,14 +65081,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65049,9 +65138,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65104,14 +65193,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  34%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65161,9 +65250,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65216,9 +65305,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65271,9 +65360,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65326,9 +65415,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65381,14 +65470,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65438,14 +65527,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65495,9 +65584,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65550,9 +65639,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65605,9 +65694,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65660,14 +65749,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65717,9 +65806,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65772,9 +65861,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65827,14 +65916,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65884,9 +65973,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65939,14 +66028,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  37%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -65996,9 +66085,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66051,9 +66140,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66106,9 +66195,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66161,9 +66250,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66216,14 +66305,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66273,14 +66362,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66330,9 +66419,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66385,9 +66474,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66440,9 +66529,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66495,14 +66584,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66552,9 +66641,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66607,9 +66696,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66662,9 +66751,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66717,14 +66806,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66774,14 +66863,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  40%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66831,9 +66920,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66886,9 +66975,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66941,9 +67030,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -66996,9 +67085,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67051,14 +67140,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67108,14 +67197,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67165,9 +67254,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67220,9 +67309,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67275,9 +67364,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67330,14 +67419,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67387,9 +67476,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67442,9 +67531,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67497,9 +67586,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67552,14 +67641,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67609,14 +67698,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  43%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67666,9 +67755,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67721,9 +67810,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67776,9 +67865,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67831,9 +67920,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67886,14 +67975,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67943,9 +68032,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -67998,14 +68087,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68055,9 +68144,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68110,9 +68199,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68165,14 +68254,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68222,9 +68311,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68277,9 +68366,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68332,9 +68421,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68387,14 +68476,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68444,14 +68533,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  46%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68501,9 +68590,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68556,9 +68645,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68611,9 +68700,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68666,9 +68755,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68721,14 +68810,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68778,9 +68867,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68833,14 +68922,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68890,9 +68979,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -68945,9 +69034,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69000,14 +69089,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  48%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69057,9 +69146,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69112,9 +69201,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69167,9 +69256,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69222,9 +69311,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69277,14 +69366,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  49%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69334,9 +69423,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69389,9 +69478,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69444,9 +69533,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69499,9 +69588,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69554,14 +69643,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69611,9 +69700,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69666,9 +69755,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69721,14 +69810,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69778,9 +69867,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69833,14 +69922,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  51%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69890,9 +69979,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -69945,9 +70034,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70000,9 +70089,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70055,9 +70144,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70110,14 +70199,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  52%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70167,9 +70256,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70222,9 +70311,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70277,9 +70366,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70332,9 +70421,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70387,14 +70476,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70444,9 +70533,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70499,9 +70588,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70554,14 +70643,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70611,9 +70700,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70666,14 +70755,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  54%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70723,9 +70812,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70778,9 +70867,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70833,9 +70922,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70888,9 +70977,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -70943,14 +71032,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71000,14 +71089,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71057,9 +71146,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71112,9 +71201,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71167,9 +71256,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71222,14 +71311,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71279,9 +71368,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71334,9 +71423,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71389,14 +71478,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71446,9 +71535,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71501,14 +71590,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  57%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71558,9 +71647,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71613,9 +71702,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71668,9 +71757,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71723,9 +71812,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71778,14 +71867,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71835,14 +71924,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71892,9 +71981,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -71947,9 +72036,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72002,9 +72091,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72057,14 +72146,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72114,9 +72203,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72169,9 +72258,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72224,9 +72313,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72279,14 +72368,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72336,14 +72425,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  60%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72393,9 +72482,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72448,9 +72537,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72503,9 +72592,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72558,9 +72647,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72613,14 +72702,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72670,14 +72759,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72727,9 +72816,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72782,9 +72871,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72837,9 +72926,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72892,14 +72981,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -72949,9 +73038,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73004,9 +73093,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73059,9 +73148,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73114,14 +73203,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73171,14 +73260,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  63%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73228,9 +73317,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73283,9 +73372,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73338,9 +73427,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73393,9 +73482,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73448,14 +73537,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73505,9 +73594,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73560,14 +73649,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73617,9 +73706,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73672,9 +73761,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73727,14 +73816,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73784,9 +73873,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73839,9 +73928,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73894,9 +73983,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -73949,14 +74038,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74006,14 +74095,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  66%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74063,9 +74152,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74118,9 +74207,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74173,9 +74262,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74228,9 +74317,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74283,14 +74372,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74340,9 +74429,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74395,14 +74484,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74452,9 +74541,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74507,9 +74596,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74562,14 +74651,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  68%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74619,9 +74708,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74674,9 +74763,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74729,9 +74818,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74784,9 +74873,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74839,14 +74928,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  69%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74896,9 +74985,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -74951,9 +75040,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75006,9 +75095,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75061,9 +75150,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75116,14 +75205,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75173,9 +75262,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75228,14 +75317,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75285,9 +75374,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75340,9 +75429,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75395,14 +75484,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  71%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75452,9 +75541,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75507,9 +75596,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75562,9 +75651,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75617,9 +75706,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75672,14 +75761,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  72%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75729,9 +75818,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75784,9 +75873,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75839,9 +75928,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75894,9 +75983,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -75949,14 +76038,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76006,9 +76095,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76061,9 +76150,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76116,14 +76205,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76173,9 +76262,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76228,14 +76317,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  74%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76285,9 +76374,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76340,9 +76429,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76395,9 +76484,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76450,9 +76539,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76505,14 +76594,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76562,14 +76651,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76619,9 +76708,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76674,9 +76763,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76729,9 +76818,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76784,14 +76873,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76841,9 +76930,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76896,9 +76985,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -76951,14 +77040,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77008,9 +77097,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77063,14 +77152,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  77%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77120,9 +77209,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77175,9 +77264,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77230,9 +77319,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77285,9 +77374,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77340,14 +77429,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77397,14 +77486,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77454,9 +77543,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77509,9 +77598,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77564,9 +77653,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77619,14 +77708,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77676,9 +77765,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77731,9 +77820,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77786,9 +77875,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77841,14 +77930,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77898,14 +77987,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  80%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -77955,9 +78044,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78010,9 +78099,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78065,9 +78154,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78120,9 +78209,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78175,14 +78264,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78232,14 +78321,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78289,9 +78378,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78344,9 +78433,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78399,9 +78488,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78454,14 +78543,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78511,9 +78600,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78566,9 +78655,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78621,9 +78710,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78676,14 +78765,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78733,14 +78822,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  83%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78790,9 +78879,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78845,9 +78934,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78900,9 +78989,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -78955,9 +79044,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79010,14 +79099,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79067,9 +79156,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79122,14 +79211,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79179,9 +79268,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79234,9 +79323,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79289,14 +79378,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79346,9 +79435,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79401,9 +79490,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79456,9 +79545,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79511,14 +79600,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79568,14 +79657,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  86%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79625,9 +79714,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79680,9 +79769,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79735,9 +79824,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79790,9 +79879,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79845,14 +79934,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79902,9 +79991,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -79957,14 +80046,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80014,9 +80103,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80069,9 +80158,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80124,14 +80213,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  88%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80181,9 +80270,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80236,9 +80325,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80291,9 +80380,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80346,9 +80435,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80401,14 +80490,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  89%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80458,9 +80547,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80513,9 +80602,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80568,9 +80657,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80623,9 +80712,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80678,14 +80767,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80735,9 +80824,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80790,9 +80879,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80845,14 +80934,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80902,9 +80991,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -80957,14 +81046,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  91%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81014,9 +81103,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81069,9 +81158,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81124,9 +81213,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81179,9 +81268,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81234,14 +81323,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  92%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81291,9 +81380,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81346,9 +81435,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81401,9 +81490,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81456,9 +81545,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81511,14 +81600,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81568,9 +81657,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81623,9 +81712,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81678,14 +81767,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81735,9 +81824,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81790,14 +81879,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  94%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81847,9 +81936,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81902,9 +81991,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -81957,9 +82046,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82012,9 +82101,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82067,14 +82156,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82124,14 +82213,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82181,9 +82270,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82236,9 +82325,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82291,9 +82380,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82346,14 +82435,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82403,9 +82492,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82458,9 +82547,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82513,14 +82602,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82570,9 +82659,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82625,14 +82714,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  97%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82682,9 +82771,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82737,9 +82826,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82792,9 +82881,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82847,9 +82936,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82902,14 +82991,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -82959,14 +83048,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83016,9 +83105,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83071,9 +83160,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83126,9 +83215,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83181,14 +83270,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83238,9 +83327,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83293,9 +83382,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83348,9 +83437,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83403,14 +83492,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================|  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83460,14 +83549,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================| 100%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83517,9 +83606,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83572,20 +83661,32 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
 ## [1] "saving MCMC output to"                                                     
 ## [2] "/fs/data3/tonygard/work/pecan/modules/allometry/vignettes/Allom.LH.6.Rdata"
 ## [1] "saving diagnostic graphs to"                                                  
 ## [2] "/fs/data3/tonygard/work/pecan/modules/allometry/vignettes/Allom.LH.6.MCMC.pdf"</code></pre>
-<pre><code>## [1] "DIC"              "399.878998334903" "pD"              
+            <pre><code>## [1] "DIC"              "399.878998334903" "pD"              
 ## [4] "241.380752079601"
 ## [1] "DICg"             "478.685032054038" "pDg"             
 ## [4] "240.109914393467"</code></pre>
-<p>If you want to run with a response variable other than the default (e.g. components = 6; stem biomass), look up the relevant component IDs in data(allom.components). The default component is 3 (total aboveground biomass). Note that if you specify multiple PFTs (as a list) and multiple components (as a vector) then AllomAve will generate allometries for all PFT x component combinations</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">allom.stats =<span class="st"> </span><span class="kw"><a href="../reference/AllomAve.html">AllomAve</a></span>(pfts,<span class="dt">ngibbs=</span><span class="dv">500</span>,<span class="dt">components=</span><span class="kw">c</span>(<span class="dv">3</span>,<span class="dv">6</span>))</code></pre></div>
-<pre><code>## [1] "writing output to"                                        
+            <p>
+              If you want to run with a response variable other than the default
+              (e.g. components = 6; stem biomass), look up the relevant
+              component IDs in data(allom.components). The default component is
+              3 (total aboveground biomass). Note that if you specify multiple
+              PFTs (as a list) and multiple components (as a vector) then
+              AllomAve will generate allometries for all PFT x component
+              combinations
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">allom.stats =<span class="st"> </span><span class="kw"><a href="../reference/AllomAve.html">AllomAve</a></span>(pfts,<span class="dt">ngibbs=</span><span class="dv">500</span>,<span class="dt">components=</span><span class="kw">c</span>(<span class="dv">3</span>,<span class="dv">6</span>))</code></pre>
+            </div>
+            <pre><code>## [1] "writing output to"                                        
 ## [2] "/fs/data3/tonygard/work/pecan/modules/allometry/vignettes"
 ## $spcd
 ## [1] 531 318
@@ -83596,14 +83697,14 @@ <h2 class="hasAnchor">
 ## 
 ## [[3]]
 ## [1] 3</code></pre>
-<pre><code>## Warning in nu(allom$parm$Component.ID): NAs introduced by coercion</code></pre>
-<pre><code>## [1] "Dropping allom rows: "
+            <pre><code>## Warning in nu(allom$parm$Component.ID): NAs introduced by coercion</code></pre>
+            <pre><code>## [1] "Dropping allom rows: "
 ## 
   |                                                                       
   |                                                                 |   0%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83617,9 +83718,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83636,9 +83737,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83655,14 +83756,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |                                                                 |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83676,14 +83777,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83697,9 +83798,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83716,9 +83817,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83735,9 +83836,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83754,14 +83855,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83775,9 +83876,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83794,9 +83895,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83813,9 +83914,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83832,14 +83933,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83853,14 +83954,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   3%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83874,9 +83975,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83893,9 +83994,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83912,9 +84013,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83931,9 +84032,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83950,14 +84051,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83971,9 +84072,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -83990,14 +84091,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84011,9 +84112,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84030,9 +84131,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84049,14 +84150,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84070,9 +84171,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84089,9 +84190,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84108,9 +84209,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84127,14 +84228,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84148,14 +84249,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   6%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84169,9 +84270,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84188,9 +84289,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84207,9 +84308,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84226,9 +84327,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84245,14 +84346,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84266,9 +84367,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84285,14 +84386,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84306,9 +84407,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84325,9 +84426,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84344,14 +84445,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   8%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84365,9 +84466,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84384,9 +84485,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84403,9 +84504,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84422,9 +84523,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84441,14 +84542,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |   9%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84462,9 +84563,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84481,9 +84582,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84500,9 +84601,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84519,9 +84620,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84538,14 +84639,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84559,9 +84660,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84578,9 +84679,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84597,14 +84698,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84618,9 +84719,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84637,14 +84738,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  11%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84658,9 +84759,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84677,9 +84778,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84696,9 +84797,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84715,9 +84816,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84734,14 +84835,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  12%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84755,9 +84856,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84774,9 +84875,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84793,9 +84894,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84812,9 +84913,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84831,14 +84932,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84852,9 +84953,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84871,9 +84972,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84890,14 +84991,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84911,9 +85012,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84930,14 +85031,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  14%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84951,9 +85052,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84970,9 +85071,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -84989,9 +85090,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85008,9 +85109,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85027,14 +85128,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85048,14 +85149,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85069,9 +85170,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85088,9 +85189,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85107,9 +85208,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85126,14 +85227,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85147,9 +85248,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85166,9 +85267,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85185,14 +85286,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85206,9 +85307,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85225,14 +85326,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  17%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85246,9 +85347,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85265,9 +85366,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85284,9 +85385,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85303,9 +85404,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85322,14 +85423,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85343,14 +85444,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85364,9 +85465,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85383,9 +85484,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85402,9 +85503,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85421,14 +85522,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85442,9 +85543,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85461,9 +85562,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85480,9 +85581,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85499,14 +85600,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85520,14 +85621,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  20%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85541,9 +85642,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85560,9 +85661,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85579,9 +85680,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85598,9 +85699,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85617,14 +85718,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85638,14 +85739,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85659,9 +85760,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85678,9 +85779,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85697,9 +85798,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85716,14 +85817,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85737,9 +85838,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85756,9 +85857,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85775,9 +85876,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85794,14 +85895,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85815,14 +85916,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  23%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85836,9 +85937,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85855,9 +85956,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85874,9 +85975,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85893,9 +85994,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85912,14 +86013,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85933,9 +86034,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85952,14 +86053,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85973,9 +86074,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -85992,9 +86093,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86011,14 +86112,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86032,9 +86133,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86051,9 +86152,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86070,9 +86171,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86089,14 +86190,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86110,14 +86211,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  26%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86131,9 +86232,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86150,9 +86251,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86169,9 +86270,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86188,9 +86289,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86207,14 +86308,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86228,9 +86329,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86247,14 +86348,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86268,9 +86369,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86287,9 +86388,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86306,14 +86407,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  28%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86327,9 +86428,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86346,9 +86447,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86365,9 +86466,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86384,9 +86485,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86403,14 +86504,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  29%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86424,9 +86525,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86443,9 +86544,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86462,9 +86563,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86481,9 +86582,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86500,14 +86601,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86521,9 +86622,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86540,14 +86641,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86561,9 +86662,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86580,9 +86681,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86599,14 +86700,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  31%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86620,9 +86721,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86639,9 +86740,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86658,9 +86759,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86677,9 +86778,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86696,14 +86797,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  32%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86717,9 +86818,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86736,9 +86837,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86755,9 +86856,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86774,9 +86875,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86793,14 +86894,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86814,9 +86915,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86833,9 +86934,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86852,14 +86953,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86873,9 +86974,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86892,14 +86993,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  34%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86913,9 +87014,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86932,9 +87033,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86951,9 +87052,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86970,9 +87071,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -86989,14 +87090,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87010,14 +87111,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87031,9 +87132,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87050,9 +87151,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87069,9 +87170,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87088,14 +87189,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87109,9 +87210,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87128,9 +87229,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87147,14 +87248,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87168,9 +87269,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87187,14 +87288,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  37%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87208,9 +87309,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87227,9 +87328,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87246,9 +87347,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87265,9 +87366,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87284,14 +87385,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87305,14 +87406,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87326,9 +87427,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87345,9 +87446,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87364,9 +87465,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87383,14 +87484,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87404,9 +87505,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87423,9 +87524,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87442,9 +87543,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87461,14 +87562,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87482,14 +87583,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  40%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87503,9 +87604,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87522,9 +87623,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87541,9 +87642,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87560,9 +87661,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87579,14 +87680,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87600,14 +87701,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87621,9 +87722,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87640,9 +87741,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87659,9 +87760,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87678,14 +87779,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87699,9 +87800,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87718,9 +87819,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87737,9 +87838,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87756,14 +87857,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87777,14 +87878,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  43%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87798,9 +87899,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87817,9 +87918,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87836,9 +87937,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87855,9 +87956,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87874,14 +87975,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87895,9 +87996,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87914,14 +88015,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87935,9 +88036,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87954,9 +88055,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87973,14 +88074,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -87994,9 +88095,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88013,9 +88114,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88032,9 +88133,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88051,14 +88152,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88072,14 +88173,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  46%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88093,9 +88194,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88112,9 +88213,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88131,9 +88232,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88150,9 +88251,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88169,14 +88270,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88190,9 +88291,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88209,14 +88310,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88230,9 +88331,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88249,9 +88350,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88268,14 +88369,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  48%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88289,9 +88390,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88308,9 +88409,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88327,9 +88428,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88346,9 +88447,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88365,14 +88466,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  49%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88386,9 +88487,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88405,9 +88506,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88424,9 +88525,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88443,9 +88544,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88462,14 +88563,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88483,9 +88584,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88502,9 +88603,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88521,14 +88622,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88542,9 +88643,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88561,14 +88662,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  51%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88582,9 +88683,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88601,9 +88702,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88620,9 +88721,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88639,9 +88740,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88658,14 +88759,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  52%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88679,9 +88780,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88698,9 +88799,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88717,9 +88818,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88736,9 +88837,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88755,14 +88856,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88776,9 +88877,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88795,9 +88896,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88814,14 +88915,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88835,9 +88936,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88854,14 +88955,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  54%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88875,9 +88976,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88894,9 +88995,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88913,9 +89014,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88932,9 +89033,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88951,14 +89052,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88972,14 +89073,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -88993,9 +89094,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89012,9 +89113,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89031,9 +89132,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89050,14 +89151,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89071,9 +89172,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89090,9 +89191,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89109,14 +89210,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89130,9 +89231,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89149,14 +89250,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  57%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89170,9 +89271,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89189,9 +89290,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89208,9 +89309,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89227,9 +89328,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89246,14 +89347,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89267,14 +89368,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89288,9 +89389,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89307,9 +89408,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89326,9 +89427,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89345,14 +89446,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89366,9 +89467,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89385,9 +89486,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89404,9 +89505,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89423,14 +89524,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89444,14 +89545,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  60%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89465,9 +89566,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89484,9 +89585,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89503,9 +89604,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89522,9 +89623,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89541,14 +89642,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89562,14 +89663,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89583,9 +89684,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89602,9 +89703,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89621,9 +89722,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89640,14 +89741,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89661,9 +89762,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89680,9 +89781,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89699,9 +89800,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89718,14 +89819,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89739,14 +89840,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  63%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89760,9 +89861,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89779,9 +89880,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89798,9 +89899,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89817,9 +89918,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89836,14 +89937,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89857,9 +89958,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89876,14 +89977,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89897,9 +89998,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89916,9 +90017,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89935,14 +90036,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89956,9 +90057,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89975,9 +90076,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -89994,9 +90095,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90013,14 +90114,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90034,14 +90135,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  66%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90055,9 +90156,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90074,9 +90175,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90093,9 +90194,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90112,9 +90213,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90131,14 +90232,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90152,9 +90253,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90171,14 +90272,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90192,9 +90293,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90211,9 +90312,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90230,14 +90331,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  68%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90251,9 +90352,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90270,9 +90371,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90289,9 +90390,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90308,9 +90409,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90327,14 +90428,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  69%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90348,9 +90449,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90367,9 +90468,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90386,9 +90487,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90405,9 +90506,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90424,14 +90525,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90445,9 +90546,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90464,14 +90565,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90485,9 +90586,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90504,9 +90605,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90523,14 +90624,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  71%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90544,9 +90645,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90563,9 +90664,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90582,9 +90683,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90601,9 +90702,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90620,14 +90721,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  72%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90641,9 +90742,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90660,9 +90761,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90679,9 +90780,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90698,9 +90799,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90717,14 +90818,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90738,9 +90839,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90757,9 +90858,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90776,14 +90877,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90797,9 +90898,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90816,14 +90917,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  74%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90837,9 +90938,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90856,9 +90957,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90875,9 +90976,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90894,9 +90995,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90913,14 +91014,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90934,14 +91035,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90955,9 +91056,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90974,9 +91075,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -90993,9 +91094,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91012,14 +91113,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91033,9 +91134,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91052,9 +91153,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91071,14 +91172,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91092,9 +91193,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91111,14 +91212,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  77%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91132,9 +91233,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91151,9 +91252,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91170,9 +91271,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91189,9 +91290,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91208,14 +91309,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91229,14 +91330,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91250,9 +91351,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91269,9 +91370,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91288,9 +91389,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91307,14 +91408,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91328,9 +91429,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91347,9 +91448,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91366,9 +91467,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91385,14 +91486,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91406,14 +91507,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  80%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91427,9 +91528,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91446,9 +91547,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91465,9 +91566,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91484,9 +91585,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91503,14 +91604,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91524,14 +91625,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91545,9 +91646,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91564,9 +91665,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91583,9 +91684,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91602,14 +91703,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91623,9 +91724,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91642,9 +91743,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91661,9 +91762,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91680,14 +91781,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91701,14 +91802,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  83%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91722,9 +91823,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91741,9 +91842,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91760,9 +91861,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91779,9 +91880,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91798,14 +91899,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91819,9 +91920,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91838,14 +91939,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91859,9 +91960,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91878,9 +91979,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91897,14 +91998,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91918,9 +92019,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91937,9 +92038,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91956,9 +92057,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91975,14 +92076,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -91996,14 +92097,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  86%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92017,9 +92118,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92036,9 +92137,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92055,9 +92156,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92074,9 +92175,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92093,14 +92194,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92114,9 +92215,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92133,14 +92234,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92154,9 +92255,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92173,9 +92274,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92192,14 +92293,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  88%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92213,9 +92314,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92232,9 +92333,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92251,9 +92352,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92270,9 +92371,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92289,14 +92390,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  89%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92310,9 +92411,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92329,9 +92430,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92348,9 +92449,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92367,9 +92468,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92386,14 +92487,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92407,9 +92508,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92426,9 +92527,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92445,14 +92546,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92466,9 +92567,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92485,14 +92586,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  91%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92506,9 +92607,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92525,9 +92626,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92544,9 +92645,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92563,9 +92664,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92582,14 +92683,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  92%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92603,9 +92704,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92622,9 +92723,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92641,9 +92742,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92660,9 +92761,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92679,14 +92780,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92700,9 +92801,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92719,9 +92820,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92738,14 +92839,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92759,9 +92860,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92778,14 +92879,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  94%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92799,9 +92900,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92818,9 +92919,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92837,9 +92938,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92856,9 +92957,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92875,14 +92976,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92896,14 +92997,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92917,9 +93018,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92936,9 +93037,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92955,9 +93056,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92974,14 +93075,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -92995,9 +93096,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93014,9 +93115,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93033,14 +93134,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93054,9 +93155,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93073,14 +93174,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  97%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93094,9 +93195,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93113,9 +93214,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93132,9 +93233,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93151,9 +93252,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93170,14 +93271,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93191,14 +93292,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93212,9 +93313,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93231,9 +93332,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93250,9 +93351,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93269,14 +93370,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93290,9 +93391,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93309,9 +93410,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93328,9 +93429,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93347,14 +93448,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================|  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93368,14 +93469,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================| 100%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93389,9 +93490,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93408,16 +93509,16 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
 ## [1] "Dropping allom rows: "
 ## 
   |                                                                       
   |                                                                 |   0%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93431,9 +93532,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93450,9 +93551,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93469,14 +93570,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |                                                                 |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93490,14 +93591,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93511,9 +93612,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93530,9 +93631,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93549,9 +93650,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93568,14 +93669,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93589,9 +93690,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93608,9 +93709,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93627,9 +93728,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93646,14 +93747,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93667,14 +93768,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   3%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93688,9 +93789,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93707,9 +93808,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93726,9 +93827,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93745,9 +93846,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93764,14 +93865,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93785,9 +93886,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93804,14 +93905,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93825,9 +93926,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93844,9 +93945,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93863,14 +93964,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93884,9 +93985,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93903,9 +94004,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93922,9 +94023,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93941,14 +94042,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93962,14 +94063,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   6%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -93983,9 +94084,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94002,9 +94103,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94021,9 +94122,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94040,9 +94141,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94059,14 +94160,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94080,9 +94181,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94099,14 +94200,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94120,9 +94221,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94139,9 +94240,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94158,14 +94259,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   8%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94179,9 +94280,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94198,9 +94299,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94217,9 +94318,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94236,9 +94337,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94255,14 +94356,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |   9%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94276,9 +94377,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94295,9 +94396,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94314,9 +94415,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94333,9 +94434,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94352,14 +94453,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94373,9 +94474,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94392,9 +94493,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94411,14 +94512,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94432,9 +94533,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94451,14 +94552,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  11%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94472,9 +94573,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94491,9 +94592,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94510,9 +94611,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94529,9 +94630,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94548,14 +94649,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  12%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94569,9 +94670,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94588,9 +94689,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94607,9 +94708,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94626,9 +94727,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94645,14 +94746,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94666,9 +94767,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94685,9 +94786,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94704,14 +94805,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94725,9 +94826,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94744,14 +94845,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  14%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94765,9 +94866,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94784,9 +94885,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94803,9 +94904,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94822,9 +94923,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94841,14 +94942,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94862,14 +94963,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94883,9 +94984,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94902,9 +95003,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94921,9 +95022,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94940,14 +95041,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94961,9 +95062,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94980,9 +95081,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -94999,14 +95100,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95020,9 +95121,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95039,14 +95140,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  17%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95060,9 +95161,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95079,9 +95180,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95098,9 +95199,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95117,9 +95218,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95136,14 +95237,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95157,14 +95258,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95178,9 +95279,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95197,9 +95298,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95216,9 +95317,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95235,14 +95336,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95256,9 +95357,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95275,9 +95376,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95294,9 +95395,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95313,14 +95414,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95334,14 +95435,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  20%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95355,9 +95456,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95374,9 +95475,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95393,9 +95494,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95412,9 +95513,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95431,14 +95532,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95452,14 +95553,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95473,9 +95574,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95492,9 +95593,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95511,9 +95612,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95530,14 +95631,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95551,9 +95652,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95570,9 +95671,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95589,9 +95690,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95608,14 +95709,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95629,14 +95730,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  23%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95650,9 +95751,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95669,9 +95770,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95688,9 +95789,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95707,9 +95808,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95726,14 +95827,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95747,9 +95848,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95766,14 +95867,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95787,9 +95888,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95806,9 +95907,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95825,14 +95926,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95846,9 +95947,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95865,9 +95966,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95884,9 +95985,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95903,14 +96004,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95924,14 +96025,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  26%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95945,9 +96046,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95964,9 +96065,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -95983,9 +96084,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96002,9 +96103,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96021,14 +96122,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96042,9 +96143,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96061,14 +96162,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96082,9 +96183,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96101,9 +96202,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96120,14 +96221,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  28%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96141,9 +96242,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96160,9 +96261,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96179,9 +96280,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96198,9 +96299,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96217,14 +96318,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  29%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96238,9 +96339,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96257,9 +96358,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96276,9 +96377,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96295,9 +96396,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96314,14 +96415,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96335,9 +96436,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96354,14 +96455,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96375,9 +96476,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96394,9 +96495,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96413,14 +96514,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  31%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96434,9 +96535,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96453,9 +96554,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96472,9 +96573,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96491,9 +96592,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96510,14 +96611,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  32%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96531,9 +96632,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96550,9 +96651,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96569,9 +96670,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96588,9 +96689,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96607,14 +96708,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96628,9 +96729,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96647,9 +96748,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96666,14 +96767,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96687,9 +96788,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96706,14 +96807,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  34%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96727,9 +96828,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96746,9 +96847,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96765,9 +96866,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96784,9 +96885,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96803,14 +96904,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96824,14 +96925,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96845,9 +96946,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96864,9 +96965,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96883,9 +96984,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96902,14 +97003,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96923,9 +97024,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96942,9 +97043,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96961,14 +97062,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -96982,9 +97083,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97001,14 +97102,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  37%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97022,9 +97123,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97041,9 +97142,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97060,9 +97161,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97079,9 +97180,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97098,14 +97199,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97119,14 +97220,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97140,9 +97241,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97159,9 +97260,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97178,9 +97279,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97197,14 +97298,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97218,9 +97319,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97237,9 +97338,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97256,9 +97357,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97275,14 +97376,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97296,14 +97397,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  40%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97317,9 +97418,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97336,9 +97437,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97355,9 +97456,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97374,9 +97475,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97393,14 +97494,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97414,14 +97515,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97435,9 +97536,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97454,9 +97555,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97473,9 +97574,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97492,14 +97593,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97513,9 +97614,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97532,9 +97633,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97551,9 +97652,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97570,14 +97671,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97591,14 +97692,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  43%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97612,9 +97713,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97631,9 +97732,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97650,9 +97751,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97669,9 +97770,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97688,14 +97789,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97709,9 +97810,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97728,14 +97829,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97749,9 +97850,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97768,9 +97869,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97787,14 +97888,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97808,9 +97909,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97827,9 +97928,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97846,9 +97947,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97865,14 +97966,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97886,14 +97987,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  46%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97907,9 +98008,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97926,9 +98027,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97945,9 +98046,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97964,9 +98065,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -97983,14 +98084,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98004,9 +98105,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98023,14 +98124,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98044,9 +98145,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98063,9 +98164,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98082,14 +98183,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  48%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98103,9 +98204,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98122,9 +98223,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98141,9 +98242,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98160,9 +98261,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98179,14 +98280,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  49%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98200,9 +98301,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98219,9 +98320,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98238,9 +98339,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98257,9 +98358,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98276,14 +98377,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98297,9 +98398,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98316,9 +98417,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98335,14 +98436,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98356,9 +98457,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98375,14 +98476,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  51%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98396,9 +98497,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98415,9 +98516,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98434,9 +98535,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98453,9 +98554,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98472,14 +98573,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  52%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98493,9 +98594,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98512,9 +98613,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98531,9 +98632,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98550,9 +98651,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98569,14 +98670,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98590,9 +98691,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98609,9 +98710,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98628,14 +98729,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98649,9 +98750,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98668,14 +98769,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  54%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98689,9 +98790,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98708,9 +98809,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98727,9 +98828,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98746,9 +98847,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98765,14 +98866,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98786,14 +98887,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98807,9 +98908,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98826,9 +98927,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98845,9 +98946,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98864,14 +98965,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98885,9 +98986,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98904,9 +99005,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98923,14 +99024,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98944,9 +99045,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98963,14 +99064,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  57%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -98984,9 +99085,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99003,9 +99104,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99022,9 +99123,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99041,9 +99142,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99060,14 +99161,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99081,14 +99182,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99102,9 +99203,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99121,9 +99222,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99140,9 +99241,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99159,14 +99260,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99180,9 +99281,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99199,9 +99300,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99218,9 +99319,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99237,14 +99338,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99258,14 +99359,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  60%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99279,9 +99380,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99298,9 +99399,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99317,9 +99418,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99336,9 +99437,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99355,14 +99456,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99376,14 +99477,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99397,9 +99498,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99416,9 +99517,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99435,9 +99536,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99454,14 +99555,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99475,9 +99576,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99494,9 +99595,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99513,9 +99614,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99532,14 +99633,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99553,14 +99654,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  63%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99574,9 +99675,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99593,9 +99694,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99612,9 +99713,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99631,9 +99732,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99650,14 +99751,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99671,9 +99772,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99690,14 +99791,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99711,9 +99812,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99730,9 +99831,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99749,14 +99850,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99770,9 +99871,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99789,9 +99890,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99808,9 +99909,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99827,14 +99928,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99848,14 +99949,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  66%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99869,9 +99970,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99888,9 +99989,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99907,9 +100008,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99926,9 +100027,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99945,14 +100046,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99966,9 +100067,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -99985,14 +100086,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100006,9 +100107,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100025,9 +100126,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100044,14 +100145,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  68%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100065,9 +100166,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100084,9 +100185,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100103,9 +100204,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100122,9 +100223,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100141,14 +100242,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  69%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100162,9 +100263,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100181,9 +100282,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100200,9 +100301,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100219,9 +100320,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100238,14 +100339,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100259,9 +100360,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100278,14 +100379,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100299,9 +100400,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100318,9 +100419,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100337,14 +100438,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  71%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100358,9 +100459,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100377,9 +100478,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100396,9 +100497,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100415,9 +100516,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100434,14 +100535,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  72%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100455,9 +100556,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100474,9 +100575,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100493,9 +100594,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100512,9 +100613,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100531,14 +100632,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100552,9 +100653,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100571,9 +100672,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100590,14 +100691,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100611,9 +100712,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100630,14 +100731,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  74%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100651,9 +100752,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100670,9 +100771,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100689,9 +100790,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100708,9 +100809,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100727,14 +100828,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100748,14 +100849,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100769,9 +100870,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100788,9 +100889,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100807,9 +100908,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100826,14 +100927,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100847,9 +100948,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100866,9 +100967,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100885,14 +100986,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100906,9 +101007,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100925,14 +101026,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  77%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100946,9 +101047,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100965,9 +101066,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -100984,9 +101085,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101003,9 +101104,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101022,14 +101123,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101043,14 +101144,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101064,9 +101165,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101083,9 +101184,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101102,9 +101203,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101121,14 +101222,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101142,9 +101243,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101161,9 +101262,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101180,9 +101281,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101199,14 +101300,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101220,14 +101321,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  80%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101241,9 +101342,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101260,9 +101361,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101279,9 +101380,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101298,9 +101399,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101317,14 +101418,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101338,14 +101439,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101359,9 +101460,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101378,9 +101479,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101397,9 +101498,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101416,14 +101517,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101437,9 +101538,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101456,9 +101557,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101475,9 +101576,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101494,14 +101595,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101515,14 +101616,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  83%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101536,9 +101637,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101555,9 +101656,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101574,9 +101675,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101593,9 +101694,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101612,14 +101713,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101633,9 +101734,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101652,14 +101753,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101673,9 +101774,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101692,9 +101793,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101711,14 +101812,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101732,9 +101833,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101751,9 +101852,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101770,9 +101871,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101789,14 +101890,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101810,14 +101911,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  86%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101831,9 +101932,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101850,9 +101951,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101869,9 +101970,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101888,9 +101989,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101907,14 +102008,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101928,9 +102029,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101947,14 +102048,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101968,9 +102069,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -101987,9 +102088,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102006,14 +102107,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  88%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102027,9 +102128,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102046,9 +102147,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102065,9 +102166,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102084,9 +102185,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102103,14 +102204,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  89%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102124,9 +102225,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102143,9 +102244,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102162,9 +102263,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102181,9 +102282,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102200,14 +102301,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102221,9 +102322,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102240,9 +102341,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102259,14 +102360,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102280,9 +102381,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102299,14 +102400,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  91%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102320,9 +102421,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102339,9 +102440,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102358,9 +102459,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102377,9 +102478,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102396,14 +102497,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  92%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102417,9 +102518,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102436,9 +102537,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102455,9 +102556,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102474,9 +102575,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102493,14 +102594,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102514,9 +102615,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102533,9 +102634,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102552,14 +102653,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102573,9 +102674,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102592,14 +102693,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  94%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102613,9 +102714,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102632,9 +102733,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102651,9 +102752,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102670,9 +102771,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102689,14 +102790,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102710,14 +102811,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102731,9 +102832,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102750,9 +102851,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102769,9 +102870,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102788,14 +102889,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102809,9 +102910,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102828,9 +102929,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102847,14 +102948,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102868,9 +102969,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102887,14 +102988,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  97%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102908,9 +103009,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102927,9 +103028,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102946,9 +103047,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102965,9 +103066,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -102984,14 +103085,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103005,14 +103106,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103026,9 +103127,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103045,9 +103146,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103064,9 +103165,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103083,14 +103184,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103104,9 +103205,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103123,9 +103224,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103142,9 +103243,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103161,14 +103262,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================|  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103182,14 +103283,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================| 100%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103203,9 +103304,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103222,16 +103323,16 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
 ## [1] "Dropping allom rows: "
 ## 
   |                                                                       
   |                                                                 |   0%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103245,9 +103346,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103264,9 +103365,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103283,14 +103384,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |                                                                 |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103304,14 +103405,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103325,9 +103426,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103344,9 +103445,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103363,9 +103464,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103382,14 +103483,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103403,9 +103504,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103422,9 +103523,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103441,9 +103542,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103460,14 +103561,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103481,14 +103582,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   3%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103502,9 +103603,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103521,9 +103622,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103540,9 +103641,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103559,9 +103660,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103578,14 +103679,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103599,9 +103700,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103618,14 +103719,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103639,9 +103740,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103658,9 +103759,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103677,14 +103778,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103698,9 +103799,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103717,9 +103818,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103736,9 +103837,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103755,14 +103856,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103776,14 +103877,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   6%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103797,9 +103898,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103816,9 +103917,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103835,9 +103936,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103854,9 +103955,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103873,14 +103974,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103894,9 +103995,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103913,14 +104014,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103934,9 +104035,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103953,9 +104054,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103972,14 +104073,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   8%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -103993,9 +104094,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104012,9 +104113,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104031,9 +104132,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104050,9 +104151,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104069,14 +104170,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |   9%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104090,9 +104191,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104109,9 +104210,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104128,9 +104229,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104147,9 +104248,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104166,14 +104267,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104187,9 +104288,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104206,9 +104307,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104225,14 +104326,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104246,9 +104347,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104265,14 +104366,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  11%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104286,9 +104387,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104305,9 +104406,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104324,9 +104425,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104343,9 +104444,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104362,14 +104463,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  12%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104383,9 +104484,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104402,9 +104503,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104421,9 +104522,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104440,9 +104541,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104459,14 +104560,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104480,9 +104581,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104499,9 +104600,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104518,14 +104619,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104539,9 +104640,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104558,14 +104659,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  14%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104579,9 +104680,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104598,9 +104699,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104617,9 +104718,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104636,9 +104737,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104655,14 +104756,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104676,14 +104777,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104697,9 +104798,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104716,9 +104817,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104735,9 +104836,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104754,14 +104855,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104775,9 +104876,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104794,9 +104895,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104813,14 +104914,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104834,9 +104935,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104853,14 +104954,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  17%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104874,9 +104975,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104893,9 +104994,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104912,9 +105013,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104931,9 +105032,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104950,14 +105051,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104971,14 +105072,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -104992,9 +105093,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105011,9 +105112,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105030,9 +105131,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105049,14 +105150,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105070,9 +105171,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105089,9 +105190,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105108,9 +105209,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105127,14 +105228,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105148,14 +105249,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  20%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105169,9 +105270,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105188,9 +105289,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105207,9 +105308,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105226,9 +105327,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105245,14 +105346,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105266,14 +105367,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105287,9 +105388,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105306,9 +105407,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105325,9 +105426,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105344,14 +105445,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105365,9 +105466,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105384,9 +105485,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105403,9 +105504,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105422,14 +105523,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105443,14 +105544,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  23%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105464,9 +105565,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105483,9 +105584,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105502,9 +105603,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105521,9 +105622,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105540,14 +105641,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105561,9 +105662,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105580,14 +105681,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105601,9 +105702,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105620,9 +105721,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105639,14 +105740,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105660,9 +105761,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105679,9 +105780,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105698,9 +105799,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105717,14 +105818,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105738,14 +105839,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  26%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105759,9 +105860,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105778,9 +105879,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105797,9 +105898,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105816,9 +105917,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105835,14 +105936,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105856,9 +105957,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105875,14 +105976,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105896,9 +105997,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105915,9 +106016,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105934,14 +106035,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  28%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105955,9 +106056,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105974,9 +106075,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -105993,9 +106094,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106012,9 +106113,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106031,14 +106132,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  29%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106052,9 +106153,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106071,9 +106172,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106090,9 +106191,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106109,9 +106210,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106128,14 +106229,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106149,9 +106250,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106168,14 +106269,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106189,9 +106290,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106208,9 +106309,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106227,14 +106328,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  31%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106248,9 +106349,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106267,9 +106368,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106286,9 +106387,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106305,9 +106406,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106324,14 +106425,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  32%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106345,9 +106446,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106364,9 +106465,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106383,9 +106484,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106402,9 +106503,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106421,14 +106522,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106442,9 +106543,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106461,9 +106562,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106480,14 +106581,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106501,9 +106602,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106520,14 +106621,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  34%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106541,9 +106642,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106560,9 +106661,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106579,9 +106680,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106598,9 +106699,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106617,14 +106718,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106638,14 +106739,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106659,9 +106760,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106678,9 +106779,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106697,9 +106798,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106716,14 +106817,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106737,9 +106838,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106756,9 +106857,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106775,14 +106876,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106796,9 +106897,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106815,14 +106916,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  37%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106836,9 +106937,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106855,9 +106956,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106874,9 +106975,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106893,9 +106994,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106912,14 +107013,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106933,14 +107034,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106954,9 +107055,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106973,9 +107074,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -106992,9 +107093,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107011,14 +107112,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107032,9 +107133,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107051,9 +107152,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107070,9 +107171,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107089,14 +107190,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107110,14 +107211,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  40%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107131,9 +107232,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107150,9 +107251,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107169,9 +107270,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107188,9 +107289,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107207,14 +107308,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107228,14 +107329,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107249,9 +107350,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107268,9 +107369,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107287,9 +107388,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107306,14 +107407,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107327,9 +107428,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107346,9 +107447,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107365,9 +107466,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107384,14 +107485,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107405,14 +107506,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  43%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107426,9 +107527,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107445,9 +107546,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107464,9 +107565,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107483,9 +107584,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107502,14 +107603,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107523,9 +107624,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107542,14 +107643,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107563,9 +107664,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107582,9 +107683,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107601,14 +107702,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107622,9 +107723,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107641,9 +107742,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107660,9 +107761,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107679,14 +107780,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107700,14 +107801,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  46%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107721,9 +107822,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107740,9 +107841,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107759,9 +107860,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107778,9 +107879,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107797,14 +107898,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107818,9 +107919,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107837,14 +107938,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107858,9 +107959,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107877,9 +107978,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107896,14 +107997,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  48%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107917,9 +108018,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107936,9 +108037,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107955,9 +108056,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107974,9 +108075,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -107993,14 +108094,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  49%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108014,9 +108115,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108033,9 +108134,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108052,9 +108153,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108071,9 +108172,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108090,14 +108191,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108111,9 +108212,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108130,9 +108231,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108149,14 +108250,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108170,9 +108271,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108189,14 +108290,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  51%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108210,9 +108311,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108229,9 +108330,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108248,9 +108349,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108267,9 +108368,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108286,14 +108387,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  52%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108307,9 +108408,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108326,9 +108427,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108345,9 +108446,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108364,9 +108465,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108383,14 +108484,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108404,9 +108505,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108423,9 +108524,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108442,14 +108543,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108463,9 +108564,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108482,14 +108583,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  54%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108503,9 +108604,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108522,9 +108623,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108541,9 +108642,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108560,9 +108661,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108579,14 +108680,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108600,14 +108701,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108621,9 +108722,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108640,9 +108741,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108659,9 +108760,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108678,14 +108779,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108699,9 +108800,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108718,9 +108819,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108737,14 +108838,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108758,9 +108859,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108777,14 +108878,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  57%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108798,9 +108899,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108817,9 +108918,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108836,9 +108937,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108855,9 +108956,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108874,14 +108975,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108895,14 +108996,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108916,9 +109017,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108935,9 +109036,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108954,9 +109055,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108973,14 +109074,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -108994,9 +109095,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109013,9 +109114,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109032,9 +109133,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109051,14 +109152,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109072,14 +109173,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  60%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109093,9 +109194,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109112,9 +109213,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109131,9 +109232,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109150,9 +109251,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109169,14 +109270,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109190,14 +109291,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109211,9 +109312,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109230,9 +109331,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109249,9 +109350,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109268,14 +109369,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109289,9 +109390,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109308,9 +109409,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109327,9 +109428,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109346,14 +109447,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109367,14 +109468,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  63%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109388,9 +109489,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109407,9 +109508,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109426,9 +109527,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109445,9 +109546,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109464,14 +109565,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109485,9 +109586,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109504,14 +109605,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109525,9 +109626,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109544,9 +109645,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109563,14 +109664,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109584,9 +109685,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109603,9 +109704,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109622,9 +109723,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109641,14 +109742,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109662,14 +109763,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  66%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109683,9 +109784,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109702,9 +109803,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109721,9 +109822,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109740,9 +109841,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109759,14 +109860,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109780,9 +109881,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109799,14 +109900,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109820,9 +109921,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109839,9 +109940,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109858,14 +109959,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  68%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109879,9 +109980,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109898,9 +109999,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109917,9 +110018,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109936,9 +110037,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109955,14 +110056,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  69%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109976,9 +110077,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -109995,9 +110096,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110014,9 +110115,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110033,9 +110134,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110052,14 +110153,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110073,9 +110174,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110092,14 +110193,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110113,9 +110214,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110132,9 +110233,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110151,14 +110252,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  71%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110172,9 +110273,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110191,9 +110292,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110210,9 +110311,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110229,9 +110330,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110248,14 +110349,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  72%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110269,9 +110370,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110288,9 +110389,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110307,9 +110408,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110326,9 +110427,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110345,14 +110446,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110366,9 +110467,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110385,9 +110486,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110404,14 +110505,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110425,9 +110526,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110444,14 +110545,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  74%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110465,9 +110566,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110484,9 +110585,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110503,9 +110604,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110522,9 +110623,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110541,14 +110642,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110562,14 +110663,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110583,9 +110684,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110602,9 +110703,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110621,9 +110722,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110640,14 +110741,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110661,9 +110762,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110680,9 +110781,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110699,14 +110800,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110720,9 +110821,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110739,14 +110840,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  77%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110760,9 +110861,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110779,9 +110880,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110798,9 +110899,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110817,9 +110918,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110836,14 +110937,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110857,14 +110958,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110878,9 +110979,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110897,9 +110998,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110916,9 +111017,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110935,14 +111036,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110956,9 +111057,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110975,9 +111076,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -110994,9 +111095,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111013,14 +111114,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111034,14 +111135,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  80%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111055,9 +111156,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111074,9 +111175,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111093,9 +111194,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111112,9 +111213,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111131,14 +111232,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111152,14 +111253,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111173,9 +111274,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111192,9 +111293,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111211,9 +111312,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111230,14 +111331,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111251,9 +111352,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111270,9 +111371,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111289,9 +111390,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111308,14 +111409,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111329,14 +111430,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  83%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111350,9 +111451,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111369,9 +111470,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111388,9 +111489,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111407,9 +111508,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111426,14 +111527,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111447,9 +111548,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111466,14 +111567,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111487,9 +111588,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111506,9 +111607,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111525,14 +111626,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111546,9 +111647,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111565,9 +111666,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111584,9 +111685,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111603,14 +111704,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111624,14 +111725,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  86%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111645,9 +111746,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111664,9 +111765,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111683,9 +111784,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111702,9 +111803,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111721,14 +111822,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111742,9 +111843,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111761,14 +111862,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111782,9 +111883,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111801,9 +111902,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111820,14 +111921,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  88%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111841,9 +111942,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111860,9 +111961,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111879,9 +111980,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111898,9 +111999,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111917,14 +112018,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  89%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111938,9 +112039,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111957,9 +112058,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111976,9 +112077,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -111995,9 +112096,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112014,14 +112115,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112035,9 +112136,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112054,9 +112155,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112073,14 +112174,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112094,9 +112195,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112113,14 +112214,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  91%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112134,9 +112235,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112153,9 +112254,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112172,9 +112273,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112191,9 +112292,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112210,14 +112311,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  92%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112231,9 +112332,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112250,9 +112351,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112269,9 +112370,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112288,9 +112389,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112307,14 +112408,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112328,9 +112429,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112347,9 +112448,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112366,14 +112467,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112387,9 +112488,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112406,14 +112507,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  94%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112427,9 +112528,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112446,9 +112547,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112465,9 +112566,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112484,9 +112585,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112503,14 +112604,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112524,14 +112625,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112545,9 +112646,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112564,9 +112665,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112583,9 +112684,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112602,14 +112703,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112623,9 +112724,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112642,9 +112743,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112661,14 +112762,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112682,9 +112783,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112701,14 +112802,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  97%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112722,9 +112823,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112741,9 +112842,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112760,9 +112861,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112779,9 +112880,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112798,14 +112899,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112819,14 +112920,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112840,9 +112941,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112859,9 +112960,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112878,9 +112979,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112897,14 +112998,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112918,9 +113019,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112937,9 +113038,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112956,9 +113057,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112975,14 +113076,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================|  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -112996,14 +113097,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================| 100%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113017,9 +113118,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113036,14 +113137,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
 ## [1] "saving MCMC output to"                                                     
 ## [2] "/fs/data3/tonygard/work/pecan/modules/allometry/vignettes/Allom.LH.3.Rdata"
 ## [1] "saving diagnostic graphs to"                                                  
 ## [2] "/fs/data3/tonygard/work/pecan/modules/allometry/vignettes/Allom.LH.3.MCMC.pdf"</code></pre>
-<pre><code>## [1] "DIC"              "404.346110407312" "pD"              
+            <pre><code>## [1] "DIC"              "404.346110407312" "pD"              
 ## [4] "189.740306201481"
 ## [1] "DICg"             "499.298462518416" "pDg"             
 ## [4] "253.9982381026"  
@@ -113056,14 +113157,14 @@ <h2 class="hasAnchor">
 ## 
 ## [[3]]
 ## [1] 6</code></pre>
-<pre><code>## Warning in nu(allom$parm$Component.ID): NAs introduced by coercion</code></pre>
-<pre><code>## [1] "Dropping allom rows: "
+            <pre><code>## Warning in nu(allom$parm$Component.ID): NAs introduced by coercion</code></pre>
+            <pre><code>## [1] "Dropping allom rows: "
 ## 
   |                                                                       
   |                                                                 |   0%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113113,9 +113214,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113168,9 +113269,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113223,14 +113324,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |                                                                 |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113280,14 +113381,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113337,9 +113438,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113392,9 +113493,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113447,9 +113548,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113502,14 +113603,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113559,9 +113660,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113614,9 +113715,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113669,9 +113770,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113724,14 +113825,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113781,14 +113882,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   3%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113838,9 +113939,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113893,9 +113994,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -113948,9 +114049,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114003,9 +114104,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114058,14 +114159,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114115,9 +114216,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114170,14 +114271,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114227,9 +114328,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114282,9 +114383,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114337,14 +114438,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114394,9 +114495,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114449,9 +114550,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114504,9 +114605,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114559,14 +114660,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114616,14 +114717,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   6%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114673,9 +114774,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114728,9 +114829,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114783,9 +114884,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114838,9 +114939,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114893,14 +114994,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -114950,9 +115051,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115005,14 +115106,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115062,9 +115163,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115117,9 +115218,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115172,14 +115273,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   8%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115229,9 +115330,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115284,9 +115385,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115339,9 +115440,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115394,9 +115495,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115449,14 +115550,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |   9%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115506,9 +115607,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115561,9 +115662,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115616,9 +115717,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115671,9 +115772,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115726,14 +115827,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115783,9 +115884,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115838,9 +115939,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115893,14 +115994,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -115950,9 +116051,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116005,14 +116106,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  11%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116062,9 +116163,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116117,9 +116218,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116172,9 +116273,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116227,9 +116328,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116282,14 +116383,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  12%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116339,9 +116440,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116394,9 +116495,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116449,9 +116550,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116504,9 +116605,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116559,14 +116660,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116616,9 +116717,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116671,9 +116772,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116726,14 +116827,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116783,9 +116884,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116838,14 +116939,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  14%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116895,9 +116996,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -116950,9 +117051,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117005,9 +117106,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117060,9 +117161,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117115,14 +117216,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117172,14 +117273,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117229,9 +117330,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117284,9 +117385,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117339,9 +117440,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117394,14 +117495,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117451,9 +117552,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117506,9 +117607,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117561,14 +117662,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117618,9 +117719,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117673,14 +117774,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  17%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117730,9 +117831,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117785,9 +117886,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117840,9 +117941,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117895,9 +117996,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -117950,14 +118051,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118007,14 +118108,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118064,9 +118165,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118119,9 +118220,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118174,9 +118275,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118229,14 +118330,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118286,9 +118387,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118341,9 +118442,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118396,9 +118497,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118451,14 +118552,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118508,14 +118609,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  20%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118565,9 +118666,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118620,9 +118721,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118675,9 +118776,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118730,9 +118831,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118785,14 +118886,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118842,14 +118943,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118899,9 +119000,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -118954,9 +119055,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119009,9 +119110,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119064,14 +119165,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119121,9 +119222,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119176,9 +119277,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119231,9 +119332,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119286,14 +119387,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119343,14 +119444,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  23%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119400,9 +119501,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119455,9 +119556,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119510,9 +119611,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119565,9 +119666,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119620,14 +119721,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119677,9 +119778,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119732,14 +119833,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119789,9 +119890,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119844,9 +119945,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119899,14 +120000,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -119956,9 +120057,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120011,9 +120112,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120066,9 +120167,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120121,14 +120222,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120178,14 +120279,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  26%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120235,9 +120336,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120290,9 +120391,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120345,9 +120446,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120400,9 +120501,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120455,14 +120556,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120512,9 +120613,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120567,14 +120668,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120624,9 +120725,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120679,9 +120780,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120734,14 +120835,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  28%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120791,9 +120892,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120846,9 +120947,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120901,9 +121002,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -120956,9 +121057,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121011,14 +121112,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  29%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121068,9 +121169,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121123,9 +121224,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121178,9 +121279,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121233,9 +121334,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121288,14 +121389,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121345,9 +121446,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121400,14 +121501,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121457,9 +121558,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121512,9 +121613,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121567,14 +121668,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  31%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121624,9 +121725,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121679,9 +121780,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121734,9 +121835,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121789,9 +121890,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121844,14 +121945,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  32%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121901,9 +122002,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -121956,9 +122057,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122011,9 +122112,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122066,9 +122167,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122121,14 +122222,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122178,9 +122279,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122233,9 +122334,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122288,14 +122389,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122345,9 +122446,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122400,14 +122501,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  34%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122457,9 +122558,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122512,9 +122613,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122567,9 +122668,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122622,9 +122723,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122677,14 +122778,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122734,14 +122835,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122791,9 +122892,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122846,9 +122947,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122901,9 +123002,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -122956,14 +123057,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123013,9 +123114,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123068,9 +123169,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123123,14 +123224,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123180,9 +123281,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123235,14 +123336,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  37%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123292,9 +123393,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123347,9 +123448,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123402,9 +123503,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123457,9 +123558,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123512,14 +123613,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123569,14 +123670,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123626,9 +123727,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123681,9 +123782,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123736,9 +123837,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123791,14 +123892,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123848,9 +123949,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123903,9 +124004,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -123958,9 +124059,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124013,14 +124114,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124070,14 +124171,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  40%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124127,9 +124228,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124182,9 +124283,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124237,9 +124338,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124292,9 +124393,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124347,14 +124448,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124404,14 +124505,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124461,9 +124562,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124516,9 +124617,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124571,9 +124672,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124626,14 +124727,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124683,9 +124784,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124738,9 +124839,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124793,9 +124894,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124848,14 +124949,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124905,14 +125006,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  43%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -124962,9 +125063,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125017,9 +125118,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125072,9 +125173,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125127,9 +125228,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125182,14 +125283,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125239,9 +125340,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125294,14 +125395,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125351,9 +125452,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125406,9 +125507,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125461,14 +125562,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125518,9 +125619,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125573,9 +125674,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125628,9 +125729,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125683,14 +125784,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125740,14 +125841,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  46%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125797,9 +125898,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125852,9 +125953,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125907,9 +126008,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -125962,9 +126063,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126017,14 +126118,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126074,9 +126175,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126129,14 +126230,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126186,9 +126287,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126241,9 +126342,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126296,14 +126397,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  48%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126353,9 +126454,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126408,9 +126509,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126463,9 +126564,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126518,9 +126619,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126573,14 +126674,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  49%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126630,9 +126731,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126685,9 +126786,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126740,9 +126841,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126795,9 +126896,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126850,14 +126951,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126907,9 +127008,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -126962,9 +127063,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127017,14 +127118,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127074,9 +127175,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127129,14 +127230,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  51%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127186,9 +127287,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127241,9 +127342,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127296,9 +127397,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127351,9 +127452,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127406,14 +127507,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  52%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127463,9 +127564,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127518,9 +127619,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127573,9 +127674,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127628,9 +127729,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127683,14 +127784,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127740,9 +127841,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127795,9 +127896,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127850,14 +127951,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127907,9 +128008,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -127962,14 +128063,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  54%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128019,9 +128120,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128074,9 +128175,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128129,9 +128230,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128184,9 +128285,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128239,14 +128340,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128296,14 +128397,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128353,9 +128454,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128408,9 +128509,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128463,9 +128564,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128518,14 +128619,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128575,9 +128676,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128630,9 +128731,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128685,14 +128786,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128742,9 +128843,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128797,14 +128898,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  57%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128854,9 +128955,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128909,9 +129010,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -128964,9 +129065,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129019,9 +129120,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129074,14 +129175,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129131,14 +129232,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129188,9 +129289,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129243,9 +129344,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129298,9 +129399,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129353,14 +129454,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129410,9 +129511,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129465,9 +129566,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129520,9 +129621,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129575,14 +129676,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129632,14 +129733,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  60%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129689,9 +129790,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129744,9 +129845,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129799,9 +129900,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129854,9 +129955,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129909,14 +130010,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -129966,14 +130067,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130023,9 +130124,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130078,9 +130179,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130133,9 +130234,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130188,14 +130289,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130245,9 +130346,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130300,9 +130401,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130355,9 +130456,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130410,14 +130511,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130467,14 +130568,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  63%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130524,9 +130625,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130579,9 +130680,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130634,9 +130735,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130689,9 +130790,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130744,14 +130845,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130801,9 +130902,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130856,14 +130957,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130913,9 +131014,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -130968,9 +131069,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131023,14 +131124,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131080,9 +131181,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131135,9 +131236,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131190,9 +131291,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131245,14 +131346,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131302,14 +131403,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  66%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131359,9 +131460,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131414,9 +131515,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131469,9 +131570,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131524,9 +131625,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131579,14 +131680,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131636,9 +131737,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131691,14 +131792,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131748,9 +131849,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131803,9 +131904,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131858,14 +131959,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  68%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131915,9 +132016,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -131970,9 +132071,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132025,9 +132126,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132080,9 +132181,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132135,14 +132236,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  69%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132192,9 +132293,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132247,9 +132348,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132302,9 +132403,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132357,9 +132458,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132412,14 +132513,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132469,9 +132570,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132524,14 +132625,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132581,9 +132682,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132636,9 +132737,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132691,14 +132792,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  71%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132748,9 +132849,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132803,9 +132904,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132858,9 +132959,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132913,9 +133014,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -132968,14 +133069,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  72%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133025,9 +133126,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133080,9 +133181,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133135,9 +133236,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133190,9 +133291,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133245,14 +133346,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133302,9 +133403,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133357,9 +133458,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133412,14 +133513,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133469,9 +133570,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133524,14 +133625,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  74%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133581,9 +133682,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133636,9 +133737,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133691,9 +133792,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133746,9 +133847,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133801,14 +133902,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133858,14 +133959,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133915,9 +134016,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -133970,9 +134071,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134025,9 +134126,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134080,14 +134181,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134137,9 +134238,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134192,9 +134293,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134247,14 +134348,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134304,9 +134405,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134359,14 +134460,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  77%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134416,9 +134517,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134471,9 +134572,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134526,9 +134627,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134581,9 +134682,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134636,14 +134737,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134693,14 +134794,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134750,9 +134851,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134805,9 +134906,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134860,9 +134961,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134915,14 +135016,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -134972,9 +135073,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135027,9 +135128,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135082,9 +135183,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135137,14 +135238,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135194,14 +135295,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  80%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135251,9 +135352,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135306,9 +135407,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135361,9 +135462,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135416,9 +135517,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135471,14 +135572,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135528,14 +135629,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135585,9 +135686,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135640,9 +135741,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135695,9 +135796,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135750,14 +135851,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135807,9 +135908,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135862,9 +135963,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135917,9 +136018,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -135972,14 +136073,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136029,14 +136130,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  83%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136086,9 +136187,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136141,9 +136242,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136196,9 +136297,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136251,9 +136352,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136306,14 +136407,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136363,9 +136464,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136418,14 +136519,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136475,9 +136576,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136530,9 +136631,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136585,14 +136686,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136642,9 +136743,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136697,9 +136798,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136752,9 +136853,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136807,14 +136908,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136864,14 +136965,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  86%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136921,9 +137022,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -136976,9 +137077,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137031,9 +137132,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137086,9 +137187,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137141,14 +137242,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137198,9 +137299,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137253,14 +137354,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137310,9 +137411,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137365,9 +137466,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137420,14 +137521,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  88%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137477,9 +137578,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137532,9 +137633,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137587,9 +137688,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137642,9 +137743,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137697,14 +137798,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  89%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137754,9 +137855,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137809,9 +137910,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137864,9 +137965,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137919,9 +138020,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -137974,14 +138075,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138031,9 +138132,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138086,9 +138187,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138141,14 +138242,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138198,9 +138299,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138253,14 +138354,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  91%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138310,9 +138411,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138365,9 +138466,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138420,9 +138521,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138475,9 +138576,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138530,14 +138631,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  92%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138587,9 +138688,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138642,9 +138743,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138697,9 +138798,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138752,9 +138853,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138807,14 +138908,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138864,9 +138965,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138919,9 +139020,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -138974,14 +139075,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139031,9 +139132,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139086,14 +139187,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  94%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139143,9 +139244,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139198,9 +139299,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139253,9 +139354,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139308,9 +139409,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139363,14 +139464,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139420,14 +139521,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139477,9 +139578,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139532,9 +139633,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139587,9 +139688,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139642,14 +139743,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139699,9 +139800,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139754,9 +139855,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139809,14 +139910,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139866,9 +139967,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139921,14 +140022,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  97%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -139978,9 +140079,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140033,9 +140134,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140088,9 +140189,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140143,9 +140244,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140198,14 +140299,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140255,14 +140356,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140312,9 +140413,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140367,9 +140468,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140422,9 +140523,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140477,14 +140578,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140534,9 +140635,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140589,9 +140690,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140644,9 +140745,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140699,14 +140800,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================|  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140756,14 +140857,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================| 100%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140813,9 +140914,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140868,16 +140969,16 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
 ## [1] "Dropping allom rows: "
 ## 
   |                                                                       
   |                                                                 |   0%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140927,9 +141028,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -140982,9 +141083,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141037,14 +141138,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |                                                                 |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141094,14 +141195,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141151,9 +141252,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141206,9 +141307,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141261,9 +141362,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141316,14 +141417,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141373,9 +141474,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141428,9 +141529,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141483,9 +141584,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141538,14 +141639,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141595,14 +141696,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   3%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141652,9 +141753,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141707,9 +141808,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141762,9 +141863,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141817,9 +141918,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141872,14 +141973,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141929,9 +142030,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -141984,14 +142085,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142041,9 +142142,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142096,9 +142197,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142151,14 +142252,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142208,9 +142309,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142263,9 +142364,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142318,9 +142419,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142373,14 +142474,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142430,14 +142531,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   6%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142487,9 +142588,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142542,9 +142643,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142597,9 +142698,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142652,9 +142753,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142707,14 +142808,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142764,9 +142865,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142819,14 +142920,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142876,9 +142977,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142931,9 +143032,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -142986,14 +143087,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   8%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143043,9 +143144,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143098,9 +143199,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143153,9 +143254,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143208,9 +143309,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143263,14 +143364,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |   9%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143320,9 +143421,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143375,9 +143476,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143430,9 +143531,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143485,9 +143586,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143540,14 +143641,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143597,9 +143698,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143652,9 +143753,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143707,14 +143808,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143764,9 +143865,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143819,14 +143920,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  11%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143876,9 +143977,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143931,9 +144032,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -143986,9 +144087,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144041,9 +144142,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144096,14 +144197,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  12%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144153,9 +144254,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144208,9 +144309,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144263,9 +144364,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144318,9 +144419,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144373,14 +144474,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144430,9 +144531,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144485,9 +144586,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144540,14 +144641,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144597,9 +144698,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144652,14 +144753,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  14%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144709,9 +144810,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144764,9 +144865,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144819,9 +144920,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144874,9 +144975,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144929,14 +145030,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -144986,14 +145087,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145043,9 +145144,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145098,9 +145199,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145153,9 +145254,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145208,14 +145309,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145265,9 +145366,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145320,9 +145421,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145375,14 +145476,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145432,9 +145533,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145487,14 +145588,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  17%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145544,9 +145645,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145599,9 +145700,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145654,9 +145755,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145709,9 +145810,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145764,14 +145865,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145821,14 +145922,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145878,9 +145979,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145933,9 +146034,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -145988,9 +146089,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146043,14 +146144,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146100,9 +146201,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146155,9 +146256,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146210,9 +146311,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146265,14 +146366,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146322,14 +146423,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  20%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146379,9 +146480,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146434,9 +146535,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146489,9 +146590,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146544,9 +146645,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146599,14 +146700,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146656,14 +146757,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146713,9 +146814,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146768,9 +146869,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146823,9 +146924,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146878,14 +146979,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146935,9 +147036,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -146990,9 +147091,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147045,9 +147146,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147100,14 +147201,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147157,14 +147258,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  23%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147214,9 +147315,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147269,9 +147370,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147324,9 +147425,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147379,9 +147480,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147434,14 +147535,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147491,9 +147592,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147546,14 +147647,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147603,9 +147704,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147658,9 +147759,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147713,14 +147814,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147770,9 +147871,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147825,9 +147926,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147880,9 +147981,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147935,14 +148036,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -147992,14 +148093,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  26%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148049,9 +148150,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148104,9 +148205,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148159,9 +148260,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148214,9 +148315,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148269,14 +148370,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148326,9 +148427,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148381,14 +148482,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148438,9 +148539,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148493,9 +148594,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148548,14 +148649,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  28%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148605,9 +148706,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148660,9 +148761,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148715,9 +148816,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148770,9 +148871,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148825,14 +148926,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  29%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148882,9 +148983,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148937,9 +149038,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -148992,9 +149093,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149047,9 +149148,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149102,14 +149203,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149159,9 +149260,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149214,14 +149315,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149271,9 +149372,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149326,9 +149427,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149381,14 +149482,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  31%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149438,9 +149539,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149493,9 +149594,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149548,9 +149649,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149603,9 +149704,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149658,14 +149759,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  32%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149715,9 +149816,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149770,9 +149871,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149825,9 +149926,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149880,9 +149981,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149935,14 +150036,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -149992,9 +150093,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150047,9 +150148,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150102,14 +150203,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150159,9 +150260,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150214,14 +150315,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  34%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150271,9 +150372,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150326,9 +150427,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150381,9 +150482,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150436,9 +150537,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150491,14 +150592,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150548,14 +150649,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150605,9 +150706,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150660,9 +150761,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150715,9 +150816,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150770,14 +150871,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150827,9 +150928,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150882,9 +150983,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150937,14 +151038,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -150994,9 +151095,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151049,14 +151150,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  37%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151106,9 +151207,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151161,9 +151262,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151216,9 +151317,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151271,9 +151372,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151326,14 +151427,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151383,14 +151484,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151440,9 +151541,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151495,9 +151596,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151550,9 +151651,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151605,14 +151706,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151662,9 +151763,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151717,9 +151818,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151772,9 +151873,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151827,14 +151928,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151884,14 +151985,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  40%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151941,9 +152042,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -151996,9 +152097,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152051,9 +152152,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152106,9 +152207,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152161,14 +152262,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152218,14 +152319,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152275,9 +152376,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152330,9 +152431,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152385,9 +152486,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152440,14 +152541,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152497,9 +152598,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152552,9 +152653,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152607,9 +152708,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152662,14 +152763,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152719,14 +152820,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  43%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152776,9 +152877,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152831,9 +152932,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152886,9 +152987,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152941,9 +153042,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -152996,14 +153097,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153053,9 +153154,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153108,14 +153209,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153165,9 +153266,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153220,9 +153321,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153275,14 +153376,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153332,9 +153433,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153387,9 +153488,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153442,9 +153543,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153497,14 +153598,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153554,14 +153655,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  46%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153611,9 +153712,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153666,9 +153767,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153721,9 +153822,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153776,9 +153877,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153831,14 +153932,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153888,9 +153989,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -153943,14 +154044,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154000,9 +154101,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154055,9 +154156,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154110,14 +154211,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  48%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154167,9 +154268,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154222,9 +154323,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154277,9 +154378,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154332,9 +154433,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154387,14 +154488,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  49%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154444,9 +154545,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154499,9 +154600,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154554,9 +154655,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154609,9 +154710,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154664,14 +154765,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154721,9 +154822,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154776,9 +154877,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154831,14 +154932,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154888,9 +154989,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -154943,14 +155044,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  51%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155000,9 +155101,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155055,9 +155156,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155110,9 +155211,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155165,9 +155266,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155220,14 +155321,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  52%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155277,9 +155378,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155332,9 +155433,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155387,9 +155488,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155442,9 +155543,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155497,14 +155598,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155554,9 +155655,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155609,9 +155710,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155664,14 +155765,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155721,9 +155822,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155776,14 +155877,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  54%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155833,9 +155934,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155888,9 +155989,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155943,9 +156044,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -155998,9 +156099,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156053,14 +156154,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156110,14 +156211,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156167,9 +156268,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156222,9 +156323,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156277,9 +156378,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156332,14 +156433,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156389,9 +156490,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156444,9 +156545,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156499,14 +156600,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156556,9 +156657,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156611,14 +156712,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  57%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156668,9 +156769,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156723,9 +156824,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156778,9 +156879,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156833,9 +156934,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156888,14 +156989,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -156945,14 +157046,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157002,9 +157103,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157057,9 +157158,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157112,9 +157213,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157167,14 +157268,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157224,9 +157325,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157279,9 +157380,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157334,9 +157435,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157389,14 +157490,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157446,14 +157547,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  60%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157503,9 +157604,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157558,9 +157659,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157613,9 +157714,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157668,9 +157769,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157723,14 +157824,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157780,14 +157881,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157837,9 +157938,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157892,9 +157993,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -157947,9 +158048,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158002,14 +158103,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158059,9 +158160,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158114,9 +158215,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158169,9 +158270,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158224,14 +158325,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158281,14 +158382,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  63%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158338,9 +158439,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158393,9 +158494,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158448,9 +158549,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158503,9 +158604,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158558,14 +158659,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158615,9 +158716,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158670,14 +158771,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158727,9 +158828,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158782,9 +158883,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158837,14 +158938,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158894,9 +158995,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -158949,9 +159050,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159004,9 +159105,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159059,14 +159160,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159116,14 +159217,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  66%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159173,9 +159274,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159228,9 +159329,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159283,9 +159384,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159338,9 +159439,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159393,14 +159494,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159450,9 +159551,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159505,14 +159606,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159562,9 +159663,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159617,9 +159718,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159672,14 +159773,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  68%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159729,9 +159830,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159784,9 +159885,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159839,9 +159940,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159894,9 +159995,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -159949,14 +160050,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  69%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160006,9 +160107,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160061,9 +160162,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160116,9 +160217,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160171,9 +160272,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160226,14 +160327,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160283,9 +160384,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160338,14 +160439,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160395,9 +160496,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160450,9 +160551,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160505,14 +160606,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  71%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160562,9 +160663,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160617,9 +160718,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160672,9 +160773,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160727,9 +160828,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160782,14 +160883,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  72%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160839,9 +160940,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160894,9 +160995,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -160949,9 +161050,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161004,9 +161105,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161059,14 +161160,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161116,9 +161217,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161171,9 +161272,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161226,14 +161327,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161283,9 +161384,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161338,14 +161439,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  74%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161395,9 +161496,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161450,9 +161551,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161505,9 +161606,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161560,9 +161661,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161615,14 +161716,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161672,14 +161773,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161729,9 +161830,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161784,9 +161885,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161839,9 +161940,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161894,14 +161995,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -161951,9 +162052,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162006,9 +162107,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162061,14 +162162,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162118,9 +162219,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162173,14 +162274,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  77%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162230,9 +162331,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162285,9 +162386,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162340,9 +162441,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162395,9 +162496,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162450,14 +162551,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162507,14 +162608,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162564,9 +162665,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162619,9 +162720,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162674,9 +162775,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162729,14 +162830,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162786,9 +162887,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162841,9 +162942,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162896,9 +162997,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -162951,14 +163052,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163008,14 +163109,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  80%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163065,9 +163166,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163120,9 +163221,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163175,9 +163276,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163230,9 +163331,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163285,14 +163386,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163342,14 +163443,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163399,9 +163500,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163454,9 +163555,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163509,9 +163610,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163564,14 +163665,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163621,9 +163722,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163676,9 +163777,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163731,9 +163832,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163786,14 +163887,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163843,14 +163944,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  83%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163900,9 +164001,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -163955,9 +164056,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164010,9 +164111,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164065,9 +164166,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164120,14 +164221,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164177,9 +164278,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164232,14 +164333,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164289,9 +164390,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164344,9 +164445,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164399,14 +164500,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164456,9 +164557,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164511,9 +164612,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164566,9 +164667,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164621,14 +164722,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164678,14 +164779,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  86%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164735,9 +164836,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164790,9 +164891,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164845,9 +164946,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164900,9 +165001,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -164955,14 +165056,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165012,9 +165113,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165067,14 +165168,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165124,9 +165225,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165179,9 +165280,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165234,14 +165335,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  88%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165291,9 +165392,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165346,9 +165447,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165401,9 +165502,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165456,9 +165557,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165511,14 +165612,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  89%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165568,9 +165669,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165623,9 +165724,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165678,9 +165779,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165733,9 +165834,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165788,14 +165889,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165845,9 +165946,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165900,9 +166001,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -165955,14 +166056,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166012,9 +166113,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166067,14 +166168,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  91%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166124,9 +166225,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166179,9 +166280,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166234,9 +166335,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166289,9 +166390,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166344,14 +166445,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  92%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166401,9 +166502,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166456,9 +166557,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166511,9 +166612,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166566,9 +166667,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166621,14 +166722,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166678,9 +166779,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166733,9 +166834,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166788,14 +166889,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166845,9 +166946,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166900,14 +167001,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  94%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -166957,9 +167058,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167012,9 +167113,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167067,9 +167168,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167122,9 +167223,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167177,14 +167278,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167234,14 +167335,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167291,9 +167392,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167346,9 +167447,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167401,9 +167502,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167456,14 +167557,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167513,9 +167614,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167568,9 +167669,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167623,14 +167724,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167680,9 +167781,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167735,14 +167836,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  97%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167792,9 +167893,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167847,9 +167948,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167902,9 +168003,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -167957,9 +168058,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168012,14 +168113,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168069,14 +168170,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168126,9 +168227,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168181,9 +168282,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168236,9 +168337,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168291,14 +168392,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168348,9 +168449,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168403,9 +168504,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168458,9 +168559,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168513,14 +168614,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================|  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168570,14 +168671,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================| 100%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168627,9 +168728,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168682,16 +168783,16 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
 ## [1] "Dropping allom rows: "
 ## 
   |                                                                       
   |                                                                 |   0%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168741,9 +168842,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168796,9 +168897,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168851,14 +168952,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |                                                                 |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168908,14 +169009,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   1%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -168965,9 +169066,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169020,9 +169121,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169075,9 +169176,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169130,14 +169231,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=                                                                |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169187,9 +169288,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169242,9 +169343,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169297,9 +169398,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169352,14 +169453,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   2%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169409,14 +169510,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   3%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169466,9 +169567,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169521,9 +169622,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169576,9 +169677,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169631,9 +169732,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169686,14 +169787,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==                                                               |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169743,9 +169844,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169798,14 +169899,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   4%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169855,9 +169956,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169910,9 +170011,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -169965,14 +170066,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===                                                              |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170022,9 +170123,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170077,9 +170178,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170132,9 +170233,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170187,14 +170288,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   5%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170244,14 +170345,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   6%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170301,9 +170402,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170356,9 +170457,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170411,9 +170512,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170466,9 +170567,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170521,14 +170622,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====                                                             |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170578,9 +170679,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170633,14 +170734,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   7%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170690,9 +170791,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170745,9 +170846,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170800,14 +170901,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====                                                            |   8%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170857,9 +170958,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170912,9 +171013,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -170967,9 +171068,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171022,9 +171123,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171077,14 +171178,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |   9%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171134,9 +171235,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171189,9 +171290,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171244,9 +171345,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171299,9 +171400,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171354,14 +171455,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======                                                           |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171411,9 +171512,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171466,9 +171567,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171521,14 +171622,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  10%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171578,9 +171679,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171633,14 +171734,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======                                                          |  11%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171690,9 +171791,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171745,9 +171846,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171800,9 +171901,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171855,9 +171956,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171910,14 +172011,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  12%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -171967,9 +172068,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172022,9 +172123,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172077,9 +172178,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172132,9 +172233,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172187,14 +172288,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========                                                         |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172244,9 +172345,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172299,9 +172400,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172354,14 +172455,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  13%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172411,9 +172512,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172466,14 +172567,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  14%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172523,9 +172624,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172578,9 +172679,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172633,9 +172734,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172688,9 +172789,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172743,14 +172844,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========                                                        |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172800,14 +172901,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  15%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172857,9 +172958,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172912,9 +173013,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -172967,9 +173068,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173022,14 +173123,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========                                                       |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173079,9 +173180,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173134,9 +173235,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173189,14 +173290,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  16%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173246,9 +173347,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173301,14 +173402,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  17%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173358,9 +173459,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173413,9 +173514,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173468,9 +173569,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173523,9 +173624,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173578,14 +173679,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========                                                      |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173635,14 +173736,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  18%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173692,9 +173793,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173747,9 +173848,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173802,9 +173903,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173857,14 +173958,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============                                                     |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173914,9 +174015,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -173969,9 +174070,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174024,9 +174125,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174079,14 +174180,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  19%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174136,14 +174237,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  20%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174193,9 +174294,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174248,9 +174349,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174303,9 +174404,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174358,9 +174459,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174413,14 +174514,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============                                                    |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174470,14 +174571,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  21%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174527,9 +174628,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174582,9 +174683,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174637,9 +174738,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174692,14 +174793,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============                                                   |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174749,9 +174850,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174804,9 +174905,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174859,9 +174960,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174914,14 +175015,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  22%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -174971,14 +175072,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  23%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175028,9 +175129,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175083,9 +175184,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175138,9 +175239,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175193,9 +175294,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175248,14 +175349,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============                                                  |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175305,9 +175406,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175360,14 +175461,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  24%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175417,9 +175518,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175472,9 +175573,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175527,14 +175628,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================                                                 |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175584,9 +175685,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175639,9 +175740,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175694,9 +175795,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175749,14 +175850,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  25%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175806,14 +175907,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  26%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175863,9 +175964,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175918,9 +176019,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -175973,9 +176074,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176028,9 +176129,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176083,14 +176184,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================                                                |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176140,9 +176241,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176195,14 +176296,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  27%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176252,9 +176353,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176307,9 +176408,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176362,14 +176463,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================                                               |  28%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176419,9 +176520,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176474,9 +176575,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176529,9 +176630,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176584,9 +176685,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176639,14 +176740,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  29%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176696,9 +176797,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176751,9 +176852,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176806,9 +176907,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176861,9 +176962,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176916,14 +177017,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================                                              |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -176973,9 +177074,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177028,14 +177129,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  30%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177085,9 +177186,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177140,9 +177241,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177195,14 +177296,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================                                             |  31%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177252,9 +177353,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177307,9 +177408,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177362,9 +177463,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177417,9 +177518,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177472,14 +177573,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  32%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177529,9 +177630,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177584,9 +177685,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177639,9 +177740,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177694,9 +177795,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177749,14 +177850,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================                                            |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177806,9 +177907,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177861,9 +177962,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177916,14 +178017,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  33%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -177973,9 +178074,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178028,14 +178129,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  34%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178085,9 +178186,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178140,9 +178241,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178195,9 +178296,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178250,9 +178351,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178305,14 +178406,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================                                           |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178362,14 +178463,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  35%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178419,9 +178520,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178474,9 +178575,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178529,9 +178630,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178584,14 +178685,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================                                          |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178641,9 +178742,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178696,9 +178797,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178751,14 +178852,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  36%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178808,9 +178909,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178863,14 +178964,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  37%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178920,9 +179021,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -178975,9 +179076,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179030,9 +179131,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179085,9 +179186,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179140,14 +179241,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================                                         |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179197,14 +179298,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  38%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179254,9 +179355,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179309,9 +179410,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179364,9 +179465,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179419,14 +179520,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================                                        |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179476,9 +179577,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179531,9 +179632,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179586,9 +179687,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179641,14 +179742,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  39%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179698,14 +179799,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  40%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179755,9 +179856,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179810,9 +179911,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179865,9 +179966,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179920,9 +180021,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -179975,14 +180076,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================                                       |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180032,14 +180133,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  41%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180089,9 +180190,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180144,9 +180245,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180199,9 +180300,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180254,14 +180355,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================                                      |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180311,9 +180412,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180366,9 +180467,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180421,9 +180522,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180476,14 +180577,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  42%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180533,14 +180634,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  43%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180590,9 +180691,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180645,9 +180746,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180700,9 +180801,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180755,9 +180856,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180810,14 +180911,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================                                     |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180867,9 +180968,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180922,14 +181023,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  44%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -180979,9 +181080,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181034,9 +181135,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181089,14 +181190,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================                                    |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181146,9 +181247,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181201,9 +181302,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181256,9 +181357,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181311,14 +181412,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  45%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181368,14 +181469,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  46%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181425,9 +181526,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181480,9 +181581,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181535,9 +181636,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181590,9 +181691,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181645,14 +181746,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================                                   |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181702,9 +181803,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181757,14 +181858,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  47%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181814,9 +181915,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181869,9 +181970,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181924,14 +182025,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================                                  |  48%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -181981,9 +182082,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182036,9 +182137,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182091,9 +182192,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182146,9 +182247,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182201,14 +182302,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  49%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182258,9 +182359,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182313,9 +182414,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182368,9 +182469,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182423,9 +182524,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182478,14 +182579,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================                                 |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182535,9 +182636,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182590,9 +182691,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182645,14 +182746,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  50%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182702,9 +182803,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182757,14 +182858,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================                                |  51%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182814,9 +182915,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182869,9 +182970,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182924,9 +183025,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -182979,9 +183080,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183034,14 +183135,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  52%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183091,9 +183192,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183146,9 +183247,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183201,9 +183302,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183256,9 +183357,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183311,14 +183412,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================                               |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183368,9 +183469,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183423,9 +183524,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183478,14 +183579,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  53%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183535,9 +183636,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183590,14 +183691,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  54%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183647,9 +183748,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183702,9 +183803,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183757,9 +183858,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183812,9 +183913,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183867,14 +183968,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================                              |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183924,14 +184025,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  55%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -183981,9 +184082,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184036,9 +184137,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184091,9 +184192,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184146,14 +184247,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================                             |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184203,9 +184304,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184258,9 +184359,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184313,14 +184414,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  56%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184370,9 +184471,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184425,14 +184526,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  57%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184482,9 +184583,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184537,9 +184638,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184592,9 +184693,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184647,9 +184748,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184702,14 +184803,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================                            |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184759,14 +184860,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  58%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184816,9 +184917,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184871,9 +184972,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184926,9 +185027,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -184981,14 +185082,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================                           |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185038,9 +185139,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185093,9 +185194,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185148,9 +185249,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185203,14 +185304,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  59%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185260,14 +185361,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  60%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185317,9 +185418,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185372,9 +185473,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185427,9 +185528,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185482,9 +185583,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185537,14 +185638,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================                          |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185594,14 +185695,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  61%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185651,9 +185752,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185706,9 +185807,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185761,9 +185862,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185816,14 +185917,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================                         |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185873,9 +185974,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185928,9 +186029,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -185983,9 +186084,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186038,14 +186139,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  62%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186095,14 +186196,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  63%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186152,9 +186253,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186207,9 +186308,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186262,9 +186363,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186317,9 +186418,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186372,14 +186473,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================                        |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186429,9 +186530,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186484,14 +186585,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  64%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186541,9 +186642,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186596,9 +186697,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186651,14 +186752,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================                       |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186708,9 +186809,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186763,9 +186864,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186818,9 +186919,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186873,14 +186974,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  65%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186930,14 +187031,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  66%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -186987,9 +187088,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187042,9 +187143,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187097,9 +187198,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187152,9 +187253,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187207,14 +187308,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================                      |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187264,9 +187365,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187319,14 +187420,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  67%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187376,9 +187477,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187431,9 +187532,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187486,14 +187587,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================                     |  68%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187543,9 +187644,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187598,9 +187699,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187653,9 +187754,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187708,9 +187809,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187763,14 +187864,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  69%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187820,9 +187921,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187875,9 +187976,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187930,9 +188031,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -187985,9 +188086,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188040,14 +188141,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================                    |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188097,9 +188198,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188152,14 +188253,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  70%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188209,9 +188310,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188264,9 +188365,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188319,14 +188420,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================                   |  71%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188376,9 +188477,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188431,9 +188532,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188486,9 +188587,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188541,9 +188642,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188596,14 +188697,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  72%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188653,9 +188754,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188708,9 +188809,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188763,9 +188864,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188818,9 +188919,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188873,14 +188974,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================                  |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188930,9 +189031,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -188985,9 +189086,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189040,14 +189141,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  73%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189097,9 +189198,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189152,14 +189253,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  74%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189209,9 +189310,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189264,9 +189365,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189319,9 +189420,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189374,9 +189475,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189429,14 +189530,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================                 |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189486,14 +189587,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  75%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189543,9 +189644,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189598,9 +189699,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189653,9 +189754,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189708,14 +189809,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================                |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189765,9 +189866,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189820,9 +189921,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189875,14 +189976,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  76%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189932,9 +190033,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -189987,14 +190088,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  77%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190044,9 +190145,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190099,9 +190200,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190154,9 +190255,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190209,9 +190310,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190264,14 +190365,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==================================================               |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190321,14 +190422,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  78%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190378,9 +190479,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190433,9 +190534,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190488,9 +190589,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190543,14 +190644,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===================================================              |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190600,9 +190701,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190655,9 +190756,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190710,9 +190811,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190765,14 +190866,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  79%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190822,14 +190923,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  80%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190879,9 +190980,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190934,9 +191035,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -190989,9 +191090,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191044,9 +191145,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191099,14 +191200,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |====================================================             |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191156,14 +191257,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  81%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191213,9 +191314,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191268,9 +191369,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191323,9 +191424,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191378,14 +191479,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=====================================================            |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191435,9 +191536,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191490,9 +191591,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191545,9 +191646,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191600,14 +191701,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  82%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191657,14 +191758,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  83%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191714,9 +191815,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191769,9 +191870,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191824,9 +191925,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191879,9 +191980,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191934,14 +192035,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |======================================================           |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -191991,9 +192092,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192046,14 +192147,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  84%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192103,9 +192204,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192158,9 +192259,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192213,14 +192314,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=======================================================          |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192270,9 +192371,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192325,9 +192426,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192380,9 +192481,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192435,14 +192536,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  85%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192492,14 +192593,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  86%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192549,9 +192650,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192604,9 +192705,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192659,9 +192760,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192714,9 +192815,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192769,14 +192870,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |========================================================         |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192826,9 +192927,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192881,14 +192982,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  87%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192938,9 +193039,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -192993,9 +193094,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193048,14 +193149,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=========================================================        |  88%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193105,9 +193206,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193160,9 +193261,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193215,9 +193316,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193270,9 +193371,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193325,14 +193426,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  89%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193382,9 +193483,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193437,9 +193538,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193492,9 +193593,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193547,9 +193648,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193602,14 +193703,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==========================================================       |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193659,9 +193760,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193714,9 +193815,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193769,14 +193870,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  90%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193826,9 +193927,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193881,14 +193982,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===========================================================      |  91%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193938,9 +194039,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -193993,9 +194094,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194048,9 +194149,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194103,9 +194204,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194158,14 +194259,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  92%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194215,9 +194316,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194270,9 +194371,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194325,9 +194426,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194380,9 +194481,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194435,14 +194536,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |============================================================     |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194492,9 +194593,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194547,9 +194648,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194602,14 +194703,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  93%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194659,9 +194760,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194714,14 +194815,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  94%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194771,9 +194872,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194826,9 +194927,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194881,9 +194982,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194936,9 +195037,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -194991,14 +195092,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=============================================================    |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195048,14 +195149,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  95%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195105,9 +195206,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195160,9 +195261,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195215,9 +195316,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195270,14 +195371,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |==============================================================   |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195327,9 +195428,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195382,9 +195483,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195437,14 +195538,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  96%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195494,9 +195595,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195549,14 +195650,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  97%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195606,9 +195707,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195661,9 +195762,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195716,9 +195817,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195771,9 +195872,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195826,14 +195927,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |===============================================================  |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195883,14 +195984,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  98%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195940,9 +196041,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -195995,9 +196096,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -196050,9 +196151,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -196105,14 +196206,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |================================================================ |  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -196162,9 +196263,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -196217,9 +196318,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -196272,9 +196373,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -196327,14 +196428,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================|  99%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -196384,14 +196485,14 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
   |                                                                       
   |=================================================================| 100%</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -196441,9 +196542,9 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
@@ -196496,22 +196597,27 @@ <h2 class="hasAnchor">
 
 ## Warning in u2 + 0.5 * crossprod(Y - X %*% beta): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
+            <pre><code>## Warning in s2 + 0.5 * crossprod(Y - X %*% Bg): Recycling array of length 1 in vector-array arithmetic is deprecated.
 ##   Use c() or as.vector() instead.</code></pre>
-<pre><code>## 
+            <pre><code>## 
 ## [1] "saving MCMC output to"                                                     
 ## [2] "/fs/data3/tonygard/work/pecan/modules/allometry/vignettes/Allom.LH.6.Rdata"
 ## [1] "saving diagnostic graphs to"                                                  
 ## [2] "/fs/data3/tonygard/work/pecan/modules/allometry/vignettes/Allom.LH.6.MCMC.pdf"</code></pre>
-<pre><code>## [1] "DIC"              "420.881895239451" "pD"              
+            <pre><code>## [1] "DIC"              "420.881895239451" "pD"              
 ## [4] "254.185258779193"
 ## [1] "DICg"             "458.579828562878" "pDg"             
 ## [4] "214.827364289522"</code></pre>
-</div>
-<div id="predict-for-individual-trees" class="section level2">
-<h2 class="hasAnchor">
-<a href="#predict-for-individual-trees" class="anchor"></a>Predict for individual trees</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">allom.fit =<span class="st"> </span><span class="kw"><a href="../reference/load.allom.html">load.allom</a></span>(<span class="kw">getwd</span>())
+          </div>
+          <div id="predict-for-individual-trees" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#predict-for-individual-trees" class="anchor"></a>Predict
+              for individual trees
+            </h2>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">allom.fit =<span class="st"> </span><span class="kw"><a href="../reference/load.allom.html">load.allom</a></span>(<span class="kw">getwd</span>())
 dbh =<span class="st"> </span><span class="dv">1</span><span class="op">:</span><span class="dv">50</span>
 pred =<span class="st"> </span><span class="kw"><a href="../reference/allom.predict.html">allom.predict</a></span>(allom.fit,<span class="dt">dbh =</span> dbh,<span class="dt">pft =</span> <span class="st">"LH"</span>,<span class="dt">component =</span> <span class="dv">3</span>,<span class="dt">use =</span> <span class="st">"Bg"</span>,<span class="dt">interval =</span> <span class="st">"prediction"</span>)
 conf =<span class="st"> </span><span class="kw"><a href="../reference/allom.predict.html">allom.predict</a></span>(allom.fit,<span class="dt">dbh =</span> dbh,<span class="dt">pft =</span> <span class="st">"LH"</span>,<span class="dt">component =</span> <span class="dv">3</span>,<span class="dt">use =</span> <span class="st">"Bg"</span>,<span class="dt">interval =</span> <span class="st">"confidence"</span>)
@@ -196521,52 +196627,90 @@ <h2 class="hasAnchor">
 <span class="kw">lines</span>(dbh,CI[<span class="dv">1</span>,],<span class="dt">lty=</span><span class="dv">2</span>,<span class="dt">col=</span><span class="st">"blue"</span>)
 <span class="kw">lines</span>(dbh,CI[<span class="dv">3</span>,],<span class="dt">lty=</span><span class="dv">2</span>,<span class="dt">col=</span><span class="st">"blue"</span>)
 <span class="kw">lines</span>(dbh,PI[<span class="dv">1</span>,],<span class="dt">lty=</span><span class="dv">3</span>,<span class="dt">col=</span><span class="st">"red"</span>)
-<span class="kw">lines</span>(dbh,PI[<span class="dv">3</span>,],<span class="dt">lty=</span><span class="dv">3</span>,<span class="dt">col=</span><span class="st">"red"</span>)</code></pre></div>
-<p><img src="AllomVignette_files/figure-html/unnamed-chunk-5-1.png" width="700"></p>
-</div>
-<div id="predict-for-a-stand" class="section level2">
-<h2 class="hasAnchor">
-<a href="#predict-for-a-stand" class="anchor"></a>Predict for a stand</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">## simulated DBH's
+<span class="kw">lines</span>(dbh,PI[<span class="dv">3</span>,],<span class="dt">lty=</span><span class="dv">3</span>,<span class="dt">col=</span><span class="st">"red"</span>)</code></pre>
+            </div>
+            <p>
+              <img
+                src="AllomVignette_files/figure-html/unnamed-chunk-5-1.png"
+                width="700"
+              />
+            </p>
+          </div>
+          <div id="predict-for-a-stand" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#predict-for-a-stand" class="anchor"></a>Predict for a
+              stand
+            </h2>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">## simulated DBH's
 dbh =<span class="st"> </span><span class="kw">rpois</span>(<span class="dv">100</span>,<span class="dv">20</span>)
-<span class="kw">hist</span>(dbh)</code></pre></div>
-<p><img src="AllomVignette_files/figure-html/unnamed-chunk-6-1.png" width="700"></p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">stand =<span class="st"> </span><span class="kw"><a href="../reference/allom.predict.html">allom.predict</a></span>(allom.fit,<span class="dt">dbh =</span> dbh,<span class="dt">pft =</span> <span class="st">"LH"</span>,<span class="dt">component =</span> <span class="dv">3</span>,<span class="dt">use =</span> <span class="st">"Bg"</span>,<span class="dt">interval =</span> <span class="st">"prediction"</span>)
+<span class="kw">hist</span>(dbh)</code></pre>
+            </div>
+            <p>
+              <img
+                src="AllomVignette_files/figure-html/unnamed-chunk-6-1.png"
+                width="700"
+              />
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">stand =<span class="st"> </span><span class="kw"><a href="../reference/allom.predict.html">allom.predict</a></span>(allom.fit,<span class="dt">dbh =</span> dbh,<span class="dt">pft =</span> <span class="st">"LH"</span>,<span class="dt">component =</span> <span class="dv">3</span>,<span class="dt">use =</span> <span class="st">"Bg"</span>,<span class="dt">interval =</span> <span class="st">"prediction"</span>)
 AGB =<span class="st"> </span><span class="kw">apply</span>(stand,<span class="dv">1</span>,sum)
-<span class="kw">hist</span>(AGB)</code></pre></div>
-<p><img src="AllomVignette_files/figure-html/unnamed-chunk-6-2.png" width="700"></p>
-</div>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#install-package-from-github">install package from Github</a></li>
-      <li><a href="#define-species-groups">Define species groups</a></li>
-      <li><a href="#run-the-bayesian-allometry-model">Run the Bayesian allometry model</a></li>
-      <li><a href="#predict-for-individual-trees">Predict for individual trees</a></li>
-      <li><a href="#predict-for-a-stand">Predict for a stand</a></li>
-      </ul>
-</div>
+<span class="kw">hist</span>(AGB)</code></pre>
+            </div>
+            <p>
+              <img
+                src="AllomVignette_files/figure-html/unnamed-chunk-6-2.png"
+                width="700"
+              />
+            </p>
+          </div>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#install-package-from-github"
+                  >install package from Github</a
+                >
+              </li>
+              <li>
+                <a href="#define-species-groups">Define species groups</a>
+              </li>
+              <li>
+                <a href="#run-the-bayesian-allometry-model"
+                  >Run the Bayesian allometry model</a
+                >
+              </li>
+              <li>
+                <a href="#predict-for-individual-trees"
+                  >Predict for individual trees</a
+                >
+              </li>
+              <li><a href="#predict-for-a-stand">Predict for a stand</a></li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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index 876d90e..c199693 100644
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+++ b/modules/allometry/docs/articles/index.html
@@ -2,133 +2,166 @@
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-      <h1>Articles</h1>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Articles</h1>
+          </div>
 
-    <div class="section ">
-      <h3>All vignettes</h3>
-      <p class="section-desc"></p>
+          <div class="section ">
+            <h3>All vignettes</h3>
+            <p class="section-desc"></p>
 
-      <ul>
-        <li><a href="AllomVignette.html">PEcAn.allometry Vignette</a></li>
-      </ul>
-    </div>
-  </div>
-</div>
+            <ul>
+              <li><a href="AllomVignette.html">PEcAn.allometry Vignette</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/modules/allometry/docs/authors.html b/modules/allometry/docs/authors.html
index 3404671..a2193e0 100644
--- a/modules/allometry/docs/authors.html
+++ b/modules/allometry/docs/authors.html
@@ -2,134 +2,163 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.allometry</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.allometry</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.allometry</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/AllomVignette.html">PEcAn.allometry Vignette</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.allometry</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/AllomVignette.html"
+                        >PEcAn.allometry Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/allometry/docs/docsearch.css b/modules/allometry/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/allometry/docs/docsearch.css
+++ b/modules/allometry/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/allometry/docs/docsearch.js b/modules/allometry/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/allometry/docs/docsearch.js
+++ b/modules/allometry/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/allometry/docs/index.html b/modules/allometry/docs/index.html
index 8dff2d3..dff9e0f 100644
--- a/modules/allometry/docs/index.html
+++ b/modules/allometry/docs/index.html
@@ -1,115 +1,175 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn allometry functions • PEcAn.allometry</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn allometry functions">
-<meta property="og:description" content="Synthesize allometric equations or fit allometries to data">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn allometry functions • PEcAn.allometry</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
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+    <script
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta property="og:title" content="PEcAn allometry functions" />
+    <meta
+      property="og:description"
+      content="Synthesize allometric equations or fit allometries to data"
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.allometry</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/AllomVignette.html">PEcAn.allometry Vignette</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    Synthesize allometric equations or fit allometries to data
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.allometry</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/AllomVignette.html"
+                        >PEcAn.allometry Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          Synthesize allometric equations or fit allometries to data
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/allometry/docs/pkgdown.css b/modules/allometry/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/allometry/docs/pkgdown.css
+++ b/modules/allometry/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/allometry/docs/pkgdown.js b/modules/allometry/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/allometry/docs/pkgdown.js
+++ b/modules/allometry/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/allometry/docs/reference/AllomAve.html b/modules/allometry/docs/reference/AllomAve.html
index a0e8b92..c2be040 100644
--- a/modules/allometry/docs/reference/AllomAve.html
+++ b/modules/allometry/docs/reference/AllomAve.html
@@ -2,192 +2,275 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>AllomAve — AllomAve • PEcAn.allometry</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="AllomAve — AllomAve" />
-
-<meta property="og:description" content="allometery wrapper function that handles loading and subsetting the data,
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>AllomAve — AllomAve • PEcAn.allometry</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
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+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="AllomAve — AllomAve" />
+
+    <meta
+      property="og:description"
+      content="allometery wrapper function that handles loading and subsetting the data,
  fitting the Bayesian models, and generating diagnostic figures. Set up to loop over
   multiple PFTs and components. 
-  Writes raw MCMC and PDF of diagnositcs to file and returns table of summary stats." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+  Writes raw MCMC and PDF of diagnositcs to file and returns table of summary stats."
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
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+                    <li>
+                      <a href="../articles/AllomVignette.html"
+                        >PEcAn.allometry Vignette</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>AllomAve</h1>
-    
-    <div class="hidden name"><code>AllomAve.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>allometery wrapper function that handles loading and subsetting the data,
- fitting the Bayesian models, and generating diagnostic figures. Set up to loop over
-  multiple PFTs and components. 
-  Writes raw MCMC and PDF of diagnositcs to file and returns table of summary stats.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>AllomAve</span>(<span class='no'>pfts</span>, <span class='kw'>components</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>outdir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>AllomAve</h1>
+
+            <div class="hidden name"><code>AllomAve.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              allometery wrapper function that handles loading and subsetting
+              the data, fitting the Bayesian models, and generating diagnostic
+              figures. Set up to loop over multiple PFTs and components. Writes
+              raw MCMC and PDF of diagnositcs to file and returns table of
+              summary stats.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>AllomAve</span>(<span class='no'>pfts</span>, <span class='kw'>components</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>outdir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>field</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>parm</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"data/Table3_GTR-NE-319.v2.csv"</span>,
   <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"PEcAn.allometry"</span>), <span class='kw'>ngibbs</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>nchain</span> <span class='kw'>=</span> <span class='fl'>3</span>,
   <span class='kw'>dmin</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>dmax</span> <span class='kw'>=</span> <span class='fl'>500</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pfts</th>
-      <td><p>pft list from PEcAn settings (if con) OR list of pft spcd's
-If the latter, the names within the list are used to identify PFTs</p><ul>
-<li><p>'acronym' - USDA species acronyms (see plants.usda.gov), used with FIELD data (vector)</p></li>
-<li><p>'spcd' - USFS species codes, use with PARM data (vector)</p></li>
-</ul></td>
-    </tr>
-    <tr>
-      <th>components</th>
-      <td><p>IDs for allometry components from Jenkins et al 2004 Table 5. Default is stem biomass (6). See data(allom.components)</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>output directory files are written to. Default is getwd()</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    <tr>
-      <th>field</th>
-      <td><p>path(s) to raw data files</p></td>
-    </tr>
-    <tr>
-      <th>parm</th>
-      <td><p>path to allometry equation file (NULL default loads Jenkins Table 3)</p></td>
-    </tr>
-    <tr>
-      <th>ngibbs</th>
-      <td><p>number of MCMC iterations (per chain) to run</p></td>
-    </tr>
-    <tr>
-      <th>nchain</th>
-      <td><p>number of MCMC chains</p></td>
-    </tr>
-    <tr>
-      <th>dmin</th>
-      <td><p>minimum dbh of interest</p></td>
-    </tr>
-    <tr>
-      <th>dmax</th>
-      <td><p>maximum dbh of interest</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nested list of parameter summary statistics</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>There are two usages of this function. 
-When running 'online' (connected to the PEcAn database), pass the database connection, con, and the pfts subsection of the PEcAn settings.
-When running 'stand alone' pass the pft list mapping species to species codes and the file paths to the allometry table and field data (optional)</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pfts</th>
+              <td>
+                <p>
+                  pft list from PEcAn settings (if con) OR list of pft spcd's If
+                  the latter, the names within the list are used to identify
+                  PFTs
+                </p>
+                <ul>
+                  <li>
+                    <p>
+                      'acronym' - USDA species acronyms (see plants.usda.gov),
+                      used with FIELD data (vector)
+                    </p>
+                  </li>
+                  <li>
+                    <p>
+                      'spcd' - USFS species codes, use with PARM data (vector)
+                    </p>
+                  </li>
+                </ul>
+              </td>
+            </tr>
+            <tr>
+              <th>components</th>
+              <td>
+                <p>
+                  IDs for allometry components from Jenkins et al 2004 Table 5.
+                  Default is stem biomass (6). See data(allom.components)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td>
+                <p>output directory files are written to. Default is getwd()</p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+            <tr>
+              <th>field</th>
+              <td><p>path(s) to raw data files</p></td>
+            </tr>
+            <tr>
+              <th>parm</th>
+              <td>
+                <p>
+                  path to allometry equation file (NULL default loads Jenkins
+                  Table 3)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ngibbs</th>
+              <td><p>number of MCMC iterations (per chain) to run</p></td>
+            </tr>
+            <tr>
+              <th>nchain</th>
+              <td><p>number of MCMC chains</p></td>
+            </tr>
+            <tr>
+              <th>dmin</th>
+              <td><p>minimum dbh of interest</p></td>
+            </tr>
+            <tr>
+              <th>dmax</th>
+              <td><p>maximum dbh of interest</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nested list of parameter summary statistics</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            There are two usages of this function. When running 'online'
+            (connected to the PEcAn database), pass the database connection,
+            con, and the pfts subsection of the PEcAn settings. When running
+            'stand alone' pass the pft list mapping species to species codes and
+            the file paths to the allometry table and field data (optional)
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='kw'>if</span>(<span class='fl'>FALSE</span>){
   <span class='no'>pfts</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>FAGR</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>spcd</span><span class='kw'>=</span><span class='fl'>531</span>,<span class='kw'>acronym</span><span class='kw'>=</span><span class='st'>'FAGR'</span>))
   <span class='no'>allom.stats</span> <span class='kw'>=</span> <span class='fu'>AllomAve</span>(<span class='no'>pfts</span>,<span class='kw'>ngibbs</span><span class='kw'>=</span><span class='fl'>500</span>)
@@ -198,40 +281,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 }
 
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Michael Dietze
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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-
diff --git a/modules/allometry/docs/reference/AllomUnitCoef.html b/modules/allometry/docs/reference/AllomUnitCoef.html
index 63d6203..7a526c8 100644
--- a/modules/allometry/docs/reference/AllomUnitCoef.html
+++ b/modules/allometry/docs/reference/AllomUnitCoef.html
@@ -2,161 +2,206 @@
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+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
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+ converts mass units TO kg FROM specificed units"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>AllomUnitCoef</h1>
-    
-    <div class="hidden name"><code>AllomUnitCoef.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>converts length units FROM cm TO specified units
- converts mass units TO kg FROM specificed units</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>AllomUnitCoef</span>(<span class='no'>x</span>, <span class='kw'>tp</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>units: mm, cm, cm2, m, in, g, kg, lb, Mg</p></td>
-    </tr>
-    <tr>
-      <th>tp</th>
-      <td><p>diameter type, leave NULL if DBH. Options: 'd.b.h.^2','cbh','crc'</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>AllomUnitCoef</h1>
+
+            <div class="hidden name"><code>AllomUnitCoef.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              converts length units FROM cm TO specified units converts mass
+              units TO kg FROM specificed units
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>AllomUnitCoef</span>(<span class='no'>x</span>, <span class='kw'>tp</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>units: mm, cm, cm2, m, in, g, kg, lb, Mg</p></td>
+            </tr>
+            <tr>
+              <th>tp</th>
+              <td>
+                <p>
+                  diameter type, leave NULL if DBH. Options:
+                  'd.b.h.^2','cbh','crc'
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/allometry/docs/reference/allom.BayesFit.html b/modules/allometry/docs/reference/allom.BayesFit.html
index 4410a93..69581df 100644
--- a/modules/allometry/docs/reference/allom.BayesFit.html
+++ b/modules/allometry/docs/reference/allom.BayesFit.html
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+    <meta property="og:title" content="allom.BayesFit — allom.BayesFit" />
+
+    <meta
+      property="og:description"
+      content="Module to fit a common power-law allometric model
 to a mixture of raw data and allometric equations
 in a Heirarchical Bayes framework with multiple imputation
-of the allometric data" />
-<meta name="twitter:card" content="summary" />
-
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+of the allometric data"
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+    <meta name="twitter:card" content="summary" />
 
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>allom.BayesFit</h1>
-    
-    <div class="hidden name"><code>allom.BayesFit.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Module to fit a common power-law allometric model
-to a mixture of raw data and allometric equations
-in a Heirarchical Bayes framework with multiple imputation
-of the allometric data</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>allom.BayesFit</span>(<span class='no'>allom</span>, <span class='kw'>nrep</span> <span class='kw'>=</span> <span class='fl'>10000</span>, <span class='kw'>form</span> <span class='kw'>=</span> <span class='st'>"power"</span>, <span class='kw'>dmin</span> <span class='kw'>=</span> <span class='fl'>0.1</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>allom.BayesFit</h1>
+
+            <div class="hidden name"><code>allom.BayesFit.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Module to fit a common power-law allometric model to a mixture of
+              raw data and allometric equations in a Heirarchical Bayes
+              framework with multiple imputation of the allometric data
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>allom.BayesFit</span>(<span class='no'>allom</span>, <span class='kw'>nrep</span> <span class='kw'>=</span> <span class='fl'>10000</span>, <span class='kw'>form</span> <span class='kw'>=</span> <span class='st'>"power"</span>, <span class='kw'>dmin</span> <span class='kw'>=</span> <span class='fl'>0.1</span>,
   <span class='kw'>dmax</span> <span class='kw'>=</span> <span class='fl'>500</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>allom</th>
-      <td><p>- object (usually generated by query.allom.data) which
-        needs to be a list with two entries:
-  'field' - contains a list, each entry for which is
-            a data frame with 'x' and 'y'. Can be NULL
-  'parm' -  a single data frame with the following components:</p><ul>
-<li><p>n     sample size</p></li>
-<li><p>a     eqn coefficient</p></li>
-<li><p>b     eqn coefficient</p></li>
-<li><p>c     eqn coefficient</p></li>
-<li><p>d     eqn coefficient</p></li>
-<li><p>e     eqn coefficient</p></li>
-<li><p>se    standard error</p></li>
-<li><p>eqn   sample size</p></li>
-<li><p>Xmin  smallest tree sampled (cm)</p></li>
-<li><p>Xmax  largest tree sampled (cm)</p></li>
-<li><p>Xcor  units correction on X</p></li>
-<li><p>Ycor  units correction on Y</p></li>
-<li><p>Xtype type of measurement on the X</p></li>
-<li><p>spp    - USFS species code</p></li>
-</ul></td>
-    </tr>
-    <tr>
-      <th>nrep</th>
-      <td><p>- number of MCMC replicates</p></td>
-    </tr>
-    <tr>
-      <th>form</th>
-      <td><p>functional form of the allometry: 'power' vs 'exp'</p></td>
-    </tr>
-    <tr>
-      <th>dmin</th>
-      <td><p>minimum dbh of interest</p></td>
-    </tr>
-    <tr>
-      <th>dmax</th>
-      <td><p>maximum dbh of interest</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>returns MCMC chain and ONE instance of 'data'
-note: in many cases the estimates are multiply imputed</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>dependencies: requires MCMCpack and mvtnorm</p>
-<p>note: runs 1 chain, but multiple chains can be simulated by
-      multiple function calls</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>allom</th>
+              <td>
+                <p>
+                  - object (usually generated by query.allom.data) which needs
+                  to be a list with two entries: 'field' - contains a list, each
+                  entry for which is a data frame with 'x' and 'y'. Can be NULL
+                  'parm' - a single data frame with the following components:
+                </p>
+                <ul>
+                  <li><p>n sample size</p></li>
+                  <li><p>a eqn coefficient</p></li>
+                  <li><p>b eqn coefficient</p></li>
+                  <li><p>c eqn coefficient</p></li>
+                  <li><p>d eqn coefficient</p></li>
+                  <li><p>e eqn coefficient</p></li>
+                  <li><p>se standard error</p></li>
+                  <li><p>eqn sample size</p></li>
+                  <li><p>Xmin smallest tree sampled (cm)</p></li>
+                  <li><p>Xmax largest tree sampled (cm)</p></li>
+                  <li><p>Xcor units correction on X</p></li>
+                  <li><p>Ycor units correction on Y</p></li>
+                  <li><p>Xtype type of measurement on the X</p></li>
+                  <li><p>spp - USFS species code</p></li>
+                </ul>
+              </td>
+            </tr>
+            <tr>
+              <th>nrep</th>
+              <td><p>- number of MCMC replicates</p></td>
+            </tr>
+            <tr>
+              <th>form</th>
+              <td><p>functional form of the allometry: 'power' vs 'exp'</p></td>
+            </tr>
+            <tr>
+              <th>dmin</th>
+              <td><p>minimum dbh of interest</p></td>
+            </tr>
+            <tr>
+              <th>dmax</th>
+              <td><p>maximum dbh of interest</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            returns MCMC chain and ONE instance of 'data' note: in many cases
+            the estimates are multiply imputed
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>dependencies: requires MCMCpack and mvtnorm</p>
+          <p>
+            note: runs 1 chain, but multiple chains can be simulated by multiple
+            function calls
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
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diff --git a/modules/allometry/docs/reference/allom.predict.html b/modules/allometry/docs/reference/allom.predict.html
index 621a290..f51c5d5 100644
--- a/modules/allometry/docs/reference/allom.predict.html
+++ b/modules/allometry/docs/reference/allom.predict.html
@@ -2,168 +2,250 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>allom.predict</h1>
-    
-    <div class="hidden name"><code>allom.predict.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>allom.predict</h1>
 
-    <div class="ref-description">
-    
-    <p>Function for making tree-level Monte Carlo predictions
-from allometric equations estimated from the PEcAn allometry module</p>
-    
-    </div>
+            <div class="hidden name"><code>allom.predict.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function for making tree-level Monte Carlo predictions from
+              allometric equations estimated from the PEcAn allometry module
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>allom.predict</span>(<span class='no'>object</span>, <span class='no'>dbh</span>, <span class='kw'>pft</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>component</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>allom.predict</span>(<span class='no'>object</span>, <span class='no'>dbh</span>, <span class='kw'>pft</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>component</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>use</span> <span class='kw'>=</span> <span class='st'>"Bg"</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='st'>"prediction"</span>, <span class='kw'>single.tree</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>object</th>
-      <td><p>Allometry model object. Option includes</p><ul>
-<li><p>'list of mcmc' - mcmc outputs in a list by PFT then component</p></li>
-<li><p>'vector of file paths' - path(s) to AllomAve RData files</p></li>
-<li><p>'directory where files are located -</p></li>
-</ul></td>
-    </tr>
-    <tr>
-      <th>dbh</th>
-      <td><p>Diameter at Breast Height (cm)</p></td>
-    </tr>
-    <tr>
-      <th>pft</th>
-      <td><p>Plant Functional Type. Needs to match the name used in AllomAve. Can be NULL if only one PFT/species exists, otherwise needs to the same length as dbh</p></td>
-    </tr>
-    <tr>
-      <th>component</th>
-      <td><p>Which component to predict. Can be NULL if only one component was analysed in AllomAve.</p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>Number of Monte Carlo samples. Defaults to the same number as in the MCMC object</p></td>
-    </tr>
-    <tr>
-      <th>use</th>
-      <td><p>c('Bg','mu','best')</p></td>
-    </tr>
-    <tr>
-      <th>interval</th>
-      <td><p>c('none','confidence','prediction') default is prediction</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>matrix of Monte Carlo predictions that has n rows and one column per DBH</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"># NOT RUN {
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>object</th>
+              <td>
+                <p>Allometry model object. Option includes</p>
+                <ul>
+                  <li>
+                    <p>
+                      'list of mcmc' - mcmc outputs in a list by PFT then
+                      component
+                    </p>
+                  </li>
+                  <li>
+                    <p>
+                      'vector of file paths' - path(s) to AllomAve RData files
+                    </p>
+                  </li>
+                  <li><p>'directory where files are located -</p></li>
+                </ul>
+              </td>
+            </tr>
+            <tr>
+              <th>dbh</th>
+              <td><p>Diameter at Breast Height (cm)</p></td>
+            </tr>
+            <tr>
+              <th>pft</th>
+              <td>
+                <p>
+                  Plant Functional Type. Needs to match the name used in
+                  AllomAve. Can be NULL if only one PFT/species exists,
+                  otherwise needs to the same length as dbh
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>component</th>
+              <td>
+                <p>
+                  Which component to predict. Can be NULL if only one component
+                  was analysed in AllomAve.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td>
+                <p>
+                  Number of Monte Carlo samples. Defaults to the same number as
+                  in the MCMC object
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>use</th>
+              <td><p>c('Bg','mu','best')</p></td>
+            </tr>
+            <tr>
+              <th>interval</th>
+              <td>
+                <p>c('none','confidence','prediction') default is prediction</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            matrix of Monte Carlo predictions that has n rows and one column per
+            DBH
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"># NOT RUN {
 # }
 <span class='co'># NOT RUN {</span>
   <span class='no'>object</span> <span class='kw'>=</span> <span class='st'>'~/Dropbox//HF C Synthesis/Allometry Papers &amp; Analysis/'</span>
@@ -173,38 +255,34 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze, Christy Rollinson
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
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-   </div>
+          <h2>Author</h2>
 
-  
+          Michael Dietze, Christy Rollinson
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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+
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index cb0cef4..71f79b6 100644
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+++ b/modules/allometry/docs/reference/index.html
@@ -2,198 +2,261 @@
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AllomVignette.html"
+                        >PEcAn.allometry Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
 
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="AllomAve.html">AllomAve()</a></code> </p>
-        </td>
-        <td><p>AllomAve</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="AllomUnitCoef.html">AllomUnitCoef()</a></code> </p>
-        </td>
-        <td><p>AllomUnitCoef</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="allom.BayesFit.html">allom.BayesFit()</a></code> </p>
-        </td>
-        <td><p>allom.BayesFit</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="allom.predict.html">allom.predict()</a></code> </p>
-        </td>
-        <td><p>allom.predict</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load.allom.html">load.allom()</a></code> </p>
-        </td>
-        <td><p>load.allom</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="nu.html">nu()</a></code> </p>
-        </td>
-        <td><p>nu</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="query.allom.data.html">query.allom.data()</a></code> </p>
-        </td>
-        <td><p>query.allom.data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.allom.data.html">read.allom.data()</a></code> </p>
-        </td>
-        <td><p>read.allom.data</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-      </footer>
-   </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="AllomAve.html">AllomAve()</a></code>
+                  </p>
+                </td>
+                <td><p>AllomAve</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="AllomUnitCoef.html">AllomUnitCoef()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>AllomUnitCoef</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="allom.BayesFit.html">allom.BayesFit()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>allom.BayesFit</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="allom.predict.html">allom.predict()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>allom.predict</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="load.allom.html">load.allom()</a></code>
+                  </p>
+                </td>
+                <td><p>load.allom</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="nu.html">nu()</a></code>
+                  </p>
+                </td>
+                <td><p>nu</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="query.allom.data.html"
+                        >query.allom.data()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>query.allom.data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.allom.data.html"
+                        >read.allom.data()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>read.allom.data</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
-  
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/allometry/docs/reference/load.allom.html b/modules/allometry/docs/reference/load.allom.html
index 96e8af8..d802560 100644
--- a/modules/allometry/docs/reference/load.allom.html
+++ b/modules/allometry/docs/reference/load.allom.html
@@ -2,140 +2,191 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+
+    <meta property="og:description" content="loads allom files" />
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              <span class="navbar-brand">
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AllomVignette.html"
+                        >PEcAn.allometry Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>load.allom</h1>
-    
-    <div class="hidden name"><code>load.allom.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>loads allom files</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>load.allom</span>(<span class='no'>object</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>object</th>
-      <td><p>Allometry model object. Option includes</p><ul>
-<li><p>'vector of file paths' - path(s) to AllomAve RData files</p></li>
-<li><p>'directory where files are located -</p></li>
-</ul></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>mcmc outputs in a list by PFT then component</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"># NOT RUN {
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load.allom</h1>
+
+            <div class="hidden name"><code>load.allom.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>loads allom files</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load.allom</span>(<span class='no'>object</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>object</th>
+              <td>
+                <p>Allometry model object. Option includes</p>
+                <ul>
+                  <li>
+                    <p>
+                      'vector of file paths' - path(s) to AllomAve RData files
+                    </p>
+                  </li>
+                  <li><p>'directory where files are located -</p></li>
+                </ul>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>mcmc outputs in a list by PFT then component</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"># NOT RUN {
 # }
 <span class='co'># NOT RUN {</span>
   <span class='no'>object</span> <span class='kw'>=</span> <span class='st'>'~/Dropbox//HF C Synthesis/Allometry Papers &amp; Analysis/'</span>
@@ -144,38 +195,34 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Michael Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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 </html>
-
diff --git a/modules/allometry/docs/reference/nu.html b/modules/allometry/docs/reference/nu.html
index c7cf41c..661f50b 100644
--- a/modules/allometry/docs/reference/nu.html
+++ b/modules/allometry/docs/reference/nu.html
@@ -2,155 +2,190 @@
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+                  >1.6.0</span
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+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/AllomVignette.html"
+                        >PEcAn.allometry Vignette</a
+                      >
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+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>nu</h1>
-    
-    <div class="hidden name"><code>nu.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>converts factors to numeric</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>nu</span>(<span class='no'>x</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>data</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>nu</h1>
+
+            <div class="hidden name"><code>nu.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>converts factors to numeric</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>nu</span>(<span class='no'>x</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>data</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/allometry/docs/reference/query.allom.data.html b/modules/allometry/docs/reference/query.allom.data.html
index e0cb3bc..d476a92 100644
--- a/modules/allometry/docs/reference/query.allom.data.html
+++ b/modules/allometry/docs/reference/query.allom.data.html
@@ -2,183 +2,229 @@
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
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+
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+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="query.allom.data — query.allom.data" />
+
+    <meta
+      property="og:description"
+      content="Module to grab allometric information from the raw data table
 Will grab both original field data and tallied equations
 Tallied equation format based on Jenkins et al 2004 USFS
-General Technical Report NE-319" />
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+General Technical Report NE-319"
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.allometry</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AllomVignette.html"
+                        >PEcAn.allometry Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>query.allom.data</h1>
-    
-    <div class="hidden name"><code>query.allom.data.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Module to grab allometric information from the raw data table
-Will grab both original field data and tallied equations</p>
-<p>Tallied equation format based on Jenkins et al 2004 USFS
-General Technical Report NE-319</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>query.allom.data</span>(<span class='no'>pft_name</span>, <span class='no'>variable</span>, <span class='no'>con</span>, <span class='kw'>nsim</span> <span class='kw'>=</span> <span class='fl'>10000</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pft_name</th>
-      <td><p>name of Plant Functional Type to be queried</p></td>
-    </tr>
-    <tr>
-      <th>variable</th>
-      <td><p>name of response variable</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>open database connection</p></td>
-    </tr>
-    <tr>
-      <th>nsim</th>
-      <td><p>number of pseudo-data simulations for estimating SE</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>database is assumed to conform to the PEcAn Schema</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>query.allom.data</h1>
+
+            <div class="hidden name"><code>query.allom.data.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Module to grab allometric information from the raw data table Will
+              grab both original field data and tallied equations
+            </p>
+            <p>
+              Tallied equation format based on Jenkins et al 2004 USFS General
+              Technical Report NE-319
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>query.allom.data</span>(<span class='no'>pft_name</span>, <span class='no'>variable</span>, <span class='no'>con</span>, <span class='kw'>nsim</span> <span class='kw'>=</span> <span class='fl'>10000</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pft_name</th>
+              <td><p>name of Plant Functional Type to be queried</p></td>
+            </tr>
+            <tr>
+              <th>variable</th>
+              <td><p>name of response variable</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>open database connection</p></td>
+            </tr>
+            <tr>
+              <th>nsim</th>
+              <td>
+                <p>number of pseudo-data simulations for estimating SE</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>database is assumed to conform to the PEcAn Schema</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/allometry/docs/reference/read.allom.data.html b/modules/allometry/docs/reference/read.allom.data.html
index 6c08629..e0879ef 100644
--- a/modules/allometry/docs/reference/read.allom.data.html
+++ b/modules/allometry/docs/reference/read.allom.data.html
@@ -2,191 +2,249 @@
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+    />
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-  <a href="../reference/index.html">Reference</a>
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-    Articles
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.allometry</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AllomVignette.html"
+                        >PEcAn.allometry Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>read.allom.data</h1>
-    
-    <div class="hidden name"><code>read.allom.data.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Extracts PFT- and component-specific data and allometeric equations from the specified files.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read.allom.data</span>(<span class='no'>pft.data</span>, <span class='no'>component</span>, <span class='no'>field</span>, <span class='no'>parm</span>, <span class='kw'>nsim</span> <span class='kw'>=</span> <span class='fl'>10000</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pft.data</th>
-      <td><p>PFT dataframe</p><ul>
-<li><p>acronymUSDA species acronyms, used with FIELD data (vector)</p></li>
-<li><p>spcdUSFS species codes, use with TALLY data (vector)</p></li>
-</ul></td>
-    </tr>
-    <tr>
-      <th>component</th>
-      <td><p>allometry ID, Jenkins table 5</p></td>
-    </tr>
-    <tr>
-      <th>field</th>
-      <td><p>raw field data</p></td>
-    </tr>
-    <tr>
-      <th>parm</th>
-      <td><p>allometry equation file, Jenkins table 3</p></td>
-    </tr>
-    <tr>
-      <th>nsim</th>
-      <td><p>number of Monte Carlo draws in numerical transforms</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    
-
-<dt>field</dt><dd><p>PFT-filtered field Data</p></dd>
-        <dt>parm</dt><dd><p>Component- and PFT-filtered Allometric Equations</p></dd>
-
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This code also estimates the standard error from R-squared, 
-which is required to simulate pseudodata from the allometric eqns.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>read.allom.data</h1>
+
+            <div class="hidden name"><code>read.allom.data.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Extracts PFT- and component-specific data and allometeric
+              equations from the specified files.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read.allom.data</span>(<span class='no'>pft.data</span>, <span class='no'>component</span>, <span class='no'>field</span>, <span class='no'>parm</span>, <span class='kw'>nsim</span> <span class='kw'>=</span> <span class='fl'>10000</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pft.data</th>
+              <td>
+                <p>PFT dataframe</p>
+                <ul>
+                  <li>
+                    <p>
+                      acronymUSDA species acronyms, used with FIELD data
+                      (vector)
+                    </p>
+                  </li>
+                  <li>
+                    <p>spcdUSFS species codes, use with TALLY data (vector)</p>
+                  </li>
+                </ul>
+              </td>
+            </tr>
+            <tr>
+              <th>component</th>
+              <td><p>allometry ID, Jenkins table 5</p></td>
+            </tr>
+            <tr>
+              <th>field</th>
+              <td><p>raw field data</p></td>
+            </tr>
+            <tr>
+              <th>parm</th>
+              <td><p>allometry equation file, Jenkins table 3</p></td>
+            </tr>
+            <tr>
+              <th>nsim</th>
+              <td>
+                <p>number of Monte Carlo draws in numerical transforms</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <dt>field</dt>
+          <dd><p>PFT-filtered field Data</p></dd>
+          <dt>parm</dt>
+          <dd><p>Component- and PFT-filtered Allometric Equations</p></dd>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This code also estimates the standard error from R-squared, which is
+            required to simulate pseudodata from the allometric eqns.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+          <p>Developed by .</p>
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-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/LICENSE-text.html b/modules/assim.batch/docs/LICENSE-text.html
index 55c373e..21dbc93 100644
--- a/modules/assim.batch/docs/LICENSE-text.html
+++ b/modules/assim.batch/docs/LICENSE-text.html
@@ -2,109 +2,146 @@
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 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<![endif]-->
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <script src="pkgdown.js"></script>
+
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+
+    <!--[if lt IE 9]>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-      <a href="articles/AssimBatchVignette.html">PEcAn.assim.batch Vignette</a>
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-      
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-        
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-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.assim.batch</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -133,27 +170,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
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+
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diff --git a/modules/assim.batch/docs/articles/AssimBatchVignette.html b/modules/assim.batch/docs/articles/AssimBatchVignette.html
index 80fd514..85097e5 100644
--- a/modules/assim.batch/docs/articles/AssimBatchVignette.html
+++ b/modules/assim.batch/docs/articles/AssimBatchVignette.html
@@ -1,115 +1,243 @@
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-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+  </head>
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
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+                  <a
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+                    role="button"
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+                  >
+                    Articles
 
-    <div id="navbar" class="navbar-collapse collapse">
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-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
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+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header toc-ignore">
+            <h1>PEcAn.assim.batch Vignette</h1>
+            <h4 class="author">Ryan Kelly</h4>
+            <h4 class="author">Istem Fer</h4>
 
-      
-      </header><div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header toc-ignore">
-      <h1>PEcAn.assim.batch Vignette</h1>
-                        <h4 class="author">Ryan Kelly</h4>
-                        <h4 class="author">Istem Fer</h4>
-            
             <h4 class="date">July 12, 2015 (Updated on 08/08/16)</h4>
-      
-      
-      <div class="hidden name"><code>AssimBatchVignette.Rmd</code></div>
 
-    </div>
+            <div class="hidden name"><code>AssimBatchVignette.Rmd</code></div>
+          </div>
 
-    
-    
-<div id="install-package-from-github" class="section level2">
-<h2 class="hasAnchor">
-<a href="#install-package-from-github" class="anchor"></a>Install package from Github</h2>
-<p>Only needs to be done the first time :</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools)
-<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>, <span class="dt">subdir=</span><span class="st">"all"</span>)</code></pre></div>
-</div>
-<div id="parameter-data-assimilation-in-pecan" class="section level2">
-<h2 class="hasAnchor">
-<a href="#parameter-data-assimilation-in-pecan" class="anchor"></a>Parameter Data Assimilation in PEcAn</h2>
-<p>Currently, there are four ways of doing Parameter Data Assimilation (PDA) in PEcAn :</p>
-<ul>
-<li>bruteforce</li>
-<li>bruteforce.bs</li>
-<li>emulator</li>
-<li>bayesian.tools</li>
-</ul>
-<p><strong>Which one to use?</strong></p>
-<p><strong>bruteforce :</strong> You can choose <em>bruteforce</em> as a method to use PEcAn’s natively implemented Metropolis-Hastings Markov Chain Monte Carlo (MCMC) algorithm. This would perform a Bayesian MCMC on model parameters by proposing one parameter value at a time, and accepting or rejecting it according to the calculated likelihood value. This algorithm also has an adaptation functionality that can be turned on (recommended) and off (see below). As each (<em>i</em>-th) parameter is dependent of the previous (<em>i-1</em>-th) one, this algorithm can only be run sequentially (but different chains can be run in parallel). Therefore, if you have just one parameter to calibrate and a relatively fast model that can be run couple of hundreds (couple of thousands would even be better) of times within an hour, it is possible to use this algorithm.</p>
-<p><strong>bruteforce.bs :</strong> This algorithm is basically identical to the <em>bruteforce</em>, but rather than proposing parameters one at a time, it proposes new values for all parameters at once (“bs” stands for “block sampling”). If you have more than one parameter to calibrate and a relatively fast model, you can use this algorithm, preferably with the adaptation functionality turned on.</p>
-<p><strong>emulator :</strong> When a model is slow, it is practically not possible to run it many times in order to explore the parameter space and draw enough samples to converge the target distribution with bruteforce algorithms. Instead, we can run the model for a relatively smaller number of times with parameter values that have been carefully chosen to give good coverage of parameter space. Then we can interpolate the likelihood calculated for each of those runs to get a surface that “emulates” the true likelihood and perform regular MCMC (just like the “bruteforce” approach), except instead of actually running the model on every iteration to get a likelihood, this time we will just get an approximation from the likelihood emulator.</p>
-<p><strong>bayesian.tools :</strong> There are other MCMC algorithms with different proposal schemes and acceptance criterion than Metropolis-Hastings. BayesianTools is an R-package that includes MCMC and SMC samplers and other tools for Bayesian parameter calibration. If you choose <em>bayesian.tools</em> option, PEcAn framework will hand the PDA calculations over to the BayesianTools package. Although this package includes algorithms that are designed to explore the parameter space more efficiently than the regular MH-MCMC, you would still need a relatively faster model to use these algorithms. The BayesianTools R-package itself is currently under development, once it is fully integrated with PEcAn it will be possible to run some of those algorithms in parallel.</p>
-</div>
-<div id="adding-pda-tags-to-pecan-xml" class="section level2">
-<h2 class="hasAnchor">
-<a href="#adding-pda-tags-to-pecan-xml" class="anchor"></a>Adding PDA tags to pecan.xml</h2>
-<p>The easiest way to use PEcAn’s parameter data assimilation module is to add an <code>&lt;assim.batch&gt;</code> block to pecan.xml, load the file with <code>read.settings</code>, and pass the resulting settings object to <code><a href="../reference/pda.mcmc.html">pda.mcmc()</a></code>. There are some differences in the settings for using different PDA methods (see below), but here is an example <code>&lt;assim.batch&gt;</code> block :</p>
-<pre><code>&lt;assim.batch&gt;
+          <div id="install-package-from-github" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#install-package-from-github" class="anchor"></a>Install
+              package from Github
+            </h2>
+            <p>Only needs to be done the first time :</p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(devtools)
+<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan"</span>, <span class="dt">subdir=</span><span class="st">"all"</span>)</code></pre>
+            </div>
+          </div>
+          <div id="parameter-data-assimilation-in-pecan" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#parameter-data-assimilation-in-pecan" class="anchor"></a
+              >Parameter Data Assimilation in PEcAn
+            </h2>
+            <p>
+              Currently, there are four ways of doing Parameter Data
+              Assimilation (PDA) in PEcAn :
+            </p>
+            <ul>
+              <li>bruteforce</li>
+              <li>bruteforce.bs</li>
+              <li>emulator</li>
+              <li>bayesian.tools</li>
+            </ul>
+            <p><strong>Which one to use?</strong></p>
+            <p>
+              <strong>bruteforce :</strong> You can choose
+              <em>bruteforce</em> as a method to use PEcAn’s natively
+              implemented Metropolis-Hastings Markov Chain Monte Carlo (MCMC)
+              algorithm. This would perform a Bayesian MCMC on model parameters
+              by proposing one parameter value at a time, and accepting or
+              rejecting it according to the calculated likelihood value. This
+              algorithm also has an adaptation functionality that can be turned
+              on (recommended) and off (see below). As each (<em>i</em>-th)
+              parameter is dependent of the previous (<em>i-1</em>-th) one, this
+              algorithm can only be run sequentially (but different chains can
+              be run in parallel). Therefore, if you have just one parameter to
+              calibrate and a relatively fast model that can be run couple of
+              hundreds (couple of thousands would even be better) of times
+              within an hour, it is possible to use this algorithm.
+            </p>
+            <p>
+              <strong>bruteforce.bs :</strong> This algorithm is basically
+              identical to the <em>bruteforce</em>, but rather than proposing
+              parameters one at a time, it proposes new values for all
+              parameters at once (“bs” stands for “block sampling”). If you have
+              more than one parameter to calibrate and a relatively fast model,
+              you can use this algorithm, preferably with the adaptation
+              functionality turned on.
+            </p>
+            <p>
+              <strong>emulator :</strong> When a model is slow, it is
+              practically not possible to run it many times in order to explore
+              the parameter space and draw enough samples to converge the target
+              distribution with bruteforce algorithms. Instead, we can run the
+              model for a relatively smaller number of times with parameter
+              values that have been carefully chosen to give good coverage of
+              parameter space. Then we can interpolate the likelihood calculated
+              for each of those runs to get a surface that “emulates” the true
+              likelihood and perform regular MCMC (just like the “bruteforce”
+              approach), except instead of actually running the model on every
+              iteration to get a likelihood, this time we will just get an
+              approximation from the likelihood emulator.
+            </p>
+            <p>
+              <strong>bayesian.tools :</strong> There are other MCMC algorithms
+              with different proposal schemes and acceptance criterion than
+              Metropolis-Hastings. BayesianTools is an R-package that includes
+              MCMC and SMC samplers and other tools for Bayesian parameter
+              calibration. If you choose <em>bayesian.tools</em> option, PEcAn
+              framework will hand the PDA calculations over to the BayesianTools
+              package. Although this package includes algorithms that are
+              designed to explore the parameter space more efficiently than the
+              regular MH-MCMC, you would still need a relatively faster model to
+              use these algorithms. The BayesianTools R-package itself is
+              currently under development, once it is fully integrated with
+              PEcAn it will be possible to run some of those algorithms in
+              parallel.
+            </p>
+          </div>
+          <div id="adding-pda-tags-to-pecan-xml" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#adding-pda-tags-to-pecan-xml" class="anchor"></a>Adding
+              PDA tags to pecan.xml
+            </h2>
+            <p>
+              The easiest way to use PEcAn’s parameter data assimilation module
+              is to add an <code>&lt;assim.batch&gt;</code> block to pecan.xml,
+              load the file with <code>read.settings</code>, and pass the
+              resulting settings object to
+              <code><a href="../reference/pda.mcmc.html">pda.mcmc()</a></code
+              >. There are some differences in the settings for using different
+              PDA methods (see below), but here is an example
+              <code>&lt;assim.batch&gt;</code> block :
+            </p>
+            <pre><code>&lt;assim.batch&gt;
   &lt;iter&gt;10000&lt;/iter&gt;
   &lt;method&gt;bruteforce&lt;/method&gt;
   &lt;chain&gt;3&lt;/chain&gt;
@@ -159,40 +287,106 @@ <h2 class="hasAnchor">
   &lt;/jump&gt;
   &lt;diag.plot.iter&gt;500&lt;/diag.plot.iter&gt;
 &lt;/assim.batch&gt;</code></pre>
-<p>Here are details about the settings:</p>
-<ul>
-<li><p><code>&lt;iter&gt;</code> Specifies the number of MCMC iterations to run. If continuing a previous MCMC, this is the number of additional iterations, which will be added to the previous total. Defaults to 100 if missing. Ignored by pda.emulator().</p></li>
-<li><p><code>&lt;chain&gt;</code> Specifies the number of MCMC chains to be run.</p></li>
-<li>
-<p><code>&lt;prior&gt;</code> Identifies the prior to be used for PDA. Can be one of either:</p>
-<ul>
-<li><p><code>&lt;posterior.id&gt;</code> A posterior ID in BETY specifying the posterior from a previous PEcAn analysis (e.g., meta-analysis or previous PDA) to be used as the prior for PDA. Defaults to the most recent relevant posterior in the database if omitted (and no <code>&lt;path&gt;</code> specified instead; see below).</p></li>
-<li><p><code>&lt;path&gt;</code> As an alternative to using a posterior ID, can specify a file path to either a <code>prior.distns.Rdata</code> or <code>post.distns.Rdata</code> file generated from an earlier analysis. Conceptually, using a posterior distribution as the prior for PDA is preferred, as this allows the multiple analyses to work together to iteratively constrain parameters. In practice, previous analyses may have over-constrained parameters to ranges that do not actually optimize model outputs, so using a less informative prior for PDA might yield better results.</p></li>
-</ul>
-<p>NOTE: It is recommended to leave the <code>&lt;prior&gt;</code> tag empty if you are doing this for the first time. PEcAn workflow will handle it for you.</p>
-</li>
-<li><p><code>&lt;param.names&gt;</code> The names of parameters to be constrained by assimilation, listed in individual <code>&lt;param&gt;</code> tags. These must be the standard names given in the <code>id</code> column of the <code>trait.dictionary</code>, i.e. :</p></li>
-</ul>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">data</span>(trait.dictionary, <span class="dt">package =</span> <span class="st">"PEcAn.utils"</span>)
+            <p>Here are details about the settings:</p>
+            <ul>
+              <li>
+                <p>
+                  <code>&lt;iter&gt;</code> Specifies the number of MCMC
+                  iterations to run. If continuing a previous MCMC, this is the
+                  number of additional iterations, which will be added to the
+                  previous total. Defaults to 100 if missing. Ignored by
+                  pda.emulator().
+                </p>
+              </li>
+              <li>
+                <p>
+                  <code>&lt;chain&gt;</code> Specifies the number of MCMC chains
+                  to be run.
+                </p>
+              </li>
+              <li>
+                <p>
+                  <code>&lt;prior&gt;</code> Identifies the prior to be used for
+                  PDA. Can be one of either:
+                </p>
+                <ul>
+                  <li>
+                    <p>
+                      <code>&lt;posterior.id&gt;</code> A posterior ID in BETY
+                      specifying the posterior from a previous PEcAn analysis
+                      (e.g., meta-analysis or previous PDA) to be used as the
+                      prior for PDA. Defaults to the most recent relevant
+                      posterior in the database if omitted (and no
+                      <code>&lt;path&gt;</code> specified instead; see below).
+                    </p>
+                  </li>
+                  <li>
+                    <p>
+                      <code>&lt;path&gt;</code> As an alternative to using a
+                      posterior ID, can specify a file path to either a
+                      <code>prior.distns.Rdata</code> or
+                      <code>post.distns.Rdata</code> file generated from an
+                      earlier analysis. Conceptually, using a posterior
+                      distribution as the prior for PDA is preferred, as this
+                      allows the multiple analyses to work together to
+                      iteratively constrain parameters. In practice, previous
+                      analyses may have over-constrained parameters to ranges
+                      that do not actually optimize model outputs, so using a
+                      less informative prior for PDA might yield better results.
+                    </p>
+                  </li>
+                </ul>
+                <p>
+                  NOTE: It is recommended to leave the
+                  <code>&lt;prior&gt;</code> tag empty if you are doing this for
+                  the first time. PEcAn workflow will handle it for you.
+                </p>
+              </li>
+              <li>
+                <p>
+                  <code>&lt;param.names&gt;</code> The names of parameters to be
+                  constrained by assimilation, listed in individual
+                  <code>&lt;param&gt;</code> tags. These must be the standard
+                  names given in the <code>id</code> column of the
+                  <code>trait.dictionary</code>, i.e. :
+                </p>
+              </li>
+            </ul>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">data</span>(trait.dictionary, <span class="dt">package =</span> <span class="st">"PEcAn.utils"</span>)
 
-<span class="kw">head</span>(trait.dictionary[,<span class="kw">c</span>(<span class="st">"id"</span>, <span class="st">"figid"</span>)])</code></pre></div>
-<pre><code>##                         id                   figid
+<span class="kw">head</span>(trait.dictionary[,<span class="kw">c</span>(<span class="st">"id"</span>, <span class="st">"figid"</span>)])</code></pre>
+            </div>
+            <pre><code>##                         id                   figid
 ## 1           plant_min_temp          Plant Min Temp
 ## 2                      GDD     Growing Degree Days
 ## 3                    leafC            Leaf C conc.
 ## 4                 c2n_leaf                Leaf C:N
 ## 5 leaf_respiration_rate_m2   Leaf Respiration Rate
 ## 6  dark_respiration_factor Dark Respiration Factor</code></pre>
-<pre><code>       NOTE : `&lt;param.names&gt;` chunk should always be on your xml file regardless of the method you use in the PDA.
+            <pre><code>       NOTE : `&lt;param.names&gt;` chunk should always be on your xml file regardless of the method you use in the PDA.
        </code></pre>
-<ul>
-<li>
-<p><code>&lt;inputs&gt;</code> Observation data to be compared to the model. In principle, can be one or more datasets, specified in a variety of ways. In practice, the code is tested for assimilating Ameriflux dataset currently, and assumes the input is Ameriflux NEE/FC or LE.</p>
-<ul>
-<li>
-<code>&lt;file&gt;</code> Denotes a set of tags for a single input. Would be repeated for multiple datasets/variables, e.g. in this case note the differences in <code>&lt;variable.id&gt;</code> and <code>&lt;variable.name&gt;</code> :</li>
-</ul>
-<pre><code>...
+            <ul>
+              <li>
+                <p>
+                  <code>&lt;inputs&gt;</code> Observation data to be compared to
+                  the model. In principle, can be one or more datasets,
+                  specified in a variety of ways. In practice, the code is
+                  tested for assimilating Ameriflux dataset currently, and
+                  assumes the input is Ameriflux NEE/FC or LE.
+                </p>
+                <ul>
+                  <li>
+                    <code>&lt;file&gt;</code> Denotes a set of tags for a single
+                    input. Would be repeated for multiple datasets/variables,
+                    e.g. in this case note the differences in
+                    <code>&lt;variable.id&gt;</code> and
+                    <code>&lt;variable.name&gt;</code> :
+                  </li>
+                </ul>
+                <pre><code>...
 &lt;inputs&gt;
   &lt;file&gt;
     &lt;input.id&gt;1000000384&lt;/input.id&gt;
@@ -222,53 +416,129 @@ <h2 class="hasAnchor">
   &lt;/file&gt;
 &lt;/inputs&gt;
 ...</code></pre>
-<ul>
-<li>
-<code>&lt;input.id&gt;</code> BETY input ID for looking up the input.</li>
-<li>
-<code>&lt;path&gt;</code> File path to the input. Both <code>&lt;id&gt;</code> and <code>&lt;path&gt;</code> of the observation data should be supplied for the PDA.</li>
-<li>
-<code>&lt;source&gt;</code> A standardized source of input data (e.g., Ameriflux). Not implemented yet, but the idea would be similar to the met workflow, PEcAn would be able to use standard data sources automatically where available. Only used if no <code>&lt;id&gt;</code> or <code>&lt;path&gt;</code> is given.</li>
-<li>
-<code>&lt;likelihood&gt;</code> Identifier for the likelihood to use. E.g., the Ameriflux NEE/FC and LE data use a Laplacian likelihood.</li>
-<li>
-<code>&lt;hyper.pars&gt;</code> Optional. Hyperparameters for your likelihood. E.g. Prior parameters of the precision for Gaussian likelihood. Defaults to scaled values if not provided.</li>
-<li>
-<p><code>&lt;variable.id&gt;</code> The BETY variable ID associated with this dataset. The idea is that specific preprocessing steps (e.g., estimating heteroskedastic error for tower NEE) would be associated with particular IDs. Could automate further by assigning default <code>&lt;likelihood&gt;</code> to variable.id values (allowing <code>&lt;likelihood&gt;</code> to be omitted from pecan.xml).</p>
-<p>NOTE : <code>&lt;inputs&gt;</code> chunk should always be on your xml file regardless of the method you use in the PDA.</p>
-</li>
-</ul>
-</li>
-<li>
-<code>&lt;jump&gt;</code> Settings for the specifics of the proposal schema and adaptation functionality.
-<ul>
-<li>
-<code>&lt;ar.target&gt;</code> Target acceptance rate for the adaptive jump algorithm. Defaults to 0.5 if missing.</li>
-<li>
-<code>&lt;adapt&gt;</code> Number of iterations between jump variance adaptations. Defaults to <code>floor(iter/10)</code> if missing. If set equal to the number of <code>&lt;iter&gt;</code>, basically turns off the adaptation functionality, it is not recommended to turn-off this functionality.</li>
-<li>
-<code>&lt;adj.min&gt;</code> Minimum factor by which to reduce jump variance when adapting. Prevents jump variances from degenerating to 0. Defaults to 0.1 if missing.</li>
-</ul>
-</li>
-<li>
-<code>&lt;diag.plot.iter&gt;</code> Interval between saving diagnostic plots. Omit or set to NULL to skip them.</li>
-<li><p><code>&lt;params.id&gt;</code> (Not shown.) A BETY dbfile ID for an MCMC output from previous PDA. If specified, that file is loaded, the new MCMC starts from the last parameter values of the previous, and when finished the extended chain is saved as a new output. If missing, then MCMC starts fresh from prior median parameter values. Regardless, the MCMC parameter values of the PDA are saved to file and inserted in BETY, and the new dbfile ID is inserted into <code>&lt;params.id&gt;</code>. The <code><a href="../reference/pda.mcmc.html">pda.mcmc()</a></code> funtion returns the <code>&lt;assim.batch&gt;</code> settings, which can then be saved. Then, calling a new round of PDA using these returned settings will automatically continue the previous MCMC.</p></li>
-</ul>
-</div>
-<div id="method-specific-settings" class="section level2">
-<h2 class="hasAnchor">
-<a href="#method-specific-settings" class="anchor"></a>Method specific settings</h2>
-<p>If you want to extend your previous <em>bruteforce</em> and <em>bruteforce.bs</em> MCMC-chains, you can add an <code>&lt;extension&gt;</code> tag within your <code>&lt;assim.batch&gt;</code> chunk after reading your post-PDA settings (which would be saved as “pecan.pda[UNIQUE_ID].xml” in your working directory) and set it to “longer”.</p>
-<pre><code>  ...
+                <ul>
+                  <li>
+                    <code>&lt;input.id&gt;</code> BETY input ID for looking up
+                    the input.
+                  </li>
+                  <li>
+                    <code>&lt;path&gt;</code> File path to the input. Both
+                    <code>&lt;id&gt;</code> and <code>&lt;path&gt;</code> of the
+                    observation data should be supplied for the PDA.
+                  </li>
+                  <li>
+                    <code>&lt;source&gt;</code> A standardized source of input
+                    data (e.g., Ameriflux). Not implemented yet, but the idea
+                    would be similar to the met workflow, PEcAn would be able to
+                    use standard data sources automatically where available.
+                    Only used if no <code>&lt;id&gt;</code> or
+                    <code>&lt;path&gt;</code> is given.
+                  </li>
+                  <li>
+                    <code>&lt;likelihood&gt;</code> Identifier for the
+                    likelihood to use. E.g., the Ameriflux NEE/FC and LE data
+                    use a Laplacian likelihood.
+                  </li>
+                  <li>
+                    <code>&lt;hyper.pars&gt;</code> Optional. Hyperparameters
+                    for your likelihood. E.g. Prior parameters of the precision
+                    for Gaussian likelihood. Defaults to scaled values if not
+                    provided.
+                  </li>
+                  <li>
+                    <p>
+                      <code>&lt;variable.id&gt;</code> The BETY variable ID
+                      associated with this dataset. The idea is that specific
+                      preprocessing steps (e.g., estimating heteroskedastic
+                      error for tower NEE) would be associated with particular
+                      IDs. Could automate further by assigning default
+                      <code>&lt;likelihood&gt;</code> to variable.id values
+                      (allowing <code>&lt;likelihood&gt;</code> to be omitted
+                      from pecan.xml).
+                    </p>
+                    <p>
+                      NOTE : <code>&lt;inputs&gt;</code> chunk should always be
+                      on your xml file regardless of the method you use in the
+                      PDA.
+                    </p>
+                  </li>
+                </ul>
+              </li>
+              <li>
+                <code>&lt;jump&gt;</code> Settings for the specifics of the
+                proposal schema and adaptation functionality.
+                <ul>
+                  <li>
+                    <code>&lt;ar.target&gt;</code> Target acceptance rate for
+                    the adaptive jump algorithm. Defaults to 0.5 if missing.
+                  </li>
+                  <li>
+                    <code>&lt;adapt&gt;</code> Number of iterations between jump
+                    variance adaptations. Defaults to
+                    <code>floor(iter/10)</code> if missing. If set equal to the
+                    number of <code>&lt;iter&gt;</code>, basically turns off the
+                    adaptation functionality, it is not recommended to turn-off
+                    this functionality.
+                  </li>
+                  <li>
+                    <code>&lt;adj.min&gt;</code> Minimum factor by which to
+                    reduce jump variance when adapting. Prevents jump variances
+                    from degenerating to 0. Defaults to 0.1 if missing.
+                  </li>
+                </ul>
+              </li>
+              <li>
+                <code>&lt;diag.plot.iter&gt;</code> Interval between saving
+                diagnostic plots. Omit or set to NULL to skip them.
+              </li>
+              <li>
+                <p>
+                  <code>&lt;params.id&gt;</code> (Not shown.) A BETY dbfile ID
+                  for an MCMC output from previous PDA. If specified, that file
+                  is loaded, the new MCMC starts from the last parameter values
+                  of the previous, and when finished the extended chain is saved
+                  as a new output. If missing, then MCMC starts fresh from prior
+                  median parameter values. Regardless, the MCMC parameter values
+                  of the PDA are saved to file and inserted in BETY, and the new
+                  dbfile ID is inserted into <code>&lt;params.id&gt;</code>. The
+                  <code
+                    ><a href="../reference/pda.mcmc.html">pda.mcmc()</a></code
+                  >
+                  funtion returns the <code>&lt;assim.batch&gt;</code> settings,
+                  which can then be saved. Then, calling a new round of PDA
+                  using these returned settings will automatically continue the
+                  previous MCMC.
+                </p>
+              </li>
+            </ul>
+          </div>
+          <div id="method-specific-settings" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#method-specific-settings" class="anchor"></a>Method
+              specific settings
+            </h2>
+            <p>
+              If you want to extend your previous <em>bruteforce</em> and
+              <em>bruteforce.bs</em> MCMC-chains, you can add an
+              <code>&lt;extension&gt;</code> tag within your
+              <code>&lt;assim.batch&gt;</code> chunk after reading your post-PDA
+              settings (which would be saved as “pecan.pda[UNIQUE_ID].xml” in
+              your working directory) and set it to “longer”.
+            </p>
+            <pre><code>  ...
   &lt;method&gt;bruteforce.bs&lt;/method&gt;
   &lt;iter&gt;10000&lt;/iter&gt;
   &lt;method&gt;bruteforce&lt;/method&gt;
   &lt;chain&gt;3&lt;/chain&gt;
   &lt;extension&gt;longer&lt;/extension&gt;
   ...</code></pre>
-<p>If you are using methods other than <em>bruteforce</em> and <em>bruteforce.bs</em>, some additional tags and different settings may apply.</p>
-<p><strong>emulator</strong> would use additional tags:</p>
-<pre><code>  ...
+            <p>
+              If you are using methods other than <em>bruteforce</em> and
+              <em>bruteforce.bs</em>, some additional tags and different
+              settings may apply.
+            </p>
+            <p><strong>emulator</strong> would use additional tags:</p>
+            <pre><code>  ...
   &lt;method&gt;emulator&lt;/method&gt;
   &lt;n.knot&gt;20&lt;/n.knot&gt;
   &lt;GPpckg&gt;GPfit&lt;/GPpckg&gt;
@@ -276,19 +546,66 @@ <h2 class="hasAnchor">
   &lt;extension&gt;round&lt;/extension&gt;
   &lt;knot.par&gt;0.75&lt;/knot.par&gt;
   ...</code></pre>
-<ul>
-<li><p><code>&lt;n.knot&gt;</code> Specifies the number of locations in parameter space to be sampled by the Latin Hypercube design. These locations are where the model will actually be run. In other words the model will be run for <code>&lt;n.knots&gt;</code> times.</p></li>
-<li><p><code>&lt;GPpckg&gt;</code> Specifies which R package to use for fitting a Gaussian process to interpolate the likelihood surface in between the calculated values that are obtained from actual model runs. Current options are <code>kernlab</code> and <code>GPfit</code> (recommended).</p></li>
-<li><p><code>&lt;chain&gt;</code> Specifies the number of MCMC chains to be run.</p></li>
-<li>
-<p><code>&lt;extension&gt;</code> Specifies the extension type of additional emulator runs, should be skipped if this a first emulator run of its own. Otherwise it is possible to extend emulator PDA runs in two ways:</p>
-<ul>
-<li><p><code>&lt;extension&gt;longer&lt;/extension&gt;</code> using the same emulator, this extension run takes the MCMC sampling from where it was left in the previous emulator run and runs a longer MCMC chain.</p></li>
-<li><p><code>&lt;extension&gt;round&lt;/extension&gt;</code> this extension run proposes new points in the parameter space in addition to the previous ones, and builds a new emulator including these additional points for a new MCMC sampling. These new points can come from both your inital PDA prior and the posterior of your first round of emulator run. You can determine the percentage of new knots coming from the posterior of your previous run in the <code>&lt;knot.par&gt;</code> tag. If you leave it empty, 75% of your new points will be drawn from the posterior of your previous run by default.</p></li>
-</ul>
-</li>
-</ul>
-<pre><code>      &lt;file&gt;
+            <ul>
+              <li>
+                <p>
+                  <code>&lt;n.knot&gt;</code> Specifies the number of locations
+                  in parameter space to be sampled by the Latin Hypercube
+                  design. These locations are where the model will actually be
+                  run. In other words the model will be run for
+                  <code>&lt;n.knots&gt;</code> times.
+                </p>
+              </li>
+              <li>
+                <p>
+                  <code>&lt;GPpckg&gt;</code> Specifies which R package to use
+                  for fitting a Gaussian process to interpolate the likelihood
+                  surface in between the calculated values that are obtained
+                  from actual model runs. Current options are
+                  <code>kernlab</code> and <code>GPfit</code> (recommended).
+                </p>
+              </li>
+              <li>
+                <p>
+                  <code>&lt;chain&gt;</code> Specifies the number of MCMC chains
+                  to be run.
+                </p>
+              </li>
+              <li>
+                <p>
+                  <code>&lt;extension&gt;</code> Specifies the extension type of
+                  additional emulator runs, should be skipped if this a first
+                  emulator run of its own. Otherwise it is possible to extend
+                  emulator PDA runs in two ways:
+                </p>
+                <ul>
+                  <li>
+                    <p>
+                      <code>&lt;extension&gt;longer&lt;/extension&gt;</code>
+                      using the same emulator, this extension run takes the MCMC
+                      sampling from where it was left in the previous emulator
+                      run and runs a longer MCMC chain.
+                    </p>
+                  </li>
+                  <li>
+                    <p>
+                      <code>&lt;extension&gt;round&lt;/extension&gt;</code> this
+                      extension run proposes new points in the parameter space
+                      in addition to the previous ones, and builds a new
+                      emulator including these additional points for a new MCMC
+                      sampling. These new points can come from both your inital
+                      PDA prior and the posterior of your first round of
+                      emulator run. You can determine the percentage of new
+                      knots coming from the posterior of your previous run in
+                      the <code>&lt;knot.par&gt;</code> tag. If you leave it
+                      empty, 75% of your new points will be drawn from the
+                      posterior of your previous run by default.
+                    </p>
+                  </li>
+                </ul>
+              </li>
+            </ul>
+            <pre><code>      &lt;file&gt;
         &lt;input.id&gt;...&lt;/input.id&gt;
         &lt;path&gt;
           &lt;path&gt;...&lt;/path&gt;
@@ -301,36 +618,59 @@ <h2 class="hasAnchor">
         &lt;/variable.name&gt;
       &lt;/file&gt;
     &lt;/inputs&gt;</code></pre>
-<ul>
-<li>
-<code>&lt;ss.positive&gt;</code> When using the emulator, it is important to let the algorithm know that you have a likelihood whose sufficient statistics is zero bound.</li>
-</ul>
-<p><strong>bayesian.tools</strong> would look for sampler specific settings that can be passed through the pecan.xml as a block under the <code>&lt;bt.settings&gt;</code> tag. Currently, the available samplers in the BayesianTools package are:</p>
-<ul>
-<li>Metropolis
-<ul>
-<li>Standard MH-MCMC</li>
-<li>With pre-optimization</li>
-<li>Adaptive MCMC</li>
-<li>Delayed rejection</li>
-<li>Gibbs updating</li>
-</ul>
-</li>
-<li>M : Another implementation of standard MH-MCMC.</li>
-<li>AM : Adaptive Metropolis</li>
-<li>DR : Delayed Rejection</li>
-<li>DRAM : Delayed Rejection Adaptive Metropolis</li>
-<li>DE : Differential Evolution</li>
-<li>DEzs : Differential Evolution with a snooker updater</li>
-<li>DREAM : Differential Evolution Adaptive Metropolis</li>
-<li>DREAMzs : Differential Evolution Adaptive Metropolis with a snooker updater</li>
-<li>Twalk : “traverse” or “thoughtful” walk, a general purpose sampling algorithm</li>
-<li>SMC : Sequential Monte Carlo</li>
-</ul>
-<p>The name of the chosen sampler would be passed under <code>&lt;sampler&gt;</code> tag within the <code>&lt;bt.settings&gt;</code> block :</p>
-<p>It is not possible to use some of the samplers in this package for univariate cases. The ones that you can use for univariate cases are: “Metropolis”, “DE”, “DEzs” and “Twalk”.</p>
-<p>For Metropolis variations:</p>
-<pre><code>  ...
+            <ul>
+              <li>
+                <code>&lt;ss.positive&gt;</code> When using the emulator, it is
+                important to let the algorithm know that you have a likelihood
+                whose sufficient statistics is zero bound.
+              </li>
+            </ul>
+            <p>
+              <strong>bayesian.tools</strong> would look for sampler specific
+              settings that can be passed through the pecan.xml as a block under
+              the <code>&lt;bt.settings&gt;</code> tag. Currently, the available
+              samplers in the BayesianTools package are:
+            </p>
+            <ul>
+              <li>
+                Metropolis
+                <ul>
+                  <li>Standard MH-MCMC</li>
+                  <li>With pre-optimization</li>
+                  <li>Adaptive MCMC</li>
+                  <li>Delayed rejection</li>
+                  <li>Gibbs updating</li>
+                </ul>
+              </li>
+              <li>M : Another implementation of standard MH-MCMC.</li>
+              <li>AM : Adaptive Metropolis</li>
+              <li>DR : Delayed Rejection</li>
+              <li>DRAM : Delayed Rejection Adaptive Metropolis</li>
+              <li>DE : Differential Evolution</li>
+              <li>DEzs : Differential Evolution with a snooker updater</li>
+              <li>DREAM : Differential Evolution Adaptive Metropolis</li>
+              <li>
+                DREAMzs : Differential Evolution Adaptive Metropolis with a
+                snooker updater
+              </li>
+              <li>
+                Twalk : “traverse” or “thoughtful” walk, a general purpose
+                sampling algorithm
+              </li>
+              <li>SMC : Sequential Monte Carlo</li>
+            </ul>
+            <p>
+              The name of the chosen sampler would be passed under
+              <code>&lt;sampler&gt;</code> tag within the
+              <code>&lt;bt.settings&gt;</code> block :
+            </p>
+            <p>
+              It is not possible to use some of the samplers in this package for
+              univariate cases. The ones that you can use for univariate cases
+              are: “Metropolis”, “DE”, “DEzs” and “Twalk”.
+            </p>
+            <p>For Metropolis variations:</p>
+            <pre><code>  ...
   &lt;method&gt;bayesian.tools&lt;/method&gt;
   &lt;bt.settings&gt;
     &lt;iter&gt;10000&lt;/iter&gt;
@@ -341,38 +681,53 @@ <h2 class="hasAnchor">
     &lt;adaptationNotBefore&gt;500&lt;/adaptationNotBefore&gt;       &lt;-- set for Adaptive Metropolis
   &lt;/bt.settings&gt;
   ...</code></pre>
-<p>Some of the samplers are also restartable : “Metropolis”, “DE”, “DEzs”, “DREAM”, “DREAMzs”, “Twalk”</p>
-</div>
-  </div>
+            <p>
+              Some of the samplers are also restartable : “Metropolis”, “DE”,
+              “DEzs”, “DREAM”, “DREAMzs”, “Twalk”
+            </p>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#install-package-from-github">Install package from Github</a></li>
-      <li><a href="#parameter-data-assimilation-in-pecan">Parameter Data Assimilation in PEcAn</a></li>
-      <li><a href="#adding-pda-tags-to-pecan-xml">Adding PDA tags to pecan.xml</a></li>
-      <li><a href="#method-specific-settings">Method specific settings</a></li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#install-package-from-github"
+                  >Install package from Github</a
+                >
+              </li>
+              <li>
+                <a href="#parameter-data-assimilation-in-pecan"
+                  >Parameter Data Assimilation in PEcAn</a
+                >
+              </li>
+              <li>
+                <a href="#adding-pda-tags-to-pecan-xml"
+                  >Adding PDA tags to pecan.xml</a
+                >
+              </li>
+              <li>
+                <a href="#method-specific-settings">Method specific settings</a>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+          <p>Developed by .</p>
+        </div>
 
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<![endif]-->
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+    <meta charset="utf-8" />
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+    <title>Authors • PEcAn.assim.batch</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.assim.batch</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="index.html">
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-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/AssimBatchVignette.html">PEcAn.assim.batch Vignette</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.assim.batch</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/docsearch.css b/modules/assim.batch/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/assim.batch/docs/docsearch.css
+++ b/modules/assim.batch/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/assim.batch/docs/docsearch.js b/modules/assim.batch/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/assim.batch/docs/docsearch.js
+++ b/modules/assim.batch/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/assim.batch/docs/index.html b/modules/assim.batch/docs/index.html
index bd7e7eb..31f96dd 100644
--- a/modules/assim.batch/docs/index.html
+++ b/modules/assim.batch/docs/index.html
@@ -1,123 +1,189 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for ecological forecasts and reanalysis • PEcAn.assim.batch</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis •
+      PEcAn.assim.batch
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    efficacy of scientific investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.assim.batch</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/AssimBatchVignette.html">PEcAn.assim.batch Vignette</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.assim.batch</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/assim.batch/docs/pkgdown.css b/modules/assim.batch/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/assim.batch/docs/pkgdown.css
+++ b/modules/assim.batch/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
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 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/assim.batch/docs/pkgdown.js b/modules/assim.batch/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/assim.batch/docs/pkgdown.js
+++ b/modules/assim.batch/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/assim.batch/docs/reference/assim.batch.html b/modules/assim.batch/docs/reference/assim.batch.html
index 4ea8e39..aa36afd 100644
--- a/modules/assim.batch/docs/reference/assim.batch.html
+++ b/modules/assim.batch/docs/reference/assim.batch.html
@@ -2,165 +2,204 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Run Batch PDA — assim.batch • PEcAn.assim.batch</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Run Batch PDA — assim.batch" />
-
-<meta property="og:description" content="Run Batch PDA" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Run Batch PDA — assim.batch • PEcAn.assim.batch</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
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+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Run Batch PDA — assim.batch" />
+
+    <meta property="og:description" content="Run Batch PDA" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
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-      <span class="navbar-brand">
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-      </span>
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-        <li>
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-  </a>
-</li>
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-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/AssimBatchVignette.html">PEcAn.assim.batch Vignette</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
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-</div><!--/.navbar -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
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+                class="navbar-toggle collapsed"
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+                data-target="#navbar"
+              >
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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-    
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-    <tr>
-      <th>settings</th>
-      <td><p>a PEcAn settings list</p></td>
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-
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-      
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+      <div class="row">
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+          <div class="page-header">
+            <h1>Run Batch PDA</h1>
+
+            <div class="hidden name"><code>assim.batch.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Run Batch PDA</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>assim.batch</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>a PEcAn settings list</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Updated settings list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
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diff --git a/modules/assim.batch/docs/reference/autoburnin.html b/modules/assim.batch/docs/reference/autoburnin.html
index 85c86ee..8d65fd5 100644
--- a/modules/assim.batch/docs/reference/autoburnin.html
+++ b/modules/assim.batch/docs/reference/autoburnin.html
@@ -2,178 +2,235 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Automatically calculate and apply burnin value</h1>
-    
-    <div class="hidden name"><code>autoburnin.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Automatically calculate and apply burnin value</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>autoburnin</span>(<span class='no'>jags_out</span>, <span class='kw'>return.burnin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>jags_out</th>
-      <td><p>List of MCMC sample matrices or `mcmc.list` object</p></td>
-    </tr>
-    <tr>
-      <th>return.burnin</th>
-      <td><p>Logical. If `TRUE`, return burnin value in addition to 
-samples (as list). Default = FALSE.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional arguments for <code>getBurnin</code>, <code>gelman_diag_mw</code>, 
-and <code>gelman.diag</code>.</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Automatically calculate and apply burnin value</h1>
+
+            <div class="hidden name"><code>autoburnin.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Automatically calculate and apply burnin value</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>autoburnin</span>(<span class='no'>jags_out</span>, <span class='kw'>return.burnin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>jags_out</th>
+              <td><p>List of MCMC sample matrices or `mcmc.list` object</p></td>
+            </tr>
+            <tr>
+              <th>return.burnin</th>
+              <td>
+                <p>
+                  Logical. If `TRUE`, return burnin value in addition to samples
+                  (as list). Default = FALSE.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  Additional arguments for <code>getBurnin</code>,
+                  <code>gelman_diag_mw</code>, and <code>gelman.diag</code>.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
      <span class='no'>z1</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>coda</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/coda/topics/mcmc'>mcmc</a></span>(<span class='fu'>c</span>(<span class='fu'>rnorm</span>(<span class='fl'>2500</span>, <span class='fl'>5</span>), <span class='fu'>rnorm</span>(<span class='fl'>2500</span>, <span class='fl'>0</span>)))
      <span class='no'>z2</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>coda</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/coda/topics/mcmc'>mcmc</a></span>(<span class='fu'>c</span>(<span class='fu'>rnorm</span>(<span class='fl'>2500</span>, -<span class='fl'>5</span>), <span class='fu'>rnorm</span>(<span class='fl'>2500</span>, <span class='fl'>0</span>)))
      <span class='no'>z</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>coda</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/coda/topics/mcmc.list'>mcmc.list</a></span>(<span class='no'>z1</span>, <span class='no'>z2</span>)
      <span class='no'>z_burned</span> <span class='kw'>&lt;-</span> <span class='fu'>autoburnin</span>(<span class='no'>z</span>)
 <span class='co'># }</span></pre>
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze, Alexey Shiklomanov
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Michael Dietze, Alexey Shiklomanov
+        </div>
+      </div>
 
+      <footer>
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+          <p>Developed by .</p>
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diff --git a/modules/assim.batch/docs/reference/correlationPlot.html b/modules/assim.batch/docs/reference/correlationPlot.html
index cb8a13b..fed99a5 100644
--- a/modules/assim.batch/docs/reference/correlationPlot.html
+++ b/modules/assim.batch/docs/reference/correlationPlot.html
@@ -2,178 +2,233 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Flexible function to create correlation density plots</h1>
-    
-    <div class="hidden name"><code>correlationPlot.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Flexible function to create correlation density plots</h1>
 
-    <div class="ref-description">
-    
-    <p>numeric matrix or data.frame</p>
-    
-    </div>
+            <div class="hidden name"><code>correlationPlot.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>numeric matrix or data.frame</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>correlationPlot</span>(<span class='no'>mat</span>, <span class='kw'>density</span> <span class='kw'>=</span> <span class='st'>"smooth"</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>correlationPlot</span>(<span class='no'>mat</span>, <span class='kw'>density</span> <span class='kw'>=</span> <span class='st'>"smooth"</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
   <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"pearson"</span>, <span class='kw'>whichParameters</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mat</th>
-      <td><p>matrix or data frame of variables</p></td>
-    </tr>
-    <tr>
-      <th>density</th>
-      <td><p>type of plot to do</p></td>
-    </tr>
-    <tr>
-      <th>thin</th>
-      <td><p>thinning of the matrix to make things faster. Default is to thin to 5000</p></td>
-    </tr>
-    <tr>
-      <th>method</th>
-      <td><p>method for calculating correlations</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
-    <p>The code for the correlation density plot originates from Hartig, F.; Dislich, C.; Wiegand, T. &amp; Huth, A. (2014) Technical Note: Approximate Bayesian parameterization of a process-based tropical forest model. Biogeosciences, 11, 1261-1272.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#references">References</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mat</th>
+              <td><p>matrix or data frame of variables</p></td>
+            </tr>
+            <tr>
+              <th>density</th>
+              <td><p>type of plot to do</p></td>
+            </tr>
+            <tr>
+              <th>thin</th>
+              <td>
+                <p>
+                  thinning of the matrix to make things faster. Default is to
+                  thin to 5000
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>method</th>
+              <td><p>method for calculating correlations</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="references">
+            <a class="anchor" href="#references"></a>References
+          </h2>
+
+          <p>
+            The code for the correlation density plot originates from Hartig,
+            F.; Dislich, C.; Wiegand, T. &amp; Huth, A. (2014) Technical Note:
+            Approximate Bayesian parameterization of a process-based tropical
+            forest model. Biogeosciences, 11, 1261-1272.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#references">References</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Florian Hartig
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Florian Hartig
+        </div>
+      </div>
 
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diff --git a/modules/assim.batch/docs/reference/gelman_diag_gelmanPlot.html b/modules/assim.batch/docs/reference/gelman_diag_gelmanPlot.html
index 9073adb..6bd8869 100644
--- a/modules/assim.batch/docs/reference/gelman_diag_gelmanPlot.html
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate Gelman Diagnostic using coda::gelman.plot</h1>
-    
-    <div class="hidden name"><code>gelman_diag_gelmanPlot.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculates Gelman diagnostic cumulatively. This is a much 
-more conservative approach than the moving-window method.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>gelman_diag_gelmanPlot</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-        
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate Gelman Diagnostic using coda::gelman.plot</h1>
+
+            <div class="hidden name">
+              <code>gelman_diag_gelmanPlot.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Calculates Gelman diagnostic cumulatively. This is a much more
+              conservative approach than the moving-window method.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>gelman_diag_gelmanPlot</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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diff --git a/modules/assim.batch/docs/reference/gelman_diag_mw.html b/modules/assim.batch/docs/reference/gelman_diag_mw.html
index 1f68e16..3074e97 100644
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate Gelman diagnostic on moving window</h1>
-    
-    <div class="hidden name"><code>gelman_diag_mw.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate Gelman diagnostic on moving window</h1>
 
-    <div class="ref-description">
-    
-    <p>Calculate Gelman diagnostic on moving window</p>
-    
-    </div>
+            <div class="hidden name"><code>gelman_diag_mw.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate Gelman diagnostic on moving window</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>gelman_diag_mw</span>(<span class='no'>x</span>, <span class='kw'>width_fraction</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fu'>ceiling</span>(<span class='kw pkg'>coda</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/coda/topics/nchain'>niter</a></span>(<span class='no'>x</span>)
+          <pre
+            class="usage"
+          ><span class='fu'>gelman_diag_mw</span>(<span class='no'>x</span>, <span class='kw'>width_fraction</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fu'>ceiling</span>(<span class='kw pkg'>coda</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/coda/topics/nchain'>niter</a></span>(<span class='no'>x</span>)
   * <span class='no'>width_fraction</span>), <span class='kw'>njump</span> <span class='kw'>=</span> <span class='fl'>50</span>, <span class='kw'>include.mpsrf</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>MCMC samples, of class <code>mcmc</code> or <code>mcmc.list</code></p></td>
-    </tr>
-    <tr>
-      <th>width_fraction</th>
-      <td><p>Fractional width of moving window. Default=0.1.</p></td>
-    </tr>
-    <tr>
-      <th>width</th>
-      <td><p>Width of moving window. Default is niter(x)*width_fraction</p></td>
-    </tr>
-    <tr>
-      <th>njump</th>
-      <td><p>Number of windows to calculate over</p></td>
-    </tr>
-    <tr>
-      <th>include.mpsrf</th>
-      <td><p>Whether to calculate multivariate PSRF and include in output (default = FALSE).</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Gelman Diagnostic 3D array. First dim -- mean (1) and 95<!-- % confidence (2). Second dim -- iteration --></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td>
+                <p>
+                  MCMC samples, of class <code>mcmc</code> or
+                  <code>mcmc.list</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>width_fraction</th>
+              <td><p>Fractional width of moving window. Default=0.1.</p></td>
+            </tr>
+            <tr>
+              <th>width</th>
+              <td>
+                <p>
+                  Width of moving window. Default is niter(x)*width_fraction
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>njump</th>
+              <td><p>Number of windows to calculate over</p></td>
+            </tr>
+            <tr>
+              <th>include.mpsrf</th>
+              <td>
+                <p>
+                  Whether to calculate multivariate PSRF and include in output
+                  (default = FALSE).
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Gelman Diagnostic 3D array. First dim -- mean (1) and 95<!-- % confidence (2). Second dim -- iteration -->
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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diff --git a/modules/assim.batch/docs/reference/getBurnin.html b/modules/assim.batch/docs/reference/getBurnin.html
index c3bd945..14698a3 100644
--- a/modules/assim.batch/docs/reference/getBurnin.html
+++ b/modules/assim.batch/docs/reference/getBurnin.html
@@ -2,193 +2,247 @@
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+                        >PEcAn.assim.batch Vignette</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate burnin value</h1>
-    
-    <div class="hidden name"><code>getBurnin.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate burnin value</h1>
 
-    <div class="ref-description">
-    
-    <p>Automatically detect burnin based on one of several methods.</p>
-    
-    </div>
+            <div class="hidden name"><code>getBurnin.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Automatically detect burnin based on one of several methods.</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>getBurnin</span>(<span class='no'>jags_out</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.1</span>, <span class='kw'>use.confidence</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>getBurnin</span>(<span class='no'>jags_out</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.1</span>, <span class='kw'>use.confidence</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"moving.window"</span>, <span class='kw'>plotfile</span> <span class='kw'>=</span> <span class='st'>"/dev/null"</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>jags_out</th>
-      <td><p>List of MCMC sample matrices or `mcmc.list` object</p></td>
-    </tr>
-    <tr>
-      <th>threshold</th>
-      <td><p>Maximum value of Gelman diagnostic</p></td>
-    </tr>
-    <tr>
-      <th>use.confidence</th>
-      <td><p>Logical. If TRUE (default), use 95<!-- % confidence  -->
-interval for Gelman Diagnostic. If FALSE, use the point estimate.</p></td>
-    </tr>
-    <tr>
-      <th>method</th>
-      <td><p>Character string indicating method. Options are 
-"moving.window" (default) or "gelman.plot".</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Other parameters to methods</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>See "gelman_diag_mw" and "gelman_diag_gelmanPlot"</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>jags_out</th>
+              <td><p>List of MCMC sample matrices or `mcmc.list` object</p></td>
+            </tr>
+            <tr>
+              <th>threshold</th>
+              <td><p>Maximum value of Gelman diagnostic</p></td>
+            </tr>
+            <tr>
+              <th>use.confidence</th>
+              <td>
+                <p>
+                  Logical. If TRUE (default), use 95<!-- % confidence  -->
+                  interval for Gelman Diagnostic. If FALSE, use the point
+                  estimate.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>method</th>
+              <td>
+                <p>
+                  Character string indicating method. Options are
+                  "moving.window" (default) or "gelman.plot".
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>Other parameters to methods</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>See "gelman_diag_mw" and "gelman_diag_gelmanPlot"</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
      <span class='no'>z1</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>coda</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/coda/topics/mcmc'>mcmc</a></span>(<span class='fu'>c</span>(<span class='fu'>rnorm</span>(<span class='fl'>2500</span>, <span class='fl'>5</span>), <span class='fu'>rnorm</span>(<span class='fl'>2500</span>, <span class='fl'>0</span>)))
      <span class='no'>z2</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>coda</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/coda/topics/mcmc'>mcmc</a></span>(<span class='fu'>c</span>(<span class='fu'>rnorm</span>(<span class='fl'>2500</span>, -<span class='fl'>5</span>), <span class='fu'>rnorm</span>(<span class='fl'>2500</span>, <span class='fl'>0</span>)))
      <span class='no'>z</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>coda</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/coda/topics/mcmc.list'>mcmc.list</a></span>(<span class='no'>z1</span>, <span class='no'>z2</span>)
      <span class='no'>burnin</span> <span class='kw'>&lt;-</span> <span class='fu'>getBurnin</span>(<span class='no'>z</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.05</span>)
 <span class='co'># }</span></pre>
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-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov, Michael Dietze
-
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+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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-      <col class="title" />
-    </colgroup>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="assim.batch.html">assim.batch()</a></code> </p>
-        </td>
-        <td><p>Run Batch PDA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="autoburnin.html">autoburnin()</a></code> </p>
-        </td>
-        <td><p>Automatically calculate and apply burnin value</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="correlationPlot.html">correlationPlot()</a></code> </p>
-        </td>
-        <td><p>Flexible function to create correlation density plots</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="gelman_diag_gelmanPlot.html">gelman_diag_gelmanPlot()</a></code> </p>
-        </td>
-        <td><p>Calculate Gelman Diagnostic using coda::gelman.plot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="gelman_diag_mw.html">gelman_diag_mw()</a></code> </p>
-        </td>
-        <td><p>Calculate Gelman diagnostic on moving window</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="getBurnin.html">getBurnin()</a></code> </p>
-        </td>
-        <td><p>Calculate burnin value</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load.pda.data.html">load.L2Ameriflux.cf()</a></code> <code><a href="load.pda.data.html">load.pda.data()</a></code> </p>
-        </td>
-        <td><p>Load Ameriflux L2 Data From NetCDF</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="makeMCMCList.html">makeMCMCList()</a></code> </p>
-        </td>
-        <td><p>Make MCMC list from samples list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.adjust.jumps.html">pda.adjust.jumps()</a></code> </p>
-        </td>
-        <td><p>Adjust PDA MCMC jump size</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.adjust.jumps.bs.html">pda.adjust.jumps.bs()</a></code> </p>
-        </td>
-        <td><p>Adjust PDA block MCMC jump size</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.autocorr.calc.html">pda.autocorr.calc()</a></code> </p>
-        </td>
-        <td><p>autocorrelation correction</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.bayesian.tools.html">pda.bayesian.tools()</a></code> </p>
-        </td>
-        <td><p>Paramater Data Assimilation using BayesianTools</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.calc.error.html">pda.calc.error()</a></code> </p>
-        </td>
-        <td><p>Calculate sufficient statistics</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.calc.llik.html">pda.calc.llik()</a></code> </p>
-        </td>
-        <td><p>Calculate Likelihoods for PDA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.calc.llik.par.html">pda.calc.llik.par()</a></code> </p>
-        </td>
-        <td><p>pda.calc.llik.par</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.create.btprior.html">pda.create.btprior()</a></code> </p>
-        </td>
-        <td><p>Create priors for BayesianTools</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.create.ensemble.html">pda.create.ensemble()</a></code> </p>
-        </td>
-        <td><p>Create ensemble record for PDA ensemble</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.define.llik.fn.html">pda.define.llik.fn()</a></code> </p>
-        </td>
-        <td><p>Define PDA Likelihood Functions</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.define.prior.fn.html">pda.define.prior.fn()</a></code> </p>
-        </td>
-        <td><p>Define PDA Prior Functions</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.emulator.html">pda.emulator()</a></code> </p>
-        </td>
-        <td><p>Paramater Data Assimilation using emulator</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.generate.knots.html">pda.generate.knots()</a></code> </p>
-        </td>
-        <td><p>Generate Parameter Knots for PDA Emulator</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.generate.sf.html">pda.generate.sf()</a></code> </p>
-        </td>
-        <td><p>Generate scaling factor knots for PDA Emulator</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.get.model.output.html">pda.get.model.output()</a></code> </p>
-        </td>
-        <td><p>Get Model Output for PDA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.init.params.html">pda.init.params()</a></code> </p>
-        </td>
-        <td><p>Initialise Parameter Matrix for PDA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.init.run.html">pda.init.run()</a></code> </p>
-        </td>
-        <td><p>Initialise Model Runs for PDA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.load.priors.html">pda.load.priors()</a></code> </p>
-        </td>
-        <td><p>Load Priors for Paramater Data Assimilation</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.mcmc.html">pda.mcmc()</a></code> </p>
-        </td>
-        <td><p>Paramater Data Assimilation using MCMC</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.mcmc.bs.html">pda.mcmc.bs()</a></code> </p>
-        </td>
-        <td><p>Paramater Data Assimilation using MCMC</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.mcmc.recover.html">pda.mcmc.recover()</a></code> </p>
-        </td>
-        <td><p>Clean up a failed PDA run</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.neff.calc.html">pda.neff.calc()</a></code> </p>
-        </td>
-        <td><p>Calculate N_eff</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.plot.params.html">pda.plot.params()</a></code> </p>
-        </td>
-        <td><p>Plot PDA Parameter Diagnostics</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.postprocess.html">pda.postprocess()</a></code> </p>
-        </td>
-        <td><p>Postprocessing for PDA Results</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.settings.html">pda.settings()</a></code> </p>
-        </td>
-        <td><p>Set PDA Settings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pda.settings.bt.html">pda.settings.bt()</a></code> </p>
-        </td>
-        <td><p>Apply settings for BayesianTools</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="return.bias.html">return.bias()</a></code> </p>
-        </td>
-        <td><p>return.bias</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="return_hyperpars.html">return_hyperpars()</a></code> </p>
-        </td>
-        <td><p>return_hyperpars</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sample_MCMC.html">sample_MCMC()</a></code> </p>
-        </td>
-        <td><p>Helper function to sample from previous MCMC chain while proposing new knots</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_sf_posterior.html">write_sf_posterior()</a></code> </p>
-        </td>
-        <td><p>Function to write posterior distributions of the scaling factors</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="assim.batch.html">assim.batch()</a></code>
+                  </p>
+                </td>
+                <td><p>Run Batch PDA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="autoburnin.html">autoburnin()</a></code>
+                  </p>
+                </td>
+                <td><p>Automatically calculate and apply burnin value</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="correlationPlot.html"
+                        >correlationPlot()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Flexible function to create correlation density plots</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="gelman_diag_gelmanPlot.html"
+                        >gelman_diag_gelmanPlot()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Calculate Gelman Diagnostic using coda::gelman.plot</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="gelman_diag_mw.html">gelman_diag_mw()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Calculate Gelman diagnostic on moving window</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="getBurnin.html">getBurnin()</a></code>
+                  </p>
+                </td>
+                <td><p>Calculate burnin value</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="load.pda.data.html"
+                        >load.L2Ameriflux.cf()</a
+                      ></code
+                    >
+                    <code
+                      ><a href="load.pda.data.html">load.pda.data()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Load Ameriflux L2 Data From NetCDF</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="makeMCMCList.html">makeMCMCList()</a></code>
+                  </p>
+                </td>
+                <td><p>Make MCMC list from samples list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.adjust.jumps.html"
+                        >pda.adjust.jumps()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Adjust PDA MCMC jump size</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.adjust.jumps.bs.html"
+                        >pda.adjust.jumps.bs()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Adjust PDA block MCMC jump size</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.autocorr.calc.html"
+                        >pda.autocorr.calc()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>autocorrelation correction</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.bayesian.tools.html"
+                        >pda.bayesian.tools()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Paramater Data Assimilation using BayesianTools</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.calc.error.html">pda.calc.error()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Calculate sufficient statistics</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.calc.llik.html">pda.calc.llik()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Calculate Likelihoods for PDA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.calc.llik.par.html"
+                        >pda.calc.llik.par()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>pda.calc.llik.par</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.create.btprior.html"
+                        >pda.create.btprior()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create priors for BayesianTools</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.create.ensemble.html"
+                        >pda.create.ensemble()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create ensemble record for PDA ensemble</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.define.llik.fn.html"
+                        >pda.define.llik.fn()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Define PDA Likelihood Functions</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.define.prior.fn.html"
+                        >pda.define.prior.fn()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Define PDA Prior Functions</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pda.emulator.html">pda.emulator()</a></code>
+                  </p>
+                </td>
+                <td><p>Paramater Data Assimilation using emulator</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.generate.knots.html"
+                        >pda.generate.knots()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Generate Parameter Knots for PDA Emulator</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.generate.sf.html"
+                        >pda.generate.sf()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Generate scaling factor knots for PDA Emulator</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.get.model.output.html"
+                        >pda.get.model.output()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get Model Output for PDA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.init.params.html"
+                        >pda.init.params()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Initialise Parameter Matrix for PDA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pda.init.run.html">pda.init.run()</a></code>
+                  </p>
+                </td>
+                <td><p>Initialise Model Runs for PDA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.load.priors.html"
+                        >pda.load.priors()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Load Priors for Paramater Data Assimilation</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pda.mcmc.html">pda.mcmc()</a></code>
+                  </p>
+                </td>
+                <td><p>Paramater Data Assimilation using MCMC</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pda.mcmc.bs.html">pda.mcmc.bs()</a></code>
+                  </p>
+                </td>
+                <td><p>Paramater Data Assimilation using MCMC</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.mcmc.recover.html"
+                        >pda.mcmc.recover()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Clean up a failed PDA run</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.neff.calc.html">pda.neff.calc()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Calculate N_eff</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.plot.params.html"
+                        >pda.plot.params()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Plot PDA Parameter Diagnostics</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.postprocess.html"
+                        >pda.postprocess()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Postprocessing for PDA Results</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pda.settings.html">pda.settings()</a></code>
+                  </p>
+                </td>
+                <td><p>Set PDA Settings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pda.settings.bt.html"
+                        >pda.settings.bt()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Apply settings for BayesianTools</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="return.bias.html">return.bias()</a></code>
+                  </p>
+                </td>
+                <td><p>return.bias</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="return_hyperpars.html"
+                        >return_hyperpars()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>return_hyperpars</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sample_MCMC.html">sample_MCMC()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Helper function to sample from previous MCMC chain while
+                    proposing new knots
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write_sf_posterior.html"
+                        >write_sf_posterior()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function to write posterior distributions of the scaling
+                    factors
+                  </p>
+                </td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/reference/load.pda.data.html b/modules/assim.batch/docs/reference/load.pda.data.html
index 9e8808f..38d13ff 100644
--- a/modules/assim.batch/docs/reference/load.pda.data.html
+++ b/modules/assim.batch/docs/reference/load.pda.data.html
@@ -2,176 +2,221 @@
 <!DOCTYPE html>
 <html>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Load Ameriflux L2 Data From NetCDF</h1>
-    
-    <div class="hidden name"><code>load.pda.data.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Load Ameriflux L2 Data From NetCDF</h1>
 
-    <div class="ref-description">
-    
-    <p>Load Ameriflux L2 Data From NetCDF</p>
-<p>Load Dataset for Paramater Data Assimilation</p>
-    
-    </div>
+            <div class="hidden name"><code>load.pda.data.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>load.L2Ameriflux.cf</span>(<span class='no'>file.in</span>)
+          <div class="ref-description">
+            <p>Load Ameriflux L2 Data From NetCDF</p>
+            <p>Load Dataset for Paramater Data Assimilation</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load.L2Ameriflux.cf</span>(<span class='no'>file.in</span>)
 
 <span class='fu'>load.pda.data</span>(<span class='no'>settings</span>, <span class='no'>bety</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>file.in</th>
-      <td><p>= the netcdf file of L2 data</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>= PEcAn settings list</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A data frame of all variables in the netcdf</p>
-<p>A list containg the loaded input data, plus metadata</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>file.in</th>
+              <td><p>= the netcdf file of L2 data</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>= PEcAn settings list</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>A data frame of all variables in the netcdf</p>
+          <p>A list containg the loaded input data, plus metadata</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
 
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
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index db783e6..ab3f1d5 100644
--- a/modules/assim.batch/docs/reference/makeMCMCList.html
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+                  <a href="../reference/index.html">Reference</a>
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Make MCMC list from samples list</h1>
-    
-    <div class="hidden name"><code>makeMCMCList.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Make MCMC list from samples list</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>makeMCMCList</span>(<span class='no'>samps</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>samps</th>
-      <td><p>samples list (output from invert.custom)</p></td>
-    </tr>
-    </table>
-    
-
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Make MCMC list from samples list</h1>
+
+            <div class="hidden name"><code>makeMCMCList.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Make MCMC list from samples list</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>makeMCMCList</span>(<span class='no'>samps</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>samps</th>
+              <td><p>samples list (output from invert.custom)</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+          <p>Developed by .</p>
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diff --git a/modules/assim.batch/docs/reference/pda.adjust.jumps.bs.html b/modules/assim.batch/docs/reference/pda.adjust.jumps.bs.html
index e4399d8..fabdfd2 100644
--- a/modules/assim.batch/docs/reference/pda.adjust.jumps.bs.html
+++ b/modules/assim.batch/docs/reference/pda.adjust.jumps.bs.html
@@ -2,165 +2,216 @@
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+    </title>
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+    ></script>
+
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+                        >PEcAn.assim.batch Vignette</a
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Adjust PDA block MCMC jump size</h1>
-    
-    <div class="hidden name"><code>pda.adjust.jumps.bs.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Adjust PDA blcok MCMC jump size</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.adjust.jumps.bs</span>(<span class='no'>settings</span>, <span class='no'>jcov</span>, <span class='no'>accept.count</span>, <span class='no'>params.recent</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A PEcAn settings list updated to reflect adjusted jump distributions</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Adjust PDA block MCMC jump size</h1>
+
+            <div class="hidden name"><code>pda.adjust.jumps.bs.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Adjust PDA blcok MCMC jump size</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.adjust.jumps.bs</span>(<span class='no'>settings</span>, <span class='no'>jcov</span>, <span class='no'>accept.count</span>, <span class='no'>params.recent</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A PEcAn settings list updated to reflect adjusted jump distributions
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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       </footer>
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 </html>
-
diff --git a/modules/assim.batch/docs/reference/pda.adjust.jumps.html b/modules/assim.batch/docs/reference/pda.adjust.jumps.html
index 320220f..be7d49e 100644
--- a/modules/assim.batch/docs/reference/pda.adjust.jumps.html
+++ b/modules/assim.batch/docs/reference/pda.adjust.jumps.html
@@ -2,165 +2,216 @@
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Adjust PDA MCMC jump size</h1>
-    
-    <div class="hidden name"><code>pda.adjust.jumps.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Adjust PDA MCMC jump size</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.adjust.jumps</span>(<span class='no'>settings</span>, <span class='no'>jmp.list</span>, <span class='no'>accept.rate</span>, <span class='kw'>pnames</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A PEcAn settings list updated to reflect adjusted jump distributions</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Adjust PDA MCMC jump size</h1>
+
+            <div class="hidden name"><code>pda.adjust.jumps.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Adjust PDA MCMC jump size</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.adjust.jumps</span>(<span class='no'>settings</span>, <span class='no'>jmp.list</span>, <span class='no'>accept.rate</span>, <span class='kw'>pnames</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A PEcAn settings list updated to reflect adjusted jump distributions
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
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index 4a0db66..bcb44ee 100644
--- a/modules/assim.batch/docs/reference/pda.autocorr.calc.html
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+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
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+                        >PEcAn.assim.batch Vignette</a
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>autocorrelation correction</h1>
-    
-    <div class="hidden name"><code>pda.autocorr.calc.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>autocorrelation correction</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.autocorr.calc</span>(<span class='no'>input</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"heteroskedastic.laplacian"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>input</th>
-      <td><p>list that contains time-series data vector and parameters for heteroskedastic.laplacian</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>data model type, for flux data heteroskedastic laplacian, normal is an example</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>rho AR(1)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>autocorrelation correction</h1>
+
+            <div class="hidden name"><code>pda.autocorr.calc.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>autocorrelation correction</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.autocorr.calc</span>(<span class='no'>input</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"heteroskedastic.laplacian"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>input</th>
+              <td>
+                <p>
+                  list that contains time-series data vector and parameters for
+                  heteroskedastic.laplacian
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td>
+                <p>
+                  data model type, for flux data heteroskedastic laplacian,
+                  normal is an example
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>rho AR(1)</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
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diff --git a/modules/assim.batch/docs/reference/pda.bayesian.tools.html b/modules/assim.batch/docs/reference/pda.bayesian.tools.html
index dbb75f6..18694d2 100644
--- a/modules/assim.batch/docs/reference/pda.bayesian.tools.html
+++ b/modules/assim.batch/docs/reference/pda.bayesian.tools.html
@@ -2,170 +2,218 @@
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+      PEcAn.assim.batch
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+                        >PEcAn.assim.batch Vignette</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Paramater Data Assimilation using BayesianTools</h1>
-    
-    <div class="hidden name"><code>pda.bayesian.tools.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Paramater Data Assimilation using BayesianTools</h1>
 
-    <div class="ref-description">
-    
-    <p>Paramater Data Assimilation using BayesianTools R Package</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.bayesian.tools.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.bayesian.tools</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>Paramater Data Assimilation using BayesianTools R Package</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.bayesian.tools</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>prior.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>chain</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>iter</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>adapt</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>adj.min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>ar.target</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>jvar</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n.knot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>= a pecan settings list</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing. Diagnostic plots, MCMC samples, and posterior distributions
- are saved as files and db records.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>= a pecan settings list</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            nothing. Diagnostic plots, MCMC samples, and posterior distributions
+            are saved as files and db records.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
 
-Istem Fer, Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze Istem Fer, Ryan Kelly
+        </div>
+      </div>
 
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diff --git a/modules/assim.batch/docs/reference/pda.calc.error.html b/modules/assim.batch/docs/reference/pda.calc.error.html
index 0792468..1c96d69 100644
--- a/modules/assim.batch/docs/reference/pda.calc.error.html
+++ b/modules/assim.batch/docs/reference/pda.calc.error.html
@@ -2,177 +2,221 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate sufficient statistics</h1>
-    
-    <div class="hidden name"><code>pda.calc.error.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate sufficient statistics</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.calc.error</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='no'>model_out</span>, <span class='no'>run.id</span>, <span class='no'>inputs</span>, <span class='no'>bias.terms</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>model_out</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>inputs</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>bias.terms</th>
-      <td><p>matrix</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>pda.errors</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate sufficient statistics</h1>
+
+            <div class="hidden name"><code>pda.calc.error.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate sufficient statistics</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.calc.error</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='no'>model_out</span>, <span class='no'>run.id</span>, <span class='no'>inputs</span>, <span class='no'>bias.terms</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>model_out</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>inputs</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>bias.terms</th>
+              <td><p>matrix</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>pda.errors</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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 </html>
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diff --git a/modules/assim.batch/docs/reference/pda.calc.llik.html b/modules/assim.batch/docs/reference/pda.calc.llik.html
index 12ff0de..aa806f3 100644
--- a/modules/assim.batch/docs/reference/pda.calc.llik.html
+++ b/modules/assim.batch/docs/reference/pda.calc.llik.html
@@ -2,165 +2,216 @@
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+    />
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+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+            <div id="navbar" class="navbar-collapse collapse">
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+                    <li>
+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
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+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate Likelihoods for PDA</h1>
-    
-    <div class="hidden name"><code>pda.calc.llik.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate Likelihoods for PDA</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.calc.llik</span>(<span class='no'>pda.errors</span>, <span class='no'>llik.fn</span>, <span class='no'>llik.par</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Total log likelihood (i.e., sum of log likelihoods for each dataset)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate Likelihoods for PDA</h1>
+
+            <div class="hidden name"><code>pda.calc.llik.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate Likelihoods for PDA</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.calc.llik</span>(<span class='no'>pda.errors</span>, <span class='no'>llik.fn</span>, <span class='no'>llik.par</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Total log likelihood (i.e., sum of log likelihoods for each dataset)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
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-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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       </footer>
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diff --git a/modules/assim.batch/docs/reference/pda.calc.llik.par.html b/modules/assim.batch/docs/reference/pda.calc.llik.par.html
index 777078b..c4cb0dd 100644
--- a/modules/assim.batch/docs/reference/pda.calc.llik.par.html
+++ b/modules/assim.batch/docs/reference/pda.calc.llik.par.html
@@ -2,171 +2,208 @@
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-    
-    <div class="hidden name"><code>pda.calc.llik.par.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate likelihood parameters</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.calc.llik.par</span>(<span class='no'>settings</span>, <span class='no'>n</span>, <span class='no'>error.stats</span>, <span class='no'>hyper.pars</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>named vector, sample sizes of inputs</p></td>
-    </tr>
-    <tr>
-      <th>error.stats</th>
-      <td><p>list, Sufficient Statistics</p></td>
-    </tr>
-    <tr>
-      <th>hyper.pars</th>
-      <td><p>list, hyperparameters</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>pda.calc.llik.par</h1>
+
+            <div class="hidden name"><code>pda.calc.llik.par.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate likelihood parameters</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.calc.llik.par</span>(<span class='no'>settings</span>, <span class='no'>n</span>, <span class='no'>error.stats</span>, <span class='no'>hyper.pars</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td><p>named vector, sample sizes of inputs</p></td>
+            </tr>
+            <tr>
+              <th>error.stats</th>
+              <td><p>list, Sufficient Statistics</p></td>
+            </tr>
+            <tr>
+              <th>hyper.pars</th>
+              <td><p>list, hyperparameters</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
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index b4dc2da..09cef9e 100644
--- a/modules/assim.batch/docs/reference/pda.create.btprior.html
+++ b/modules/assim.batch/docs/reference/pda.create.btprior.html
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create priors for BayesianTools</h1>
-    
-    <div class="hidden name"><code>pda.create.btprior.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Helper function for creating log-priors compatible with BayesianTools package</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.create.btprior</span>(<span class='no'>prior.sel</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>prior.sel</th>
-      <td><p>`data.frame` containing prior distributions of the selected parameters</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>out Prior class object for BayesianTools package</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>`prior.sel` must contain the following columns:
-  * `distn` -- String describing a distribution; e.g. `norm` for `dnorm`, `rnorm`, etc.
-  * `parama`, `paramb` -- First and second parameters, respectively, of the corresponding distribution</p>
-<p>Optionally, `prior.sel` may also contain the following columns:
-  * `param_name` -- Parameter name, which will be carried through to the prior object and sampler
-  * `lower`, `upper` -- Lower and upper bounds, respectively. These can be leveraged by the BayesianTools samplers.
-  * `best` -- Best guess for a parameter estimate. BayesianTools can also use this, though I'm not sure how...</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create priors for BayesianTools</h1>
+
+            <div class="hidden name"><code>pda.create.btprior.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Helper function for creating log-priors compatible with
+              BayesianTools package
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.create.btprior</span>(<span class='no'>prior.sel</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>prior.sel</th>
+              <td>
+                <p>
+                  `data.frame` containing prior distributions of the selected
+                  parameters
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>out Prior class object for BayesianTools package</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            `prior.sel` must contain the following columns: * `distn` -- String
+            describing a distribution; e.g. `norm` for `dnorm`, `rnorm`, etc. *
+            `parama`, `paramb` -- First and second parameters, respectively, of
+            the corresponding distribution
+          </p>
+          <p>
+            Optionally, `prior.sel` may also contain the following columns: *
+            `param_name` -- Parameter name, which will be carried through to the
+            prior object and sampler * `lower`, `upper` -- Lower and upper
+            bounds, respectively. These can be leveraged by the BayesianTools
+            samplers. * `best` -- Best guess for a parameter estimate.
+            BayesianTools can also use this, though I'm not sure how...
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer, Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer, Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/assim.batch/docs/reference/pda.create.ensemble.html b/modules/assim.batch/docs/reference/pda.create.ensemble.html
index 93e5594..905f4a1 100644
--- a/modules/assim.batch/docs/reference/pda.create.ensemble.html
+++ b/modules/assim.batch/docs/reference/pda.create.ensemble.html
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create ensemble record for PDA ensemble</h1>
-    
-    <div class="hidden name"><code>pda.create.ensemble.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Create PDA Ensemble</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.create.ensemble</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='no'>workflow.id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Ensemble ID of the created ensemble</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create ensemble record for PDA ensemble</h1>
+
+            <div class="hidden name"><code>pda.create.ensemble.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Create PDA Ensemble</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.create.ensemble</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='no'>workflow.id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Ensemble ID of the created ensemble</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
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+        </div>
+
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diff --git a/modules/assim.batch/docs/reference/pda.define.llik.fn.html b/modules/assim.batch/docs/reference/pda.define.llik.fn.html
index 3a9c1fd..83667e6 100644
--- a/modules/assim.batch/docs/reference/pda.define.llik.fn.html
+++ b/modules/assim.batch/docs/reference/pda.define.llik.fn.html
@@ -2,165 +2,217 @@
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Define PDA Likelihood Functions</h1>
-    
-    <div class="hidden name"><code>pda.define.llik.fn.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Define PDA Likelihood Functions</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.define.llik.fn</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>List of likelihood functions, one for each dataset to be assimilated against.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Define PDA Likelihood Functions</h1>
+
+            <div class="hidden name"><code>pda.define.llik.fn.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Define PDA Likelihood Functions</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.define.llik.fn</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            List of likelihood functions, one for each dataset to be assimilated
+            against.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
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index 5f52e79..fd8fbd3 100644
--- a/modules/assim.batch/docs/reference/pda.define.prior.fn.html
+++ b/modules/assim.batch/docs/reference/pda.define.prior.fn.html
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Define PDA Prior Functions</h1>
-    
-    <div class="hidden name"><code>pda.define.prior.fn.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Define PDA Prior Functions</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.define.prior.fn</span>(<span class='no'>prior</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>List of prior functions containing dprior, rprior, qprior, dmvprior, rmvprior.
-        Each of these is a list with one distribution function per parameter.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Define PDA Prior Functions</h1>
+
+            <div class="hidden name"><code>pda.define.prior.fn.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Define PDA Prior Functions</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.define.prior.fn</span>(<span class='no'>prior</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            List of prior functions containing dprior, rprior, qprior, dmvprior,
+            rmvprior. Each of these is a list with one distribution function per
+            parameter.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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   </body>
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-
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index 3eb52d4..bb638d1 100644
--- a/modules/assim.batch/docs/reference/pda.emulator.html
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@@ -2,179 +2,227 @@
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+                        >PEcAn.assim.batch Vignette</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Paramater Data Assimilation using emulator</h1>
-    
-    <div class="hidden name"><code>pda.emulator.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Paramater Data Assimilation using emulator</h1>
 
-    <div class="ref-description">
-    
-    <p>Paramater Data Assimilation using emulator</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.emulator.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.emulator</span>(<span class='no'>settings</span>, <span class='kw'>external.data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>external.priors</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>Paramater Data Assimilation using emulator</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.emulator</span>(<span class='no'>settings</span>, <span class='kw'>external.data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>external.priors</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>prior.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>chain</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>iter</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>adapt</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>adj.min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>ar.target</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>jvar</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n.knot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>= a pecan settings list</p></td>
-    </tr>
-    <tr>
-      <th>external.data</th>
-      <td><p>= list of inputs</p></td>
-    </tr>
-    <tr>
-      <th>external.priors</th>
-      <td><p>= list or priors</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing. Diagnostic plots, MCMC samples, and posterior distributions
- are saved as files and db records.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>= a pecan settings list</p></td>
+            </tr>
+            <tr>
+              <th>external.data</th>
+              <td><p>= list of inputs</p></td>
+            </tr>
+            <tr>
+              <th>external.priors</th>
+              <td><p>= list or priors</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            nothing. Diagnostic plots, MCMC samples, and posterior distributions
+            are saved as files and db records.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
 
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
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diff --git a/modules/assim.batch/docs/reference/pda.generate.knots.html b/modules/assim.batch/docs/reference/pda.generate.knots.html
index 4cf0e71..4cb5383 100644
--- a/modules/assim.batch/docs/reference/pda.generate.knots.html
+++ b/modules/assim.batch/docs/reference/pda.generate.knots.html
@@ -2,166 +2,222 @@
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+      PEcAn.assim.batch
+    </title>
+
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate Parameter Knots for PDA Emulator</h1>
-    
-    <div class="hidden name"><code>pda.generate.knots.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generate Parameter Knots for PDA Emulator</h1>
 
-    <div class="ref-description">
-    
-    <p>Generate Parameter Knots for PDA Emulator</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.generate.knots.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Generate Parameter Knots for PDA Emulator</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.generate.knots</span>(<span class='no'>n.knot</span>, <span class='no'>sf</span>, <span class='no'>probs.sf</span>, <span class='no'>n.param.all</span>, <span class='no'>prior.ind</span>, <span class='no'>prior.fn</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>pda.generate.knots</span>(<span class='no'>n.knot</span>, <span class='no'>sf</span>, <span class='no'>probs.sf</span>, <span class='no'>n.param.all</span>, <span class='no'>prior.ind</span>, <span class='no'>prior.fn</span>,
   <span class='no'>pname</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A list of probabilities and parameter values, with one row for each knot in the emulator.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A list of probabilities and parameter values, with one row for each
+            knot in the emulator.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/reference/pda.generate.sf.html b/modules/assim.batch/docs/reference/pda.generate.sf.html
index 9a98d7f..dde37c9 100644
--- a/modules/assim.batch/docs/reference/pda.generate.sf.html
+++ b/modules/assim.batch/docs/reference/pda.generate.sf.html
@@ -2,149 +2,189 @@
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+      PEcAn.assim.batch
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+
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+      crossorigin="anonymous"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <script src="../pkgdown.js"></script>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
+                  <a
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate scaling factor knots for PDA Emulator</h1>
-    
-    <div class="hidden name"><code>pda.generate.sf.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generate scaling factor knots for PDA Emulator</h1>
 
-    <div class="ref-description">
-    
-    <p>Generate scaling factor knots for PDA Emulator</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.generate.sf.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.generate.sf</span>(<span class='no'>n.knot</span>, <span class='no'>sf</span>, <span class='no'>prior.list</span>)</pre>
-        
+          <div class="ref-description">
+            <p>Generate scaling factor knots for PDA Emulator</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>pda.generate.sf</span>(<span class='no'>n.knot</span>, <span class='no'>sf</span>, <span class='no'>prior.list</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-
diff --git a/modules/assim.batch/docs/reference/pda.get.model.output.html b/modules/assim.batch/docs/reference/pda.get.model.output.html
index ad37acb..8b2136a 100644
--- a/modules/assim.batch/docs/reference/pda.get.model.output.html
+++ b/modules/assim.batch/docs/reference/pda.get.model.output.html
@@ -2,166 +2,217 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-
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-
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+    </title>
+
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+      crossorigin="anonymous"
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+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get Model Output for PDA</h1>
-    
-    <div class="hidden name"><code>pda.get.model.output.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get Model Output for PDA</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.get.model.output</span>(<span class='no'>settings</span>, <span class='no'>run.id</span>, <span class='no'>bety</span>, <span class='no'>inputs</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A list containing model outputs extracted to correspond to each observational
-        dataset being used for PDA.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get Model Output for PDA</h1>
+
+            <div class="hidden name"><code>pda.get.model.output.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get Model Output for PDA</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.get.model.output</span>(<span class='no'>settings</span>, <span class='no'>run.id</span>, <span class='no'>bety</span>, <span class='no'>inputs</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A list containing model outputs extracted to correspond to each
+            observational dataset being used for PDA.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
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index a3a0c89..b0615e2 100644
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+++ b/modules/assim.batch/docs/reference/pda.init.params.html
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Initialise Parameter Matrix for PDA</h1>
-    
-    <div class="hidden name"><code>pda.init.params.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Initialise Parameter Matrix for PDA</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.init.params</span>(<span class='no'>settings</span>, <span class='no'>chain</span>, <span class='no'>pname</span>, <span class='no'>n.param.all</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A list containing 'start' and 'finish' counters for MCMC, as well as the params
-        table, which is an empty matrix concatenated to any param samples from a previous
-        PDA run, if provided.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Initialise Parameter Matrix for PDA</h1>
+
+            <div class="hidden name"><code>pda.init.params.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Initialise Parameter Matrix for PDA</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.init.params</span>(<span class='no'>settings</span>, <span class='no'>chain</span>, <span class='no'>pname</span>, <span class='no'>n.param.all</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A list containing 'start' and 'finish' counters for MCMC, as well as
+            the params table, which is an empty matrix concatenated to any param
+            samples from a previous PDA run, if provided.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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+    </div>
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 </html>
-
diff --git a/modules/assim.batch/docs/reference/pda.init.run.html b/modules/assim.batch/docs/reference/pda.init.run.html
index f3e2b02..610eaf3 100644
--- a/modules/assim.batch/docs/reference/pda.init.run.html
+++ b/modules/assim.batch/docs/reference/pda.init.run.html
@@ -2,167 +2,219 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                        >PEcAn.assim.batch Vignette</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Initialise Model Runs for PDA</h1>
-    
-    <div class="hidden name"><code>pda.init.run.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Initialise Model Runs for PDA</h1>
 
-    <div class="ref-description">
-    
-    <p>Initialise Model Runs for PDA</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.init.run.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Initialise Model Runs for PDA</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.init.run</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='no'>my.write.config</span>, <span class='no'>workflow.id</span>, <span class='no'>params</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>pda.init.run</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='no'>my.write.config</span>, <span class='no'>workflow.id</span>, <span class='no'>params</span>,
   <span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'>ifelse</span>(<span class='fu'>is.null</span>(<span class='fu'>dim</span>(<span class='no'>params</span>)), <span class='fl'>1</span>, <span class='fu'>nrow</span>(<span class='no'>params</span>)),
   <span class='kw'>run.names</span> <span class='kw'>=</span> <span class='fu'>paste</span>(<span class='st'>"run"</span>, <span class='fl'>1</span>:<span class='no'>n</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"."</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Vector of run IDs for all model runs that were set up (including write.configs)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Vector of run IDs for all model runs that were set up (including
+            write.configs)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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diff --git a/modules/assim.batch/docs/reference/pda.load.priors.html b/modules/assim.batch/docs/reference/pda.load.priors.html
index e0873d3..0bf823c 100644
--- a/modules/assim.batch/docs/reference/pda.load.priors.html
+++ b/modules/assim.batch/docs/reference/pda.load.priors.html
@@ -2,165 +2,221 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                  >PEcAn.assim.batch</a
+                >
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+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
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+                        >PEcAn.assim.batch Vignette</a
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Load Priors for Paramater Data Assimilation</h1>
-    
-    <div class="hidden name"><code>pda.load.priors.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Load Priors for Paramater Data Assimilation</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.load.priors</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='kw'>extension.check</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A previously-generated posterior distribution, to be used as the prior for PDA.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Load Priors for Paramater Data Assimilation</h1>
+
+            <div class="hidden name"><code>pda.load.priors.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Load Priors for Paramater Data Assimilation</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.load.priors</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='kw'>extension.check</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A previously-generated posterior distribution, to be used as the
+            prior for PDA.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/assim.batch/docs/reference/pda.mcmc.bs.html b/modules/assim.batch/docs/reference/pda.mcmc.bs.html
index a229abe..964607b 100644
--- a/modules/assim.batch/docs/reference/pda.mcmc.bs.html
+++ b/modules/assim.batch/docs/reference/pda.mcmc.bs.html
@@ -2,176 +2,225 @@
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+                  >PEcAn.assim.batch</a
+                >
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+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
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+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
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+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Paramater Data Assimilation using MCMC</h1>
-    
-    <div class="hidden name"><code>pda.mcmc.bs.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Paramater Data Assimilation using MCMC</h1>
 
-    <div class="ref-description">
-    
-    <p>Parameter Data Assimilation using MCMC with block sampling</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.mcmc.bs.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.mcmc.bs</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>Parameter Data Assimilation using MCMC with block sampling</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.mcmc.bs</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>prior.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>chain</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>iter</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>adapt</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>adj.min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>ar.target</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>jvar</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n.knot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>= a pecan settings list</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing. Diagnostic plots, MCMC samples, and posterior distributions
- are saved as files and db records.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Brute-force, only to be used on simple models</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-          </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>= a pecan settings list</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            nothing. Diagnostic plots, MCMC samples, and posterior distributions
+            are saved as files and db records.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Brute-force, only to be used on simple models</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+          </ul>
 
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
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-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/assim.batch/docs/reference/pda.mcmc.html b/modules/assim.batch/docs/reference/pda.mcmc.html
index 32143a3..724390d 100644
--- a/modules/assim.batch/docs/reference/pda.mcmc.html
+++ b/modules/assim.batch/docs/reference/pda.mcmc.html
@@ -2,176 +2,225 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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+                        >PEcAn.assim.batch Vignette</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Paramater Data Assimilation using MCMC</h1>
-    
-    <div class="hidden name"><code>pda.mcmc.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Paramater Data Assimilation using MCMC</h1>
 
-    <div class="ref-description">
-    
-    <p>Paramater Data Assimilation using MCMC</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.mcmc.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.mcmc</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>Paramater Data Assimilation using MCMC</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.mcmc</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>prior.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>chain</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>iter</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>adapt</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>adj.min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>ar.target</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>jvar</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n.knot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>= a pecan settings list</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing. Diagnostic plots, MCMC samples, and posterior distributions
- are saved as files and db records.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Brute-force, only to be used on simple models</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-          </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>= a pecan settings list</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            nothing. Diagnostic plots, MCMC samples, and posterior distributions
+            are saved as files and db records.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Brute-force, only to be used on simple models</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+          </ul>
 
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze Ryan Kelly
+        </div>
+      </div>
 
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index 3632041..7cfe6fa 100644
--- a/modules/assim.batch/docs/reference/pda.mcmc.recover.html
+++ b/modules/assim.batch/docs/reference/pda.mcmc.recover.html
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+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Clean up a failed PDA run</h1>
-    
-    <div class="hidden name"><code>pda.mcmc.recover.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Clean up a failed PDA run</h1>
 
-    <div class="ref-description">
-    
-    <p>Clean up a failed PDA run</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.mcmc.recover.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Clean up a failed PDA run</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.mcmc.recover</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>pda.mcmc.recover</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>prior.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>chain</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>iter</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>adapt</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>adj.min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>ar.target</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>jvar</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n.knot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>burnin</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>An updated settings list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>An updated settings list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/reference/pda.neff.calc.html b/modules/assim.batch/docs/reference/pda.neff.calc.html
index e113277..79c8d3a 100644
--- a/modules/assim.batch/docs/reference/pda.neff.calc.html
+++ b/modules/assim.batch/docs/reference/pda.neff.calc.html
@@ -2,172 +2,223 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
-<!-- clipboard.js -->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Calculate N_eff — pda.neff.calc" />
+
+    <meta
+      property="og:description"
+      content="Autocorelation correction and efficient sample size calculation on latent process"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.assim.batch</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/AssimBatchVignette.html">PEcAn.assim.batch Vignette</a>
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-        
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate N_eff</h1>
-    
-    <div class="hidden name"><code>pda.neff.calc.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Autocorelation correction and efficient sample size calculation on latent process</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.neff.calc</span>(<span class='no'>inputs</span>, <span class='kw'>recalculate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>inputs</th>
-      <td><p>list</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>inputs list, updated inputs with n_eff</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>What we're trying to do is to calculate the autocorrelation of the latent state, after attempting to "remove" the observation error. 
-The first step is thus to estimate the latent state using a simple 'process free' state-space model (e.g. random walk).</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate N_eff</h1>
+
+            <div class="hidden name"><code>pda.neff.calc.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Autocorelation correction and efficient sample size calculation on
+              latent process
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.neff.calc</span>(<span class='no'>inputs</span>, <span class='kw'>recalculate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>inputs</th>
+              <td><p>list</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>inputs list, updated inputs with n_eff</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            What we're trying to do is to calculate the autocorrelation of the
+            latent state, after attempting to "remove" the observation error.
+            The first step is thus to estimate the latent state using a simple
+            'process free' state-space model (e.g. random walk).
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/reference/pda.plot.params.html b/modules/assim.batch/docs/reference/pda.plot.params.html
index 40ab3f6..452964f 100644
--- a/modules/assim.batch/docs/reference/pda.plot.params.html
+++ b/modules/assim.batch/docs/reference/pda.plot.params.html
@@ -2,166 +2,215 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
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+                        >PEcAn.assim.batch Vignette</a
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Plot PDA Parameter Diagnostics</h1>
-    
-    <div class="hidden name"><code>pda.plot.params.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Plot PDA Parameter Diagnostics</h1>
 
-    <div class="ref-description">
-    
-    <p>Plot PDA Parameter Diagnostics</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.plot.params.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Plot PDA Parameter Diagnostics</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.plot.params</span>(<span class='no'>settings</span>, <span class='no'>mcmc.param.list</span>, <span class='no'>prior.ind</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>pda.plot.params</span>(<span class='no'>settings</span>, <span class='no'>mcmc.param.list</span>, <span class='no'>prior.ind</span>,
   <span class='kw'>par.file.name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Nothing. Plot is generated and saved to PDF.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Nothing. Plot is generated and saved to PDF.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
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diff --git a/modules/assim.batch/docs/reference/pda.postprocess.html b/modules/assim.batch/docs/reference/pda.postprocess.html
index 1c9ad40..f5f666b 100644
--- a/modules/assim.batch/docs/reference/pda.postprocess.html
+++ b/modules/assim.batch/docs/reference/pda.postprocess.html
@@ -2,165 +2,217 @@
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+
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                        >PEcAn.assim.batch Vignette</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Postprocessing for PDA Results</h1>
-    
-    <div class="hidden name"><code>pda.postprocess.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Postprocessing for PDA Results</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.postprocess</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='no'>mcmc.param.list</span>, <span class='no'>pname</span>, <span class='no'>prior</span>, <span class='no'>prior.ind</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>PEcAn settings list, updated with &lt;params.id&gt; pointing to the new params file.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Postprocessing for PDA Results</h1>
+
+            <div class="hidden name"><code>pda.postprocess.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Postprocessing for PDA Results</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.postprocess</span>(<span class='no'>settings</span>, <span class='no'>con</span>, <span class='no'>mcmc.param.list</span>, <span class='no'>pname</span>, <span class='no'>prior</span>, <span class='no'>prior.ind</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            PEcAn settings list, updated with &lt;params.id&gt; pointing to the
+            new params file.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/reference/pda.settings.bt.html b/modules/assim.batch/docs/reference/pda.settings.bt.html
index 7c1f612..787e846 100644
--- a/modules/assim.batch/docs/reference/pda.settings.bt.html
+++ b/modules/assim.batch/docs/reference/pda.settings.bt.html
@@ -2,165 +2,215 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
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-
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-
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-
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-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Apply settings for BayesianTools — pda.settings.bt" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Apply settings for BayesianTools — pda.settings.bt • PEcAn.assim.batch
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Apply settings for BayesianTools — pda.settings.bt"
+    />
+
+    <meta
+      property="og:description"
+      content="Helper function for applying BayesianTools specific settings from PEcAn general settings"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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+          <div class="container">
+            <div class="navbar-header">
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+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Apply settings for BayesianTools</h1>
-    
-    <div class="hidden name"><code>pda.settings.bt.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Helper function for applying BayesianTools specific settings from PEcAn general settings</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pda.settings.bt</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>bt.settings list of runMCMCBayesianTools settings</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Apply settings for BayesianTools</h1>
+
+            <div class="hidden name"><code>pda.settings.bt.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Helper function for applying BayesianTools specific settings from
+              PEcAn general settings
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pda.settings.bt</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>bt.settings list of runMCMCBayesianTools settings</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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-
+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/reference/pda.settings.html b/modules/assim.batch/docs/reference/pda.settings.html
index 05168aa..a9097c8 100644
--- a/modules/assim.batch/docs/reference/pda.settings.html
+++ b/modules/assim.batch/docs/reference/pda.settings.html
@@ -2,168 +2,212 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
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-
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
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+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Set PDA Settings</h1>
-    
-    <div class="hidden name"><code>pda.settings.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Set PDA Settings</h1>
 
-    <div class="ref-description">
-    
-    <p>Set PDA Settings</p>
-    
-    </div>
+            <div class="hidden name"><code>pda.settings.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Set PDA Settings</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>pda.settings</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>pda.settings</span>(<span class='no'>settings</span>, <span class='kw'>params.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>prior.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>chain</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>iter</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>adapt</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>adj.min</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>ar.target</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>jvar</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n.knot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>run.round</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>all</th>
-      <td><p>params are the identically named variables in pda.mcmc / pda.emulator</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>An updated settings list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>all</th>
+              <td>
+                <p>
+                  params are the identically named variables in pda.mcmc /
+                  pda.emulator
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>An updated settings list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/reference/return.bias.html b/modules/assim.batch/docs/reference/return.bias.html
index 829d63c..bcce5b9 100644
--- a/modules/assim.batch/docs/reference/return.bias.html
+++ b/modules/assim.batch/docs/reference/return.bias.html
@@ -2,184 +2,226 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<![endif]-->
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
   </head>
 
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.batch</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/AssimBatchVignette.html"
+                        >PEcAn.assim.batch Vignette</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>return.bias</h1>
-    
-    <div class="hidden name"><code>return.bias.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>return.bias</h1>
 
-    <div class="ref-description">
-    
-    <p>return.bias</p>
-    
-    </div>
+            <div class="hidden name"><code>return.bias.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>return.bias</span>(<span class='no'>settings</span>, <span class='no'>isbias</span>, <span class='no'>model.out</span>, <span class='no'>inputs</span>, <span class='no'>prior.list.bias</span>,
-  <span class='kw'>run.round</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>pass2bias</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings list</p></td>
-    </tr>
-    <tr>
-      <th>isbias</th>
-      <td><p>bias variable index</p></td>
-    </tr>
-    <tr>
-      <th>model.out</th>
-      <td><p>model output list</p></td>
-    </tr>
-    <tr>
-      <th>inputs</th>
-      <td><p>inputs list</p></td>
-    </tr>
-    <tr>
-      <th>prior.list.bias</th>
-      <td><p>prior list, bias prior to be added</p></td>
-    </tr>
-    <tr>
-      <th>run.round</th>
-      <td><p>extension flag</p></td>
-    </tr>
-    <tr>
-      <th>pass2bias</th>
-      <td><p>if this is another round, this is re-sampled MCMC samples, will go with the rest of model params</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>return.bias</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>return.bias</span>(<span class='no'>settings</span>, <span class='no'>isbias</span>, <span class='no'>model.out</span>, <span class='no'>inputs</span>, <span class='no'>prior.list.bias</span>,
+  <span class='kw'>run.round</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>pass2bias</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings list</p></td>
+            </tr>
+            <tr>
+              <th>isbias</th>
+              <td><p>bias variable index</p></td>
+            </tr>
+            <tr>
+              <th>model.out</th>
+              <td><p>model output list</p></td>
+            </tr>
+            <tr>
+              <th>inputs</th>
+              <td><p>inputs list</p></td>
+            </tr>
+            <tr>
+              <th>prior.list.bias</th>
+              <td><p>prior list, bias prior to be added</p></td>
+            </tr>
+            <tr>
+              <th>run.round</th>
+              <td><p>extension flag</p></td>
+            </tr>
+            <tr>
+              <th>pass2bias</th>
+              <td>
+                <p>
+                  if this is another round, this is re-sampled MCMC samples,
+                  will go with the rest of model params
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.batch/docs/reference/return_hyperpars.html b/modules/assim.batch/docs/reference/return_hyperpars.html
index a86f97d..5d9ef3c 100644
--- a/modules/assim.batch/docs/reference/return_hyperpars.html
+++ b/modules/assim.batch/docs/reference/return_hyperpars.html
@@ -2,149 +2,180 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>return_hyperpars</h1>
-    
-    <div class="hidden name"><code>return_hyperpars.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>return_hyperpars</h1>
 
-    <div class="ref-description">
-    
-    <p>return_hyperpars</p>
-    
-    </div>
+            <div class="hidden name"><code>return_hyperpars.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>return_hyperpars</span>(<span class='no'>assim.settings</span>, <span class='no'>inputs</span>)</pre>
-        
+          <div class="ref-description">
+            <p>return_hyperpars</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>return_hyperpars</span>(<span class='no'>assim.settings</span>, <span class='no'>inputs</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
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diff --git a/modules/assim.batch/docs/reference/sample_MCMC.html b/modules/assim.batch/docs/reference/sample_MCMC.html
index c97547b..3448bb8 100644
--- a/modules/assim.batch/docs/reference/sample_MCMC.html
+++ b/modules/assim.batch/docs/reference/sample_MCMC.html
@@ -2,192 +2,257 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Helper function to sample from previous MCMC chain while proposing new knots</h1>
-    
-    <div class="hidden name"><code>sample_MCMC.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Helper function to sample from previous MCMC chain while proposing new knots</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sample_MCMC</span>(<span class='no'>mcmc_path</span>, <span class='no'>n.param.orig</span>, <span class='no'>prior.ind.orig</span>, <span class='no'>n.post.knots</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Helper function to sample from previous MCMC chain while proposing
+              new knots
+            </h1>
+
+            <div class="hidden name"><code>sample_MCMC.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Helper function to sample from previous MCMC chain while proposing
+              new knots
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sample_MCMC</span>(<span class='no'>mcmc_path</span>, <span class='no'>n.param.orig</span>, <span class='no'>prior.ind.orig</span>, <span class='no'>n.post.knots</span>,
   <span class='no'>knots.params.temp</span>, <span class='no'>prior.list</span>, <span class='no'>prior.fn</span>, <span class='no'>sf</span>, <span class='no'>sf.samp</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mcmc_path</th>
-      <td><p>path to previous emulator mcmc samples object</p></td>
-    </tr>
-    <tr>
-      <th>n.param.orig</th>
-      <td><p>vector, number of parameters targeted in each (pft) sublist</p></td>
-    </tr>
-    <tr>
-      <th>prior.ind.orig</th>
-      <td><p>list, actual indices of parameters targeted in each (pft) sublist</p></td>
-    </tr>
-    <tr>
-      <th>n.post.knots</th>
-      <td><p>number of new samples requested</p></td>
-    </tr>
-    <tr>
-      <th>knots.params.temp</th>
-      <td><p>list of parameter samples proposed from the original PDA-prior</p></td>
-    </tr>
-    <tr>
-      <th>prior.list</th>
-      <td><p>PDA-prior list</p></td>
-    </tr>
-    <tr>
-      <th>prior.fn</th>
-      <td><p>list for parameter d/r/q/p functions</p></td>
-    </tr>
-    <tr>
-      <th>sf</th>
-      <td><p>SF parameter names</p></td>
-    </tr>
-    <tr>
-      <th>sf.samp</th>
-      <td><p>SF parameters MCMC samples</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
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-</div>
 
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-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mcmc_path</th>
+              <td><p>path to previous emulator mcmc samples object</p></td>
+            </tr>
+            <tr>
+              <th>n.param.orig</th>
+              <td>
+                <p>
+                  vector, number of parameters targeted in each (pft) sublist
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prior.ind.orig</th>
+              <td>
+                <p>
+                  list, actual indices of parameters targeted in each (pft)
+                  sublist
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.post.knots</th>
+              <td><p>number of new samples requested</p></td>
+            </tr>
+            <tr>
+              <th>knots.params.temp</th>
+              <td>
+                <p>
+                  list of parameter samples proposed from the original PDA-prior
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prior.list</th>
+              <td><p>PDA-prior list</p></td>
+            </tr>
+            <tr>
+              <th>prior.fn</th>
+              <td><p>list for parameter d/r/q/p functions</p></td>
+            </tr>
+            <tr>
+              <th>sf</th>
+              <td><p>SF parameter names</p></td>
+            </tr>
+            <tr>
+              <th>sf.samp</th>
+              <td><p>SF parameters MCMC samples</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
+        </div>
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index 6f38bce..545139f 100644
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to write posterior distributions of the scaling factors</h1>
-    
-    <div class="hidden name"><code>write_sf_posterior.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to write posterior distributions of the scaling factors</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write_sf_posterior</span>(<span class='no'>sf.samp.list</span>, <span class='no'>sf.prior</span>, <span class='no'>sf.samp.filename</span>)</pre>
-        
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function to write posterior distributions of the scaling factors
+            </h1>
+
+            <div class="hidden name"><code>write_sf_posterior.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to write posterior distributions of the scaling factors
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write_sf_posterior</span>(<span class='no'>sf.samp.list</span>, <span class='no'>sf.prior</span>, <span class='no'>sf.samp.filename</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html"
+                  >PEcAn.assim.sequential</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +152,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.sequential/docs/authors.html b/modules/assim.sequential/docs/authors.html
index 2f0cdd8..e3a647e 100644
--- a/modules/assim.sequential/docs/authors.html
+++ b/modules/assim.sequential/docs/authors.html
@@ -2,122 +2,145 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.assim.sequential</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.assim.sequential</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.assim.sequential</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html"
+                  >PEcAn.assim.sequential</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/assim.sequential/docs/docsearch.css b/modules/assim.sequential/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/assim.sequential/docs/docsearch.css
+++ b/modules/assim.sequential/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/assim.sequential/docs/docsearch.js b/modules/assim.sequential/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/assim.sequential/docs/docsearch.js
+++ b/modules/assim.sequential/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/assim.sequential/docs/index.html b/modules/assim.sequential/docs/index.html
index 0205c40..198ffe9 100644
--- a/modules/assim.sequential/docs/index.html
+++ b/modules/assim.sequential/docs/index.html
@@ -1,111 +1,171 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for ecological forecasts and reanalysis • PEcAn.assim.sequential</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis •
+      PEcAn.assim.sequential
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    <!-- Font Awesome icons -->
+    <link
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+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    efficacy of scientific investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
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-  <div class="container">
-    <div class="navbar-header">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.assim.sequential</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
-  </div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html"
+                  >PEcAn.assim.sequential</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-  </div>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/assim.sequential/docs/pkgdown.css b/modules/assim.sequential/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/assim.sequential/docs/pkgdown.css
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@@ -13,7 +13,8 @@
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+.contents h1,
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-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
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+}
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+}
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-.ref-index .title {width: 60%;}
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+}
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+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
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+}
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+  width: 20%;
+}
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+  width: 80%;
+}
 
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@@ -162,7 +186,8 @@ pre {
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+pre,
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@@ -183,7 +208,8 @@ pre .img img {
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 }
 
-code a, pre a {
+code a,
+pre a {
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@@ -191,15 +217,35 @@ a.sourceLine:hover {
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-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
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+} /* function */
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+.st {
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+}
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+}
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+}
 
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diff --git a/modules/assim.sequential/docs/pkgdown.js b/modules/assim.sequential/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/assim.sequential/docs/pkgdown.js
+++ b/modules/assim.sequential/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
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-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
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@@ -23,8 +26,7 @@
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     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
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     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
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-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
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@@ -88,23 +88,23 @@
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       // Initialize tooltips:
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+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
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       });
 
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-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/assim.sequential/docs/reference/Analysis.sda.html b/modules/assim.sequential/docs/reference/Analysis.sda.html
index c4429eb..867d3ff 100644
--- a/modules/assim.sequential/docs/reference/Analysis.sda.html
+++ b/modules/assim.sequential/docs/reference/Analysis.sda.html
@@ -2,182 +2,266 @@
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 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<script src="../pkgdown.js"></script>
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-
-
-<meta property="og:title" content="Analysis.sda — Analysis.sda" />
-
-<meta property="og:description" content="This functions uses the FUN to perform the analysis. EnKF function is developed inside the PEcAn.assim.sequential package which can be sent to this function to perform the Ensemble Kalman Filter. 
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>Analysis.sda — Analysis.sda • PEcAn.assim.sequential</title>
+
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Analysis.sda — Analysis.sda" />
+
+    <meta
+      property="og:description"
+      content="This functions uses the FUN to perform the analysis. EnKF function is developed inside the PEcAn.assim.sequential package which can be sent to this function to perform the Ensemble Kalman Filter. 
 The other option is GEF function inside the same package allowing to perform Generalized Ensemble kalman Filter.
-If you're using an arbitrary function you can use the ... to send any other variables to your desired analysis function." />
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+If you're using an arbitrary function you can use the ... to send any other variables to your desired analysis function."
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.sequential</a
+                >
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+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Analysis.sda</h1>
-    
-    <div class="hidden name"><code>Analysis.sda.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This functions uses the FUN to perform the analysis. EnKF function is developed inside the PEcAn.assim.sequential package which can be sent to this function to perform the Ensemble Kalman Filter. 
-The other option is GEF function inside the same package allowing to perform Generalized Ensemble kalman Filter.</p>
-<p>If you're using an arbitrary function you can use the ... to send any other variables to your desired analysis function.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>Analysis.sda</span>(<span class='no'>settings</span>, <span class='no'>FUN</span>, <span class='kw'>Forecast</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>Pf</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>mu.f</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>Q</span> <span class='kw'>=</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Analysis.sda</h1>
+
+            <div class="hidden name"><code>Analysis.sda.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This functions uses the FUN to perform the analysis. EnKF function
+              is developed inside the PEcAn.assim.sequential package which can
+              be sent to this function to perform the Ensemble Kalman Filter.
+              The other option is GEF function inside the same package allowing
+              to perform Generalized Ensemble kalman Filter.
+            </p>
+            <p>
+              If you're using an arbitrary function you can use the ... to send
+              any other variables to your desired analysis function.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>Analysis.sda</span>(<span class='no'>settings</span>, <span class='no'>FUN</span>, <span class='kw'>Forecast</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>Pf</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>mu.f</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>Q</span> <span class='kw'>=</span>
   <span class='kw'>NULL</span>, <span class='kw'>X</span> <span class='kw'>=</span> <span class='kw'>NULL</span>), <span class='kw'>Observed</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>Y</span> <span class='kw'>=</span> <span class='kw'>NULL</span>), <span class='no'>H</span>, <span class='no'>extraArg</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>pecan standard settings list.</p></td>
-    </tr>
-    <tr>
-      <th>FUN</th>
-      <td><p>A Function for performing the analysis step. Two available options are: 1-EnKF and 2-GEF.</p></td>
-    </tr>
-    <tr>
-      <th>Forecast</th>
-      <td><p>A list containing the forecasts variables including Q (process variance) and X (a dataframe of forecasts state variables for different ensemble)</p></td>
-    </tr>
-    <tr>
-      <th>Observed</th>
-      <td><p>A list containing the observed variables including R (cov of observed state variables) and Y (vector of estimated mean of observed state variables)</p></td>
-    </tr>
-    <tr>
-      <th>H</th>
-      <td><p>is a mtrix of 1's and 0's specifying which observations go with which variables.</p></td>
-    </tr>
-    <tr>
-      <th>extraArg</th>
-      <td><p>This argument is a list containing aqq, bqq and t. The aqq and bqq are shape parameters estimated over time for the proccess covariance and t gives the time in terms of index of obs.list. See Details.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Extra argument sent to the analysis function. In case you're using the `GEF` function, this function requires nt, obs.mean, obs.cov, which are the total number of steps, list of observed means and list of observed cov respectively.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Returns whatever the FUN is returning. In case of EnKF and GEF, this function returns a list with estimated mean and cov matrix of forecast state variables as well as mean and cov estimated as a result of assimilation/analysis .</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>pecan standard settings list.</p></td>
+            </tr>
+            <tr>
+              <th>FUN</th>
+              <td>
+                <p>
+                  A Function for performing the analysis step. Two available
+                  options are: 1-EnKF and 2-GEF.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>Forecast</th>
+              <td>
+                <p>
+                  A list containing the forecasts variables including Q (process
+                  variance) and X (a dataframe of forecasts state variables for
+                  different ensemble)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>Observed</th>
+              <td>
+                <p>
+                  A list containing the observed variables including R (cov of
+                  observed state variables) and Y (vector of estimated mean of
+                  observed state variables)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>H</th>
+              <td>
+                <p>
+                  is a mtrix of 1's and 0's specifying which observations go
+                  with which variables.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>extraArg</th>
+              <td>
+                <p>
+                  This argument is a list containing aqq, bqq and t. The aqq and
+                  bqq are shape parameters estimated over time for the proccess
+                  covariance and t gives the time in terms of index of obs.list.
+                  See Details.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  Extra argument sent to the analysis function. In case you're
+                  using the `GEF` function, this function requires nt, obs.mean,
+                  obs.cov, which are the total number of steps, list of observed
+                  means and list of observed cov respectively.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Returns whatever the FUN is returning. In case of EnKF and GEF, this
+            function returns a list with estimated mean and cov matrix of
+            forecast state variables as well as mean and cov estimated as a
+            result of assimilation/analysis .
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze <a href='mailto:dietze@bu.edu'>dietze@bu.edu</a>, Ann Raiho and Hamze Dokoohaki
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze <a href="mailto:dietze@bu.edu">dietze@bu.edu</a>, Ann
+          Raiho and Hamze Dokoohaki
+        </div>
+      </div>
 
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Construc_H</h1>
-    
-    <div class="hidden name"><code>Construc_H.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function creates a mtrix mapping obsereved data to their forecast state variable.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>Construct_H</span>(<span class='no'>choose</span>, <span class='no'>Y</span>, <span class='no'>X</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>choose</th>
-      <td><p>a vector of observations indices oredered based on their appearances in the list of state variable names.</p></td>
-    </tr>
-    <tr>
-      <th>Y</th>
-      <td><p>vector of observations</p></td>
-    </tr>
-    <tr>
-      <th>X</th>
-      <td><p>Dataframe or matrix of forecast state variables for different ensembles.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>This returns a mtrix specifying which observation go with which state variables.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Construc_H</h1>
+
+            <div class="hidden name"><code>Construc_H.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function creates a mtrix mapping obsereved data to their
+              forecast state variable.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>Construct_H</span>(<span class='no'>choose</span>, <span class='no'>Y</span>, <span class='no'>X</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>choose</th>
+              <td>
+                <p>
+                  a vector of observations indices oredered based on their
+                  appearances in the list of state variable names.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>Y</th>
+              <td><p>vector of observations</p></td>
+            </tr>
+            <tr>
+              <th>X</th>
+              <td>
+                <p>
+                  Dataframe or matrix of forecast state variables for different
+                  ensembles.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            This returns a mtrix specifying which observation go with which
+            state variables.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Hamze Dokoohaki
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Hamze Dokoohaki
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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index 8293d0c..6caea3d 100644
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@@ -2,173 +2,239 @@
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+
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+      property="og:description"
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+    />
+    <meta name="twitter:card" content="summary" />
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>EnKF</h1>
-    
-    <div class="hidden name"><code>EnKF.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Given the Forecast and Observed this function performs the Ensemble Kalamn Filter.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>EnKF</span>(<span class='no'>setting</span>, <span class='no'>Forecast</span>, <span class='no'>Observed</span>, <span class='no'>H</span>, <span class='kw'>extraArg</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>Forecast</th>
-      <td><p>A list containing the forecasts variables including Q (process variance) and X (a dataframe of forecasts state variables for different ensemble)</p></td>
-    </tr>
-    <tr>
-      <th>Observed</th>
-      <td><p>A list containing the observed variables including R (cov of observed state variables) and Y (vector of estimated mean of observed state variables)</p></td>
-    </tr>
-    <tr>
-      <th>H</th>
-      <td><p>is a mtrix of 1's and 0's specifying which observations go with which variables.</p></td>
-    </tr>
-    <tr>
-      <th>extraArg</th>
-      <td><p>This argument is NOT used inside this function but it is a list containing aqq, bqq and t. The aqq and bqq are shape parameters estimated over time for the proccess covariance and t gives the time in terms of index of obs.list. See Details.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Extra argument sent to the analysis function.</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>pecan standard settings list.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>It returns a list with estimated mean and cov matrix of forecast state variables as well as mean and cov estimated as a result of assimilation/analysis .</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>EnKF</h1>
+
+            <div class="hidden name"><code>EnKF.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Given the Forecast and Observed this function performs the
+              Ensemble Kalamn Filter.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>EnKF</span>(<span class='no'>setting</span>, <span class='no'>Forecast</span>, <span class='no'>Observed</span>, <span class='no'>H</span>, <span class='kw'>extraArg</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>Forecast</th>
+              <td>
+                <p>
+                  A list containing the forecasts variables including Q (process
+                  variance) and X (a dataframe of forecasts state variables for
+                  different ensemble)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>Observed</th>
+              <td>
+                <p>
+                  A list containing the observed variables including R (cov of
+                  observed state variables) and Y (vector of estimated mean of
+                  observed state variables)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>H</th>
+              <td>
+                <p>
+                  is a mtrix of 1's and 0's specifying which observations go
+                  with which variables.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>extraArg</th>
+              <td>
+                <p>
+                  This argument is NOT used inside this function but it is a
+                  list containing aqq, bqq and t. The aqq and bqq are shape
+                  parameters estimated over time for the proccess covariance and
+                  t gives the time in terms of index of obs.list. See Details.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>Extra argument sent to the analysis function.</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>pecan standard settings list.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            It returns a list with estimated mean and cov matrix of forecast
+            state variables as well as mean and cov estimated as a result of
+            assimilation/analysis .
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze <a href='mailto:dietze@bu.edu'>dietze@bu.edu</a>, Ann Raiho and Hamze Dokoohaki
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze <a href="mailto:dietze@bu.edu">dietze@bu.edu</a>, Ann
+          Raiho and Hamze Dokoohaki
+        </div>
+      </div>
 
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/assim.sequential/docs/reference/GEF.html b/modules/assim.sequential/docs/reference/GEF.html
index 835e0c1..8a91a43 100644
--- a/modules/assim.sequential/docs/reference/GEF.html
+++ b/modules/assim.sequential/docs/reference/GEF.html
@@ -2,178 +2,255 @@
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 <html>
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-<meta property="og:title" content="GEF — GEF" />
-
-<meta property="og:description" content="Given the Forecast and Observed this function performs the Generalized Ensemble Kalamn Filter. The generalized ensemble filter follows generally the three steps of sequential state data assimilation. But, in the generalized ensemble filter we add a latent state vector that accounts for added process variance. Furthermore, instead of solving the analysis analytically like the EnKF, we have to estimate the mean analysis vector and covariance matrix with MCMC." />
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+
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+
+    <meta property="og:title" content="GEF — GEF" />
+
+    <meta
+      property="og:description"
+      content="Given the Forecast and Observed this function performs the Generalized Ensemble Kalamn Filter. The generalized ensemble filter follows generally the three steps of sequential state data assimilation. But, in the generalized ensemble filter we add a latent state vector that accounts for added process variance. Furthermore, instead of solving the analysis analytically like the EnKF, we have to estimate the mean analysis vector and covariance matrix with MCMC."
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-<div class="row">
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-    <div class="page-header">
-    <h1>GEF</h1>
-    
-    <div class="hidden name"><code>GEF.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Given the Forecast and Observed this function performs the Generalized Ensemble Kalamn Filter. The generalized ensemble filter follows generally the three steps of sequential state data assimilation. But, in the generalized ensemble filter we add a latent state vector that accounts for added process variance. Furthermore, instead of solving the analysis analytically like the EnKF, we have to estimate the mean analysis vector and covariance matrix with MCMC.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>GEF</span>(<span class='no'>setting</span>, <span class='no'>Forecast</span>, <span class='no'>Observed</span>, <span class='no'>H</span>, <span class='no'>extraArg</span>, <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fl'>50000</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>GEF</h1>
+
+            <div class="hidden name"><code>GEF.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Given the Forecast and Observed this function performs the
+              Generalized Ensemble Kalamn Filter. The generalized ensemble
+              filter follows generally the three steps of sequential state data
+              assimilation. But, in the generalized ensemble filter we add a
+              latent state vector that accounts for added process variance.
+              Furthermore, instead of solving the analysis analytically like the
+              EnKF, we have to estimate the mean analysis vector and covariance
+              matrix with MCMC.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>GEF</span>(<span class='no'>setting</span>, <span class='no'>Forecast</span>, <span class='no'>Observed</span>, <span class='no'>H</span>, <span class='no'>extraArg</span>, <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fl'>50000</span>,
   <span class='kw'>nburnin</span> <span class='kw'>=</span> <span class='fl'>10000</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>Forecast</th>
-      <td><p>A list containing the forecasts variables including Q (process variance) and X (a dataframe of forecast state variables for different ensemble)</p></td>
-    </tr>
-    <tr>
-      <th>Observed</th>
-      <td><p>A list containing the observed variables including R (cov of observed state variables) and Y (vector of estimated mean of observed state variables)</p></td>
-    </tr>
-    <tr>
-      <th>extraArg</th>
-      <td><p>This argument is a list containing aqq, bqq and t. The aqq and bqq are shape parameters estimated over time for the process covariance and t gives the time in terms of index of obs.list. See Details.</p></td>
-    </tr>
-    <tr>
-      <th>nitr</th>
-      <td><p>Number of iterations to run each MCMC chain.</p></td>
-    </tr>
-    <tr>
-      <th>nburnin</th>
-      <td><p>Number of initial, pre-thinning, MCMC iterations to discard.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>This function requires nt, obs.mean, obs.cov, which are the total number of steps, list of observed means and list of observed cov respectively.</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>pecan standard settings list.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>It returns a list with estimated mean and cov matrix of forecast state variables as well as mean and cov estimated as a result of assimilation/analysis .</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>Forecast</th>
+              <td>
+                <p>
+                  A list containing the forecasts variables including Q (process
+                  variance) and X (a dataframe of forecast state variables for
+                  different ensemble)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>Observed</th>
+              <td>
+                <p>
+                  A list containing the observed variables including R (cov of
+                  observed state variables) and Y (vector of estimated mean of
+                  observed state variables)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>extraArg</th>
+              <td>
+                <p>
+                  This argument is a list containing aqq, bqq and t. The aqq and
+                  bqq are shape parameters estimated over time for the process
+                  covariance and t gives the time in terms of index of obs.list.
+                  See Details.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>nitr</th>
+              <td><p>Number of iterations to run each MCMC chain.</p></td>
+            </tr>
+            <tr>
+              <th>nburnin</th>
+              <td>
+                <p>
+                  Number of initial, pre-thinning, MCMC iterations to discard.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  This function requires nt, obs.mean, obs.cov, which are the
+                  total number of steps, list of observed means and list of
+                  observed cov respectively.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>pecan standard settings list.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            It returns a list with estimated mean and cov matrix of forecast
+            state variables as well as mean and cov estimated as a result of
+            assimilation/analysis .
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze <a href='mailto:dietze@bu.edu'>dietze@bu.edu</a>, Ann Raiho and Hamze Dokoohaki
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze <a href="mailto:dietze@bu.edu">dietze@bu.edu</a>, Ann
+          Raiho and Hamze Dokoohaki
+        </div>
+      </div>
 
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index 6fc0cb6..61882a0 100644
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>adj.ens</h1>
-    
-    <div class="hidden name"><code>adj.ens.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This functions gives weights to different ensemble members based on their likelihood during the analysis step. Then it adjusts the analysis mean estimates of state variables based on the estimated weights.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>adj.ens</span>(<span class='no'>Pf</span>, <span class='no'>X</span>, <span class='no'>mu.f</span>, <span class='no'>mu.a</span>, <span class='no'>Pa</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>Pf</th>
-      <td><p>A cov matrix of forecast state variables.</p></td>
-    </tr>
-    <tr>
-      <th>X</th>
-      <td><p>Dataframe or matrix of forecast state variables for different ensembles.</p></td>
-    </tr>
-    <tr>
-      <th>mu.f</th>
-      <td><p>A vector with forecast mean estimates of state variables.</p></td>
-    </tr>
-    <tr>
-      <th>mu.a</th>
-      <td><p>A vector with analysis mean estimates of state variables.</p></td>
-    </tr>
-    <tr>
-      <th>Pa</th>
-      <td><p>The state estimate cov matrix of analysis.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Returns a vector of adjusted analysis mean estimates of state variables.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>adj.ens</h1>
+
+            <div class="hidden name"><code>adj.ens.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This functions gives weights to different ensemble members based
+              on their likelihood during the analysis step. Then it adjusts the
+              analysis mean estimates of state variables based on the estimated
+              weights.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>adj.ens</span>(<span class='no'>Pf</span>, <span class='no'>X</span>, <span class='no'>mu.f</span>, <span class='no'>mu.a</span>, <span class='no'>Pa</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>Pf</th>
+              <td><p>A cov matrix of forecast state variables.</p></td>
+            </tr>
+            <tr>
+              <th>X</th>
+              <td>
+                <p>
+                  Dataframe or matrix of forecast state variables for different
+                  ensembles.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>mu.f</th>
+              <td>
+                <p>A vector with forecast mean estimates of state variables.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>mu.a</th>
+              <td>
+                <p>A vector with analysis mean estimates of state variables.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>Pa</th>
+              <td><p>The state estimate cov matrix of analysis.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Returns a vector of adjusted analysis mean estimates of state
+            variables.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze <a href='mailto:dietze@bu.edu'>dietze@bu.edu</a>, Ann Raiho and Hamze Dokoohaki
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze <a href="mailto:dietze@bu.edu">dietze@bu.edu</a>, Ann
+          Raiho and Hamze Dokoohaki
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/assim.sequential/docs/reference/assess.params.html b/modules/assim.sequential/docs/reference/assess.params.html
index 18c6f21..27e7510 100644
--- a/modules/assim.sequential/docs/reference/assess.params.html
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+    />
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>assess.params</h1>
-    
-    <div class="hidden name"><code>assess.params.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Assessing parameter estimations after mapping model output to tobit space</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>assessParams</span>(<span class='no'>dat</span>, <span class='no'>Xt</span>, <span class='kw'>mu_f_TRUE</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>P_f_TRUE</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>MCMC output</p></td>
-    </tr>
-    <tr>
-      <th>Xt</th>
-      <td><p>ensemble output matrix</p></td>
-    </tr>
-    <tr>
-      <th>mu_f_TRUE</th>
-      <td><p>muf before tobit2space</p></td>
-    </tr>
-    <tr>
-      <th>P_f_TRUE</th>
-      <td><p>Pf before tobit2space</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>make plots</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>assess.params</h1>
+
+            <div class="hidden name"><code>assess.params.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Assessing parameter estimations after mapping model output to
+              tobit space
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>assessParams</span>(<span class='no'>dat</span>, <span class='no'>Xt</span>, <span class='kw'>mu_f_TRUE</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>P_f_TRUE</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td><p>MCMC output</p></td>
+            </tr>
+            <tr>
+              <th>Xt</th>
+              <td><p>ensemble output matrix</p></td>
+            </tr>
+            <tr>
+              <th>mu_f_TRUE</th>
+              <td><p>muf before tobit2space</p></td>
+            </tr>
+            <tr>
+              <th>P_f_TRUE</th>
+              <td><p>Pf before tobit2space</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>make plots</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze and Ann Raiho <a href='mailto:dietze@bu.edu'>dietze@bu.edu</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze and Ann Raiho
+          <a href="mailto:dietze@bu.edu">dietze@bu.edu</a>
+        </div>
+      </div>
 
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+          </p>
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diff --git a/modules/assim.sequential/docs/reference/generate_colors_sda.html b/modules/assim.sequential/docs/reference/generate_colors_sda.html
index 4f96661..c76a786 100644
--- a/modules/assim.sequential/docs/reference/generate_colors_sda.html
+++ b/modules/assim.sequential/docs/reference/generate_colors_sda.html
@@ -2,137 +2,169 @@
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+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
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+      content="generate_colors_sda — generate_colors_sda"
+    />
+
+    <meta
+      property="og:description"
+      content="This function generates a series of colors in its parents enviroment. This is mainly used in assim.sequential package."
+    />
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+
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+    <![endif]-->
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+                  >PEcAn.assim.sequential</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>generate_colors_sda</h1>
-    
-    <div class="hidden name"><code>generate_colors_sda.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>generate_colors_sda</h1>
 
-    <div class="ref-description">
-    
-    <p>This function generates a series of colors in its parents enviroment. This is mainly used in assim.sequential package.</p>
-    
-    </div>
+            <div class="hidden name"><code>generate_colors_sda.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>generate_colors_sda</span>()</pre>
-        
+          <div class="ref-description">
+            <p>
+              This function generates a series of colors in its parents
+              enviroment. This is mainly used in assim.sequential package.
+            </p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre class="usage"><span class='fu'>generate_colors_sda</span>()</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
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 </html>
-
diff --git a/modules/assim.sequential/docs/reference/hop_test.html b/modules/assim.sequential/docs/reference/hop_test.html
index 98c0ac9..4d49ba0 100644
--- a/modules/assim.sequential/docs/reference/hop_test.html
+++ b/modules/assim.sequential/docs/reference/hop_test.html
@@ -2,157 +2,194 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    <meta property="og:title" content="hop_test — hop_test" />
+
+    <meta
+      property="og:description"
+      content="Hop test. This script tests that the model successfully reads it's own restart and can restart without loss of information."
+    />
+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.sequential</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+                <li>
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>hop_test</h1>
-    
-    <div class="hidden name"><code>hop_test.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Hop test. This script tests that the model successfully reads it's own restart and can restart without loss of information.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>hop_test</span>(<span class='no'>settings</span>, <span class='kw'>ens.runid</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>nyear</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>SDA PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>nyear</th>
-      <td><p>number of years to run hop test over</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>NONE</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>hop_test</h1>
+
+            <div class="hidden name"><code>hop_test.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Hop test. This script tests that the model successfully reads it's
+              own restart and can restart without loss of information.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>hop_test</span>(<span class='no'>settings</span>, <span class='kw'>ens.runid</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>nyear</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>SDA PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>nyear</th>
+              <td><p>number of years to run hop test over</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>NONE</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho <a href='mailto:araiho@nd.edu'>araiho@nd.edu</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho <a href="mailto:araiho@nd.edu">araiho@nd.edu</a>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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 </html>
-
diff --git a/modules/assim.sequential/docs/reference/index.html b/modules/assim.sequential/docs/reference/index.html
index cb7e3c8..f7276a2 100644
--- a/modules/assim.sequential/docs/reference/index.html
+++ b/modules/assim.sequential/docs/reference/index.html
@@ -2,216 +2,317 @@
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-  <meta charset="utf-8">
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
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+    <title>Function reference • PEcAn.assim.sequential</title>
 
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
 
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
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-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="Analysis.sda.html">Analysis.sda()</a></code> </p>
-        </td>
-        <td><p>Analysis.sda</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="Construc_H.html">Construct_H()</a></code> </p>
-        </td>
-        <td><p>Construc_H</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="EnKF.html">EnKF()</a></code> </p>
-        </td>
-        <td><p>EnKF</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="GEF.html">GEF()</a></code> </p>
-        </td>
-        <td><p>GEF</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="adj.ens.html">adj.ens()</a></code> </p>
-        </td>
-        <td><p>adj.ens</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="assess.params.html">assessParams()</a></code> </p>
-        </td>
-        <td><p>assess.params</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="generate_colors_sda.html">generate_colors_sda()</a></code> </p>
-        </td>
-        <td><p>generate_colors_sda</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="hop_test.html">hop_test()</a></code> </p>
-        </td>
-        <td><p>hop_test</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="interactive.plotting.sda.html">interactive.plotting.sda()</a></code> <code><a href="interactive.plotting.sda.html">postana.timeser.plotting.sda()</a></code> <code><a href="interactive.plotting.sda.html">postana.bias.plotting.sda()</a></code> <code><a href="interactive.plotting.sda.html">postana.bias.plotting.sda.corr()</a></code> <code><a href="interactive.plotting.sda.html">post.analysis.ggplot()</a></code> <code><a href="interactive.plotting.sda.html">post.analysis.ggplot.violin()</a></code> </p>
-        </td>
-        <td><p>Internal functions for plotting SDA outputs. Interactive, post analysis time-series and bias plots in base plotting system and ggplot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load_data_paleon_sda.html">load_data_paleon_sda()</a></code> </p>
-        </td>
-        <td><p>load_data_paleon_sda</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load_nimble.html">load_nimble()</a></code> </p>
-        </td>
-        <td><p>load_nimble</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sample.parameters.html">sample.parameters()</a></code> </p>
-        </td>
-        <td><p>sample parameters</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sda.enkf.html">sda.enkf.original()</a></code> <code><a href="sda.enkf.html">sda.enkf()</a></code> </p>
-        </td>
-        <td><p>sda.enkf</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="Analysis.sda.html">Analysis.sda()</a></code>
+                  </p>
+                </td>
+                <td><p>Analysis.sda</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="Construc_H.html">Construct_H()</a></code>
+                  </p>
+                </td>
+                <td><p>Construc_H</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="EnKF.html">EnKF()</a></code>
+                  </p>
+                </td>
+                <td><p>EnKF</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="GEF.html">GEF()</a></code>
+                  </p>
+                </td>
+                <td><p>GEF</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="adj.ens.html">adj.ens()</a></code>
+                  </p>
+                </td>
+                <td><p>adj.ens</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="assess.params.html">assessParams()</a></code>
+                  </p>
+                </td>
+                <td><p>assess.params</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="generate_colors_sda.html"
+                        >generate_colors_sda()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>generate_colors_sda</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="hop_test.html">hop_test()</a></code>
+                  </p>
+                </td>
+                <td><p>hop_test</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="interactive.plotting.sda.html"
+                        >interactive.plotting.sda()</a
+                      ></code
+                    >
+                    <code
+                      ><a href="interactive.plotting.sda.html"
+                        >postana.timeser.plotting.sda()</a
+                      ></code
+                    >
+                    <code
+                      ><a href="interactive.plotting.sda.html"
+                        >postana.bias.plotting.sda()</a
+                      ></code
+                    >
+                    <code
+                      ><a href="interactive.plotting.sda.html"
+                        >postana.bias.plotting.sda.corr()</a
+                      ></code
+                    >
+                    <code
+                      ><a href="interactive.plotting.sda.html"
+                        >post.analysis.ggplot()</a
+                      ></code
+                    >
+                    <code
+                      ><a href="interactive.plotting.sda.html"
+                        >post.analysis.ggplot.violin()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Internal functions for plotting SDA outputs. Interactive,
+                    post analysis time-series and bias plots in base plotting
+                    system and ggplot
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="load_data_paleon_sda.html"
+                        >load_data_paleon_sda()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>load_data_paleon_sda</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="load_nimble.html">load_nimble()</a></code>
+                  </p>
+                </td>
+                <td><p>load_nimble</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="sample.parameters.html"
+                        >sample.parameters()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>sample parameters</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sda.enkf.html">sda.enkf.original()</a></code>
+                    <code><a href="sda.enkf.html">sda.enkf()</a></code>
+                  </p>
+                </td>
+                <td><p>sda.enkf</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
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-   </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
+        </div>
 
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/assim.sequential/docs/reference/interactive.plotting.sda.html b/modules/assim.sequential/docs/reference/interactive.plotting.sda.html
index 16c3a8b..01713cc 100644
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+++ b/modules/assim.sequential/docs/reference/interactive.plotting.sda.html
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+      Internal functions for plotting SDA outputs. Interactive, post analysis
+      time-series and bias plots in base plotting system and ggplot —
+      interactive.plotting.sda • PEcAn.assim.sequential
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
+    <!-- Bootstrap -->
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+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    <script src="../pkgdown.js"></script>
+
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+    />
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+      content="Internal functions for plotting SDA outputs. Interactive, post analysis time-series and bias plots in base plotting system and ggplot"
+    />
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.assim.sequential</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
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+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Internal functions for plotting SDA outputs. Interactive, post analysis time-series and bias plots in base plotting system and ggplot</h1>
-    
-    <div class="hidden name"><code>interactive.plotting.sda.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Internal functions for plotting SDA outputs. Interactive, post analysis time-series and bias plots in base plotting system and ggplot</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>interactive.plotting.sda</span>(<span class='no'>settings</span>, <span class='no'>t</span>, <span class='no'>obs.times</span>, <span class='no'>obs.mean</span>, <span class='no'>obs.cov</span>, <span class='no'>obs</span>, <span class='no'>X</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Internal functions for plotting SDA outputs. Interactive, post
+              analysis time-series and bias plots in base plotting system and
+              ggplot
+            </h1>
+
+            <div class="hidden name">
+              <code>interactive.plotting.sda.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Internal functions for plotting SDA outputs. Interactive, post
+              analysis time-series and bias plots in base plotting system and
+              ggplot
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>interactive.plotting.sda</span>(<span class='no'>settings</span>, <span class='no'>t</span>, <span class='no'>obs.times</span>, <span class='no'>obs.mean</span>, <span class='no'>obs.cov</span>, <span class='no'>obs</span>, <span class='no'>X</span>,
   <span class='no'>FORECAST</span>, <span class='no'>ANALYSIS</span>)
 
 <span class='fu'>postana.timeser.plotting.sda</span>(<span class='no'>settings</span>, <span class='no'>t</span>, <span class='no'>obs.times</span>, <span class='no'>obs.mean</span>, <span class='no'>obs.cov</span>,
@@ -119,77 +169,93 @@ <h1>Internal functions for plotting SDA outputs. Interactive, post analysis time
 
 <span class='fu'>post.analysis.ggplot.violin</span>(<span class='no'>settings</span>, <span class='no'>t</span>, <span class='no'>obs.times</span>, <span class='no'>obs.mean</span>, <span class='no'>obs.cov</span>, <span class='no'>obs</span>,
   <span class='no'>X</span>, <span class='no'>FORECAST</span>, <span class='no'>ANALYSIS</span>, <span class='kw'>plot.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>pecan standard settings list.</p></td>
-    </tr>
-    <tr>
-      <th>t</th>
-      <td><p>current time - int number giving the position of the current time in obs.time.</p></td>
-    </tr>
-    <tr>
-      <th>obs.mean</th>
-      <td><p>list of vectors of the means of observed data named by the measured date.</p></td>
-    </tr>
-    <tr>
-      <th>obs.cov</th>
-      <td><p>list of cov matrices of the observed data named by the measured date.</p></td>
-    </tr>
-    <tr>
-      <th>obs</th>
-      <td><p>list containing the mean and cov object</p></td>
-    </tr>
-    <tr>
-      <th>X</th>
-      <td><p>dataframe of state variables for each ensemble</p></td>
-    </tr>
-    <tr>
-      <th>FORECAST</th>
-      <td><p>dataframe of state variables for each ensemble</p></td>
-    </tr>
-    <tr>
-      <th>ANALYSIS</th>
-      <td><p>vector of mean of state variable after analysis</p></td>
-    </tr>
-    <tr>
-      <th>plot.title</th>
-      <td><p>character giving the title for post visualization ggplots</p></td>
-    </tr>
-    <tr>
-      <th>obs.time</th>
-      <td><p>vector of dates of measurements</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>pecan standard settings list.</p></td>
+            </tr>
+            <tr>
+              <th>t</th>
+              <td>
+                <p>
+                  current time - int number giving the position of the current
+                  time in obs.time.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>obs.mean</th>
+              <td>
+                <p>
+                  list of vectors of the means of observed data named by the
+                  measured date.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>obs.cov</th>
+              <td>
+                <p>
+                  list of cov matrices of the observed data named by the
+                  measured date.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>obs</th>
+              <td><p>list containing the mean and cov object</p></td>
+            </tr>
+            <tr>
+              <th>X</th>
+              <td><p>dataframe of state variables for each ensemble</p></td>
+            </tr>
+            <tr>
+              <th>FORECAST</th>
+              <td><p>dataframe of state variables for each ensemble</p></td>
+            </tr>
+            <tr>
+              <th>ANALYSIS</th>
+              <td><p>vector of mean of state variable after analysis</p></td>
+            </tr>
+            <tr>
+              <th>plot.title</th>
+              <td>
+                <p>character giving the title for post visualization ggplots</p>
+              </td>
+            </tr>
+            <tr>
+              <th>obs.time</th>
+              <td><p>vector of dates of measurements</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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   </body>
 </html>
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diff --git a/modules/assim.sequential/docs/reference/load_data_paleon_sda.html b/modules/assim.sequential/docs/reference/load_data_paleon_sda.html
index c67e6b0..925129d 100644
--- a/modules/assim.sequential/docs/reference/load_data_paleon_sda.html
+++ b/modules/assim.sequential/docs/reference/load_data_paleon_sda.html
@@ -2,153 +2,192 @@
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+    </title>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="load_data_paleon_sda — load_data_paleon_sda"
+    />
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+      content="Load data function for paleon SDA data products"
+    />
+    <meta name="twitter:card" content="summary" />
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+    <![endif]-->
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+                  >PEcAn.assim.sequential</a
+                >
+                <span
+                  class="label label-default"
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+                  title="Released package"
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+            </div>
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                  <a href="../reference/index.html">Reference</a>
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>load_data_paleon_sda</h1>
-    
-    <div class="hidden name"><code>load_data_paleon_sda.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Load data function for paleon SDA data products</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>load_data_paleon_sda</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn SDA settings object</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>obs.mean and obs.cov for sda.enkf</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load_data_paleon_sda</h1>
+
+            <div class="hidden name"><code>load_data_paleon_sda.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Load data function for paleon SDA data products</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load_data_paleon_sda</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn SDA settings object</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>obs.mean and obs.cov for sda.enkf</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho <a href='mailto:araiho@nd.edu'>araiho@nd.edu</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho <a href="mailto:araiho@nd.edu">araiho@nd.edu</a>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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-</div>
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+          <p>Developed by .</p>
+        </div>
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diff --git a/modules/assim.sequential/docs/reference/load_nimble.html b/modules/assim.sequential/docs/reference/load_nimble.html
index 61bdf9b..f6dba41 100644
--- a/modules/assim.sequential/docs/reference/load_nimble.html
+++ b/modules/assim.sequential/docs/reference/load_nimble.html
@@ -2,137 +2,164 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<div class="row">
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-    <div class="page-header">
-    <h1>load_nimble</h1>
-    
-    <div class="hidden name"><code>load_nimble.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load_nimble</h1>
 
-    <div class="ref-description">
-    
-    <p>This functions is internally used to register a series of nimble functions inside GEF analysis function.</p>
-    
-    </div>
+            <div class="hidden name"><code>load_nimble.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>load_nimble</span>()</pre>
-        
+          <div class="ref-description">
+            <p>
+              This functions is internally used to register a series of nimble
+              functions inside GEF analysis function.
+            </p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre class="usage"><span class='fu'>load_nimble</span>()</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Ann Raiho, Hamze Dokoohaki
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ann Raiho, Hamze Dokoohaki
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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diff --git a/modules/assim.sequential/docs/reference/sample.parameters.html b/modules/assim.sequential/docs/reference/sample.parameters.html
index 49fd869..da4883d 100644
--- a/modules/assim.sequential/docs/reference/sample.parameters.html
+++ b/modules/assim.sequential/docs/reference/sample.parameters.html
@@ -2,161 +2,196 @@
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+
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+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>sample parameters</h1>
-    
-    <div class="hidden name"><code>sample.parameters.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>sample parameters</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sample.parameters</span>(<span class='no'>ne</span>, <span class='no'>settings</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ne</th>
-      <td><p>number of ensemble members</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>PEcAn database connection</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data frame of sampled parameters from the posterior distribution</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>sample parameters</h1>
+
+            <div class="hidden name"><code>sample.parameters.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>sample parameters</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sample.parameters</span>(<span class='no'>ne</span>, <span class='no'>settings</span>, <span class='no'>con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ne</th>
+              <td><p>number of ensemble members</p></td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>PEcAn database connection</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            data frame of sampled parameters from the posterior distribution
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze <a href='mailto:dietze@bu.edu'>dietze@bu.edu</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze <a href="mailto:dietze@bu.edu">dietze@bu.edu</a>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
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index 3e78731..18a28d3 100644
--- a/modules/assim.sequential/docs/reference/sda.enkf.html
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@@ -2,212 +2,306 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>sda.enkf</h1>
-    
-    <div class="hidden name"><code>sda.enkf.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>State Variable Data Assimilation: Ensemble Kalman Filter</p>
-<p>State Variable Data Assimilation: Ensemble Kalman Filter and Generalized ensemble filter</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sda.enkf.original</span>(<span class='no'>settings</span>, <span class='no'>obs.mean</span>, <span class='no'>obs.cov</span>, <span class='kw'>IC</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>Q</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>sda.enkf</h1>
+
+            <div class="hidden name"><code>sda.enkf.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>State Variable Data Assimilation: Ensemble Kalman Filter</p>
+            <p>
+              State Variable Data Assimilation: Ensemble Kalman Filter and
+              Generalized ensemble filter
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sda.enkf.original</span>(<span class='no'>settings</span>, <span class='no'>obs.mean</span>, <span class='no'>obs.cov</span>, <span class='kw'>IC</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>Q</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>adjustment</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>restart</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
 
 <span class='fu'>sda.enkf</span>(<span class='no'>settings</span>, <span class='no'>obs.mean</span>, <span class='no'>obs.cov</span>, <span class='kw'>Q</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>restart</span> <span class='kw'>=</span> <span class='no'>F</span>,
   <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>trace</span> <span class='kw'>=</span> <span class='no'>T</span>, <span class='kw'>interactivePlot</span> <span class='kw'>=</span> <span class='no'>T</span>, <span class='kw'>TimeseriesPlot</span> <span class='kw'>=</span> <span class='no'>T</span>,
   <span class='kw'>BiasPlot</span> <span class='kw'>=</span> <span class='no'>F</span>, <span class='kw'>plot.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>debug</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>obs.mean</th>
-      <td><p>list of observations of the means of state variable (time X nstate)</p></td>
-    </tr>
-    <tr>
-      <th>obs.cov</th>
-      <td><p>list of observations of covariance matrices of state variables (time X nstate X nstate)</p></td>
-    </tr>
-    <tr>
-      <th>IC</th>
-      <td><p>initial conditions</p></td>
-    </tr>
-    <tr>
-      <th>Q</th>
-      <td><p>process covariance matrix given if there is no data to estimate it</p></td>
-    </tr>
-    <tr>
-      <th>adjustment</th>
-      <td><p>flag for using ensemble adjustment filter or not</p></td>
-    </tr>
-    <tr>
-      <th>restart</th>
-      <td><p>Used for iterative updating previous forecasts. This is a list that includes ens.inputs, the list of inputs by ensemble member, params, the parameters, and old_outdir, the output directory from the previous workflow. These three things are needed to ensure that if a new workflow is started that ensemble members keep there run-specific met and params. See Details</p></td>
-    </tr>
-    <tr>
-      <th>control</th>
-      <td><p>List of flags controlling the behaviour of the SDA. trace for reporting back the SDA outcomes, interactivePlot for plotting the outcomes after each step, 
-TimeseriesPlot for post analysis examination, BiasPlot for plotting the correlation between state variables, plot.title is the title of post analysis plots and debug mode allows for pausing the code and examinign the variables inside the function.</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings object</p></td>
-    </tr>
-    <tr>
-      <th>obs.mean</th>
-      <td><p>List of dataframe of observation means, named with observation datetime.</p></td>
-    </tr>
-    <tr>
-      <th>obs.cov</th>
-      <td><p>List of covariance matrices of state variables , named with observation datetime.</p></td>
-    </tr>
-    <tr>
-      <th>Q</th>
-      <td><p>Process covariance matrix given if there is no data to estimate it.</p></td>
-    </tr>
-    <tr>
-      <th>restart</th>
-      <td><p>Used for iterative updating previous forecasts. When the restart is TRUE it read the object in SDA folder written from previous SDA.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>NONE</p>
-<p>NONE</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>obs.mean</th>
+              <td>
+                <p>
+                  list of observations of the means of state variable (time X
+                  nstate)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>obs.cov</th>
+              <td>
+                <p>
+                  list of observations of covariance matrices of state variables
+                  (time X nstate X nstate)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>IC</th>
+              <td><p>initial conditions</p></td>
+            </tr>
+            <tr>
+              <th>Q</th>
+              <td>
+                <p>
+                  process covariance matrix given if there is no data to
+                  estimate it
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>adjustment</th>
+              <td><p>flag for using ensemble adjustment filter or not</p></td>
+            </tr>
+            <tr>
+              <th>restart</th>
+              <td>
+                <p>
+                  Used for iterative updating previous forecasts. This is a list
+                  that includes ens.inputs, the list of inputs by ensemble
+                  member, params, the parameters, and old_outdir, the output
+                  directory from the previous workflow. These three things are
+                  needed to ensure that if a new workflow is started that
+                  ensemble members keep there run-specific met and params. See
+                  Details
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>control</th>
+              <td>
+                <p>
+                  List of flags controlling the behaviour of the SDA. trace for
+                  reporting back the SDA outcomes, interactivePlot for plotting
+                  the outcomes after each step, TimeseriesPlot for post analysis
+                  examination, BiasPlot for plotting the correlation between
+                  state variables, plot.title is the title of post analysis
+                  plots and debug mode allows for pausing the code and examinign
+                  the variables inside the function.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings object</p></td>
+            </tr>
+            <tr>
+              <th>obs.mean</th>
+              <td>
+                <p>
+                  List of dataframe of observation means, named with observation
+                  datetime.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>obs.cov</th>
+              <td>
+                <p>
+                  List of covariance matrices of state variables , named with
+                  observation datetime.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>Q</th>
+              <td>
+                <p>
+                  Process covariance matrix given if there is no data to
+                  estimate it.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>restart</th>
+              <td>
+                <p>
+                  Used for iterative updating previous forecasts. When the
+                  restart is TRUE it read the object in SDA folder written from
+                  previous SDA.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>NONE</p>
+          <p>NONE</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze and Ann Raiho <a href='mailto:dietze@bu.edu'>dietze@bu.edu</a>
+          <h2>Author</h2>
 
-Michael Dietze and Ann Raiho <a href='mailto:dietze@bu.edu'>dietze@bu.edu</a>
+          Michael Dietze and Ann Raiho
+          <a href="mailto:dietze@bu.edu">dietze@bu.edu</a>
 
-  </div>
-</div>
+          Michael Dietze and Ann Raiho
+          <a href="mailto:dietze@bu.edu">dietze@bu.edu</a>
+        </div>
+      </div>
 
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-</div>
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+          <p>Developed by .</p>
+        </div>
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index 54549ef..974bd23 100644
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@@ -2,97 +2,126 @@
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>License • PEcAn.benchmark</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.benchmark</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/benchmark/docs/authors.html b/modules/benchmark/docs/authors.html
index 6ccb3df..2e1307c 100644
--- a/modules/benchmark/docs/authors.html
+++ b/modules/benchmark/docs/authors.html
@@ -2,142 +2,158 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.benchmark</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.benchmark</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.benchmark</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Elizabeth Cowdery</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Toni Viskari</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Elizabeth Cowdery</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Toni Viskari</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/benchmark/docs/docsearch.css b/modules/benchmark/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/benchmark/docs/docsearch.css
+++ b/modules/benchmark/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/benchmark/docs/docsearch.js b/modules/benchmark/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/benchmark/docs/docsearch.js
+++ b/modules/benchmark/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/benchmark/docs/index.html b/modules/benchmark/docs/index.html
index cc7c691..a7a08dc 100644
--- a/modules/benchmark/docs/index.html
+++ b/modules/benchmark/docs/index.html
@@ -1,111 +1,163 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for benchmarking • PEcAn.benchmark</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for benchmarking">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn functions used for benchmarking • PEcAn.benchmark</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta property="og:title" content="PEcAn functions used for benchmarking" />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PEcAn is to
     streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    efficacy of scientific investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.benchmark</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PEcAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
-  </div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PEcAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-  </div>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/benchmark/docs/pkgdown.css b/modules/benchmark/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/benchmark/docs/pkgdown.css
+++ b/modules/benchmark/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/benchmark/docs/pkgdown.js b/modules/benchmark/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/benchmark/docs/pkgdown.js
+++ b/modules/benchmark/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/benchmark/docs/reference/add_workflow_info.html b/modules/benchmark/docs/reference/add_workflow_info.html
index 85ee299..307e8e0 100644
--- a/modules/benchmark/docs/reference/add_workflow_info.html
+++ b/modules/benchmark/docs/reference/add_workflow_info.html
@@ -2,151 +2,189 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Add workflow specific info to settings list for benchmarking — add_workflow_info • PEcAn.benchmark</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
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-    <h1>Add workflow specific info to settings list for benchmarking</h1>
-    
-    <div class="hidden name"><code>add_workflow_info.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Add workflow specific info to settings list for benchmarking</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>add_workflow_info</span>(<span class='no'>settings</span>, <span class='no'>bety</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings or multisettings object</p></td>
-    </tr>
-    <tr>
-      <th>bety</th>
-      <td><p>connection to the database</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Add workflow specific info to settings list for benchmarking
+            </h1>
+
+            <div class="hidden name"><code>add_workflow_info.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Add workflow specific info to settings list for benchmarking</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>add_workflow_info</span>(<span class='no'>settings</span>, <span class='no'>bety</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings or multisettings object</p></td>
+            </tr>
+            <tr>
+              <th>bety</th>
+              <td><p>connection to the database</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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diff --git a/modules/benchmark/docs/reference/align_by_first_observation.html b/modules/benchmark/docs/reference/align_by_first_observation.html
index ae7ab75..657d69b 100644
--- a/modules/benchmark/docs/reference/align_by_first_observation.html
+++ b/modules/benchmark/docs/reference/align_by_first_observation.html
@@ -2,134 +2,195 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>align_first_observation</h1>
-    
-    <div class="hidden name"><code>align_by_first_observation.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>align_first_observation</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>align_by_first_observation</span>(<span class='no'>observation_one</span>, <span class='no'>observation_two</span>, <span class='no'>custom_table</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>observation_one</th>
-      <td><p>a vector of plant fucntional types, or species. Provides species/pft names.</p></td>
-    </tr>
-    <tr>
-      <th>observation_two</th>
-      <td><p>another vector of plant fucntional types, or species. Provides the order.</p></td>
-    </tr>
-    <tr>
-      <th>custom_table</th>
-      <td><p>a table that either maps two pft's to one another or maps custom species codes to bety id codes. 
-In the second case, must be passable to match_species_id.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>vector</code> Returns a vector of PFT's/species from observation_one that matches the order of observation_two</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>align_first_observation</h1>
+
+            <div class="hidden name">
+              <code>align_by_first_observation.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>align_first_observation</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>align_by_first_observation</span>(<span class='no'>observation_one</span>, <span class='no'>observation_two</span>, <span class='no'>custom_table</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>observation_one</th>
+              <td>
+                <p>
+                  a vector of plant fucntional types, or species. Provides
+                  species/pft names.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>observation_two</th>
+              <td>
+                <p>
+                  another vector of plant fucntional types, or species. Provides
+                  the order.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>custom_table</th>
+              <td>
+                <p>
+                  a table that either maps two pft's to one another or maps
+                  custom species codes to bety id codes. In the second case,
+                  must be passable to match_species_id.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            <code>vector</code> Returns a vector of PFT's/species from
+            observation_one that matches the order of observation_two
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>observation_one</span><span class='kw'>&lt;-</span><span class='fu'>c</span>(<span class='st'>"AMCA3"</span>,<span class='st'>"AMCA3"</span>,<span class='st'>"AMCA3"</span>,<span class='st'>"AMCA3"</span>)
 <span class='no'>observation_two</span><span class='kw'>&lt;-</span><span class='fu'>c</span>(<span class='st'>"a"</span>, <span class='st'>"b"</span>, <span class='st'>"a"</span>, <span class='st'>"a"</span>)
 
@@ -143,38 +204,34 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 
 <span class='co'># aligned should be a vector '[1] "AMCA3" "ARHY"  "AMCA3" "AMCA3"'</span>
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Tempest McCabe
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Tempest McCabe
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
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-
diff --git a/modules/benchmark/docs/reference/align_data.html b/modules/benchmark/docs/reference/align_data.html
index 7529c11..f63a07e 100644
--- a/modules/benchmark/docs/reference/align_data.html
+++ b/modules/benchmark/docs/reference/align_data.html
@@ -2,161 +2,190 @@
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+    ></script>
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+    />
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+    ></script>
+
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+      crossorigin="anonymous"
+    />
+
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+      crossorigin="anonymous"
+    ></script>
+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Align timeseries data</h1>
-    
-    <div class="hidden name"><code>align_data.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Align timeseries data</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>align_data</span>(<span class='no'>model.calc</span>, <span class='no'>obvs.calc</span>, <span class='no'>var</span>, <span class='kw'>align_method</span> <span class='kw'>=</span> <span class='st'>"match_timestep"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>model.calc</th>
-      <td><p>data.frame</p></td>
-    </tr>
-    <tr>
-      <th>obvs.calc</th>
-      <td><p>data.frame</p></td>
-    </tr>
-    <tr>
-      <th>var</th>
-      <td><p>data.frame</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dat</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Align timeseries data</h1>
+
+            <div class="hidden name"><code>align_data.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Align timeseries data</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>align_data</span>(<span class='no'>model.calc</span>, <span class='no'>obvs.calc</span>, <span class='no'>var</span>, <span class='kw'>align_method</span> <span class='kw'>=</span> <span class='st'>"match_timestep"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>model.calc</th>
+              <td><p>data.frame</p></td>
+            </tr>
+            <tr>
+              <th>obvs.calc</th>
+              <td><p>data.frame</p></td>
+            </tr>
+            <tr>
+              <th>var</th>
+              <td><p>data.frame</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>dat</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Betsy Cowdery
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
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-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/benchmark/docs/reference/align_data_to_data_pft.html b/modules/benchmark/docs/reference/align_data_to_data_pft.html
index effe6d6..6f4d3f2 100644
--- a/modules/benchmark/docs/reference/align_data_to_data_pft.html
+++ b/modules/benchmark/docs/reference/align_data_to_data_pft.html
@@ -2,170 +2,266 @@
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>align_data_to_data_pft</h1>
-    
-    <div class="hidden name"><code>align_data_to_data_pft.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>align_data_to_data_pft</h1>
 
-    <div class="ref-description">
-    
-    <p>align_data_to_data_pft</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>align_data_to_data_pft.Rd</code>
+            </div>
+          </div>
 
-    <pre class="usage"><span class='fu'>align_data_to_data_pft</span>(<span class='no'>con</span>, <span class='no'>observation_one</span>, <span class='no'>observation_two</span>,
+          <div class="ref-description">
+            <p>align_data_to_data_pft</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>align_data_to_data_pft</span>(<span class='no'>con</span>, <span class='no'>observation_one</span>, <span class='no'>observation_two</span>,
   <span class='kw'>custom_table</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>format_one</span>, <span class='no'>format_two</span>, <span class='kw'>subset_is_ok</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    <tr>
-      <th>observation_one</th>
-      <td><p>a vector of plant functional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>observation_two</th>
-      <td><p>another vector of plant functional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>custom_table</th>
-      <td><p>a table that either maps two pft's to one another or maps custom species codes to bety id codes.
-In the second case, must be passable to match_species_id.</p></td>
-    </tr>
-    <tr>
-      <th>format_one</th>
-      <td><p>The output of query.format.vars() of observation one of the form output$vars$bety_names</p></td>
-    </tr>
-    <tr>
-      <th>format_two</th>
-      <td><p>The output of query.format.vars() of observation two of the form output$vars$bety_names</p></td>
-    </tr>
-    <tr>
-      <th>subset_is_ok</th>
-      <td><p>When aligning two species lists, this allows for alignment when species lists aren't identical.
-set to FALSE by default.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>list</code> containing the following columns:</p><dl class='dl-horizontal'>
- <dt><code>$original</code></dt><dd><p>Will spit back out original vectors pre-alignment</p></dd>
- <dt><code>$aligned$aligned_by_observation_one</code></dt><dd><p>Where possible, will return a vector of observation_one pft's/species in the order of observation_two</p></dd>
- <dt><code>species</code></dt><dd><p>Where possible, will return a vector of observation_two's pft's/species in the order of observation_one</p></dd>
- <dt><code>$bety_species_id</code></dt><dd><p>Where possible, will return the bety_species_id's for one or both observations</p></dd>
- <dt><code>$bety_species_intersection</code></dt><dd><p>Where possible, will return the intersection of two aligned lists of species. subset_is_ok must be set to TRUE.</p></dd>
-</dl>
-
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Aligns vectors of Plant Fucntional Typed and species.
-Can align: 
-- two vectors of plant fucntional types (pft's) if a custom map is provided
-- a list of species (usda, fia, or latin_name format) to a plant fucntional type
-- a list of species in a custom format, with a table mapping it to bety_species_id's</p>
-<p>Will return a list of what was originally provided, bety_species_codes if possible, 
- and an aligned output. Because some alignement is order-sensitive, alignment based on observation_one
- and observation_two are both provided.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+            <tr>
+              <th>observation_one</th>
+              <td><p>a vector of plant functional types, or species</p></td>
+            </tr>
+            <tr>
+              <th>observation_two</th>
+              <td>
+                <p>another vector of plant functional types, or species</p>
+              </td>
+            </tr>
+            <tr>
+              <th>custom_table</th>
+              <td>
+                <p>
+                  a table that either maps two pft's to one another or maps
+                  custom species codes to bety id codes. In the second case,
+                  must be passable to match_species_id.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>format_one</th>
+              <td>
+                <p>
+                  The output of query.format.vars() of observation one of the
+                  form output$vars$bety_names
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>format_two</th>
+              <td>
+                <p>
+                  The output of query.format.vars() of observation two of the
+                  form output$vars$bety_names
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>subset_is_ok</th>
+              <td>
+                <p>
+                  When aligning two species lists, this allows for alignment
+                  when species lists aren't identical. set to FALSE by default.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>list</code> containing the following columns:</p>
+          <dl class="dl-horizontal">
+            <dt><code>$original</code></dt>
+            <dd><p>Will spit back out original vectors pre-alignment</p></dd>
+            <dt><code>$aligned$aligned_by_observation_one</code></dt>
+            <dd>
+              <p>
+                Where possible, will return a vector of observation_one
+                pft's/species in the order of observation_two
+              </p>
+            </dd>
+            <dt><code>species</code></dt>
+            <dd>
+              <p>
+                Where possible, will return a vector of observation_two's
+                pft's/species in the order of observation_one
+              </p>
+            </dd>
+            <dt><code>$bety_species_id</code></dt>
+            <dd>
+              <p>
+                Where possible, will return the bety_species_id's for one or
+                both observations
+              </p>
+            </dd>
+            <dt><code>$bety_species_intersection</code></dt>
+            <dd>
+              <p>
+                Where possible, will return the intersection of two aligned
+                lists of species. subset_is_ok must be set to TRUE.
+              </p>
+            </dd>
+          </dl>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Aligns vectors of Plant Fucntional Typed and species. Can align: -
+            two vectors of plant fucntional types (pft's) if a custom map is
+            provided - a list of species (usda, fia, or latin_name format) to a
+            plant fucntional type - a list of species in a custom format, with a
+            table mapping it to bety_species_id's
+          </p>
+          <p>
+            Will return a list of what was originally provided,
+            bety_species_codes if possible, and an aligned output. Because some
+            alignement is order-sensitive, alignment based on observation_one
+            and observation_two are both provided.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>observation_one</span><span class='kw'>&lt;-</span><span class='fu'>c</span>(<span class='st'>"AMCA3"</span>,<span class='st'>"AMCA3"</span>,<span class='st'>"AMCA3"</span>,<span class='st'>"AMCA3"</span>)
 <span class='no'>observation_two</span><span class='kw'>&lt;-</span><span class='fu'>c</span>(<span class='st'>"a"</span>, <span class='st'>"b"</span>, <span class='st'>"a"</span>, <span class='st'>"a"</span>)
 
@@ -183,40 +279,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
  <span class='kw'>format_one</span> <span class='kw'>=</span> <span class='no'>format_one</span>, <span class='kw'>format_two</span> <span class='kw'>=</span> <span class='no'>format_two</span>,
  <span class='kw'>custom_table</span> <span class='kw'>=</span> <span class='no'>table</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Tempest McCabe
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
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+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Tempest McCabe
+        </div>
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+
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-
diff --git a/modules/benchmark/docs/reference/align_pft.html b/modules/benchmark/docs/reference/align_pft.html
index 12f60ec..fd1dcd1 100644
--- a/modules/benchmark/docs/reference/align_pft.html
+++ b/modules/benchmark/docs/reference/align_pft.html
@@ -2,175 +2,267 @@
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <![endif]-->
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-    
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-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>align_pft</h1>
 
-    <div class="ref-description">
-    
-    <p>align_pft</p>
-    
-    </div>
+            <div class="hidden name"><code>align_pft.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>align_pft</span>(<span class='no'>con</span>, <span class='no'>observation_one</span>, <span class='no'>observation_two</span>, <span class='kw'>custom_table</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>align_pft</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>align_pft</span>(<span class='no'>con</span>, <span class='no'>observation_one</span>, <span class='no'>observation_two</span>, <span class='kw'>custom_table</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='no'>format_one</span>, <span class='no'>format_two</span>, <span class='kw'>subset_is_ok</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>comparison_type</span> <span class='kw'>=</span> <span class='st'>"data_to_data"</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    <tr>
-      <th>observation_one</th>
-      <td><p>a vector of plant fucntional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>observation_two</th>
-      <td><p>anouther vector of plant fucntional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>custom_table</th>
-      <td><p>a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
-In the second case, must be passable to match_species_id.</p></td>
-    </tr>
-    <tr>
-      <th>format_one</th>
-      <td><p>The output of query.format.vars() of observation one of the form output$vars$bety_names</p></td>
-    </tr>
-    <tr>
-      <th>format_two</th>
-      <td><p>The output of query.format.vars() of observation two of the form output$vars$bety_names</p></td>
-    </tr>
-    <tr>
-      <th>subset_is_ok</th>
-      <td><p>When aligning two species lists, this allows for alignement when species lists aren't identical. 
-set to FALSE by default.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>list</code> containing the following columns:</p><dl class='dl-horizontal'>
- <dt><code>$original</code></dt><dd><p>Will spit back out original vectors pre-alignment</p></dd>
- <dt><code>$aligned$aligned_by_observation_one</code></dt><dd><p>Where possible, will return a vector of observation_one pft's/species in the order of observation_two</p></dd>
- <dt><code>species</code></dt><dd><p>Where possible, will return a vector of observation_two's pft's/species in the order of observation_one</p></dd>
- <dt><code>$bety_species_id</code></dt><dd><p>Where possible, will return the bety_species_id's for one or both observations</p></dd>
-</dl>
-
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Aligns vectors of Plant Fucntional Typed and species.
-Can align: 
-- two vectors of plant fucntional types (pft's) if a custom map is provided
-- a list of species (usda, fia, or latin_name format) to a plant fucntional type
-- a list of species in a custom format, with a table mapping it to bety_species_id's</p>
-<p>Will return a list of what was originally provided, bety_speceis_codes if possible, 
- and an aligned output. Becuase some alignement is order-sensitive, alignment based on observation_one
- and observation_two are both provided.</p>
-<p><code>comparison_type</code> can be one of the following:</p><dl class='dl-horizontal'>
- <dt><code>data_to_data</code></dt><dd><p>Will align lists of pfts and species. Must be assosiated with inputs.</p></dd>
- <dt><code>data_to_model</code></dt><dd><p>Not yet implemented</p></dd>
- <dt><code>model_to_model</code></dt><dd><p>Not yet implemented</p></dd>
- </dl>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+            <tr>
+              <th>observation_one</th>
+              <td><p>a vector of plant fucntional types, or species</p></td>
+            </tr>
+            <tr>
+              <th>observation_two</th>
+              <td>
+                <p>anouther vector of plant fucntional types, or species</p>
+              </td>
+            </tr>
+            <tr>
+              <th>custom_table</th>
+              <td>
+                <p>
+                  a table that either maps two pft's to one anouther or maps
+                  custom species codes to bety id codes. In the second case,
+                  must be passable to match_species_id.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>format_one</th>
+              <td>
+                <p>
+                  The output of query.format.vars() of observation one of the
+                  form output$vars$bety_names
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>format_two</th>
+              <td>
+                <p>
+                  The output of query.format.vars() of observation two of the
+                  form output$vars$bety_names
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>subset_is_ok</th>
+              <td>
+                <p>
+                  When aligning two species lists, this allows for alignement
+                  when species lists aren't identical. set to FALSE by default.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>list</code> containing the following columns:</p>
+          <dl class="dl-horizontal">
+            <dt><code>$original</code></dt>
+            <dd><p>Will spit back out original vectors pre-alignment</p></dd>
+            <dt><code>$aligned$aligned_by_observation_one</code></dt>
+            <dd>
+              <p>
+                Where possible, will return a vector of observation_one
+                pft's/species in the order of observation_two
+              </p>
+            </dd>
+            <dt><code>species</code></dt>
+            <dd>
+              <p>
+                Where possible, will return a vector of observation_two's
+                pft's/species in the order of observation_one
+              </p>
+            </dd>
+            <dt><code>$bety_species_id</code></dt>
+            <dd>
+              <p>
+                Where possible, will return the bety_species_id's for one or
+                both observations
+              </p>
+            </dd>
+          </dl>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Aligns vectors of Plant Fucntional Typed and species. Can align: -
+            two vectors of plant fucntional types (pft's) if a custom map is
+            provided - a list of species (usda, fia, or latin_name format) to a
+            plant fucntional type - a list of species in a custom format, with a
+            table mapping it to bety_species_id's
+          </p>
+          <p>
+            Will return a list of what was originally provided,
+            bety_speceis_codes if possible, and an aligned output. Becuase some
+            alignement is order-sensitive, alignment based on observation_one
+            and observation_two are both provided.
+          </p>
+          <p><code>comparison_type</code> can be one of the following:</p>
+          <dl class="dl-horizontal">
+            <dt><code>data_to_data</code></dt>
+            <dd>
+              <p>
+                Will align lists of pfts and species. Must be assosiated with
+                inputs.
+              </p>
+            </dd>
+            <dt><code>data_to_model</code></dt>
+            <dd><p>Not yet implemented</p></dd>
+            <dt><code>model_to_model</code></dt>
+            <dd><p>Not yet implemented</p></dd>
+          </dl>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 
 <span class='co'>#------------ A species to PFT alignment -----------</span>
 <span class='no'>observation_one</span><span class='kw'>&lt;-</span><span class='fu'>c</span>(<span class='st'>"AMCA3"</span>,<span class='st'>"AMCA3"</span>,<span class='st'>"AMCA3"</span>,<span class='st'>"AMCA3"</span>)
@@ -190,40 +282,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Tempest McCabe
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Tempest McCabe
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
-
diff --git a/modules/benchmark/docs/reference/bm_settings2pecan_settings.html b/modules/benchmark/docs/reference/bm_settings2pecan_settings.html
index 27652c6..6926685 100644
--- a/modules/benchmark/docs/reference/bm_settings2pecan_settings.html
+++ b/modules/benchmark/docs/reference/bm_settings2pecan_settings.html
@@ -2,147 +2,191 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Move benchmarking settings back in to original pecan settings object</h1>
-    
-    <div class="hidden name"><code>bm_settings2pecan_settings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Move benchmarking settings back in to original pecan settings object</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>bm_settings2pecan_settings</span>(<span class='no'>bm.settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bm.settings</th>
-      <td><p>settings or multisettings object</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Move benchmarking settings back in to original pecan settings
+              object
+            </h1>
+
+            <div class="hidden name">
+              <code>bm_settings2pecan_settings.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Move benchmarking settings back in to original pecan settings
+              object
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>bm_settings2pecan_settings</span>(<span class='no'>bm.settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bm.settings</th>
+              <td><p>settings or multisettings object</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/benchmark/docs/reference/calc_benchmark.html b/modules/benchmark/docs/reference/calc_benchmark.html
index a07f56b..dc53220 100644
--- a/modules/benchmark/docs/reference/calc_benchmark.html
+++ b/modules/benchmark/docs/reference/calc_benchmark.html
@@ -2,151 +2,189 @@
 <!DOCTYPE html>
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate benchmarking statistics</h1>
-    
-    <div class="hidden name"><code>calc_benchmark.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>For each benchmark id, calculate metrics and update benchmarks_ensemble_scores</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>calc_benchmark</span>(<span class='no'>settings</span>, <span class='no'>bety</span>, <span class='kw'>start_year</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>end_year</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety</th>
-      <td><p>database connection</p></td>
-    </tr>
-    <tr>
-      <th>bm.ensemble</th>
-      <td><p>object, either from create_BRR or start.bm.ensemle</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate benchmarking statistics</h1>
+
+            <div class="hidden name"><code>calc_benchmark.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              For each benchmark id, calculate metrics and update
+              benchmarks_ensemble_scores
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>calc_benchmark</span>(<span class='no'>settings</span>, <span class='no'>bety</span>, <span class='kw'>start_year</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>end_year</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety</th>
+              <td><p>database connection</p></td>
+            </tr>
+            <tr>
+              <th>bm.ensemble</th>
+              <td><p>object, either from create_BRR or start.bm.ensemle</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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diff --git a/modules/benchmark/docs/reference/calc_metrics.html b/modules/benchmark/docs/reference/calc_metrics.html
index b34e281..92ce49a 100644
--- a/modules/benchmark/docs/reference/calc_metrics.html
+++ b/modules/benchmark/docs/reference/calc_metrics.html
@@ -2,167 +2,194 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+
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+    <meta name="twitter:card" content="summary" />
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+
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+    <![endif]-->
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+                type="button"
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+                  >1.6.0</span
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+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>calc_metrics</h1>
-    
-    <div class="hidden name"><code>calc_metrics.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>calc_metrics</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>calc_metrics</span>(<span class='no'>model.calc</span>, <span class='no'>obvs.calc</span>, <span class='no'>var</span>, <span class='no'>metrics</span>, <span class='no'>ensemble.id</span>, <span class='no'>bm_dir</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>model.calc</th>
-      <td><p>model data</p></td>
-    </tr>
-    <tr>
-      <th>obvs.calc</th>
-      <td><p>observational data</p></td>
-    </tr>
-    <tr>
-      <th>var</th>
-      <td><p>variables to be used</p></td>
-    </tr>
-    <tr>
-      <th>metrics</th>
-      <td><p>metrics to be used</p></td>
-    </tr>
-    <tr>
-      <th>ensemble.id</th>
-      <td><p>id of ensemble run</p></td>
-    </tr>
-    <tr>
-      <th>bm_dir</th>
-      <td><p>directory where benchmarking outputs will be saved</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>calc_metrics</h1>
+
+            <div class="hidden name"><code>calc_metrics.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>calc_metrics</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>calc_metrics</span>(<span class='no'>model.calc</span>, <span class='no'>obvs.calc</span>, <span class='no'>var</span>, <span class='no'>metrics</span>, <span class='no'>ensemble.id</span>, <span class='no'>bm_dir</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>model.calc</th>
+              <td><p>model data</p></td>
+            </tr>
+            <tr>
+              <th>obvs.calc</th>
+              <td><p>observational data</p></td>
+            </tr>
+            <tr>
+              <th>var</th>
+              <td><p>variables to be used</p></td>
+            </tr>
+            <tr>
+              <th>metrics</th>
+              <td><p>metrics to be used</p></td>
+            </tr>
+            <tr>
+              <th>ensemble.id</th>
+              <td><p>id of ensemble run</p></td>
+            </tr>
+            <tr>
+              <th>bm_dir</th>
+              <td><p>directory where benchmarking outputs will be saved</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/benchmark/docs/reference/check_BRR.html b/modules/benchmark/docs/reference/check_BRR.html
index 928ecbf..7fb027e 100644
--- a/modules/benchmark/docs/reference/check_BRR.html
+++ b/modules/benchmark/docs/reference/check_BRR.html
@@ -2,151 +2,193 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Check whether a run has been registered as a reference run in BETY —
+      check_BRR • PEcAn.benchmark
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      content="Check whether a run has been registered as a reference run in BETY — check_BRR"
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+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check whether a run has been registered as a reference run in BETY</h1>
-    
-    <div class="hidden name"><code>check_BRR.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check whether a run has been registered as a reference run in BETY</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check_BRR</span>(<span class='no'>settings_xml</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings_xml</th>
-      <td><p>cleaned settings to be compared with BRR in the database</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Check whether a run has been registered as a reference run in BETY
+            </h1>
+
+            <div class="hidden name"><code>check_BRR.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Check whether a run has been registered as a reference run in BETY
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_BRR</span>(<span class='no'>settings_xml</span>, <span class='no'>con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings_xml</th>
+              <td>
+                <p>cleaned settings to be compared with BRR in the database</p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/modules/benchmark/docs/reference/check_if_legal_table.html b/modules/benchmark/docs/reference/check_if_legal_table.html
index 582d2ef..19257f1 100644
--- a/modules/benchmark/docs/reference/check_if_legal_table.html
+++ b/modules/benchmark/docs/reference/check_if_legal_table.html
@@ -2,171 +2,213 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+
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+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>check_if_legal_table</h1>
-    
-    <div class="hidden name"><code>check_if_legal_table.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>check_if_legal_table</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check_if_legal_table</span>(<span class='no'>table</span>, <span class='no'>observation_one</span>, <span class='no'>observation_two</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>observation_one</th>
-      <td><p>a vector of plant functional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>observation_two</th>
-      <td><p>anouther vector of plant functional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>custom_table</th>
-      <td><p>a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
-In the second case, must be passable to match_species_id.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>boolean</code></p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Checks if custom_table:
-1. is formated correctly
-2. is complete (has all of the species/pft's in both observations)
-3. is condense-able (Could be represented as a hierachry)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>check_if_legal_table</h1>
+
+            <div class="hidden name"><code>check_if_legal_table.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>check_if_legal_table</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_if_legal_table</span>(<span class='no'>table</span>, <span class='no'>observation_one</span>, <span class='no'>observation_two</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>observation_one</th>
+              <td><p>a vector of plant functional types, or species</p></td>
+            </tr>
+            <tr>
+              <th>observation_two</th>
+              <td>
+                <p>anouther vector of plant functional types, or species</p>
+              </td>
+            </tr>
+            <tr>
+              <th>custom_table</th>
+              <td>
+                <p>
+                  a table that either maps two pft's to one anouther or maps
+                  custom species codes to bety id codes. In the second case,
+                  must be passable to match_species_id.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>boolean</code></p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Checks if custom_table: 1. is formated correctly 2. is complete (has
+            all of the species/pft's in both observations) 3. is condense-able
+            (Could be represented as a hierachry)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Tempest McCabe
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Tempest McCabe
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
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diff --git a/modules/benchmark/docs/reference/check_if_list_of_pfts.html b/modules/benchmark/docs/reference/check_if_list_of_pfts.html
index 0f3b43d..78b40ac 100644
--- a/modules/benchmark/docs/reference/check_if_list_of_pfts.html
+++ b/modules/benchmark/docs/reference/check_if_list_of_pfts.html
@@ -2,168 +2,213 @@
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+    </title>
+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
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+                <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+            </div>
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+                  <a href="../reference/index.html">Reference</a>
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>check_if_list_of_pfts</h1>
-    
-    <div class="hidden name"><code>check_if_list_of_pfts.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>check_if_list_of_pfts</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check_if_list_of_pfts</span>(<span class='no'>vars</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>observation_one</th>
-      <td><p>a vector of plant fucntional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>observation_two</th>
-      <td><p>anouther vector of plant fucntional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>custom_table</th>
-      <td><p>a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
-In the second case, must be passable to match_species_id.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>boolean</code></p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Checks if format contains a variable named "plant_functional_type"</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>check_if_list_of_pfts</h1>
+
+            <div class="hidden name"><code>check_if_list_of_pfts.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>check_if_list_of_pfts</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_if_list_of_pfts</span>(<span class='no'>vars</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>observation_one</th>
+              <td><p>a vector of plant fucntional types, or species</p></td>
+            </tr>
+            <tr>
+              <th>observation_two</th>
+              <td>
+                <p>anouther vector of plant fucntional types, or species</p>
+              </td>
+            </tr>
+            <tr>
+              <th>custom_table</th>
+              <td>
+                <p>
+                  a table that either maps two pft's to one anouther or maps
+                  custom species codes to bety id codes. In the second case,
+                  must be passable to match_species_id.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>boolean</code></p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Checks if format contains a variable named "plant_functional_type"
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Tempest McCabe
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Tempest McCabe
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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-
diff --git a/modules/benchmark/docs/reference/check_if_species_list.html b/modules/benchmark/docs/reference/check_if_species_list.html
index 2e25eb4..3595ad6 100644
--- a/modules/benchmark/docs/reference/check_if_species_list.html
+++ b/modules/benchmark/docs/reference/check_if_species_list.html
@@ -2,168 +2,214 @@
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<div class="row">
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-    <h1>check_if_species_list</h1>
-    
-    <div class="hidden name"><code>check_if_species_list.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>check_if_species_list</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check_if_species_list</span>(<span class='no'>vars</span>, <span class='kw'>custom_table</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>custom_table</th>
-      <td><p>a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. 
-In the second case, must be passable to match_species_id.</p></td>
-    </tr>
-    <tr>
-      <th>observation_one</th>
-      <td><p>a vector of plant functional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>observation_two</th>
-      <td><p>another vector of plant functional types, or species</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>boolean</code></p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Checks if format contains a species list in a known format, or a declared custom format.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>check_if_species_list</h1>
+
+            <div class="hidden name"><code>check_if_species_list.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>check_if_species_list</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_if_species_list</span>(<span class='no'>vars</span>, <span class='kw'>custom_table</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>custom_table</th>
+              <td>
+                <p>
+                  a table that either maps two pft's to one anouther or maps
+                  custom species codes to bety id codes. In the second case,
+                  must be passable to match_species_id.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>observation_one</th>
+              <td><p>a vector of plant functional types, or species</p></td>
+            </tr>
+            <tr>
+              <th>observation_two</th>
+              <td>
+                <p>another vector of plant functional types, or species</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>boolean</code></p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Checks if format contains a species list in a known format, or a
+            declared custom format.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Tempest McCabe
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Tempest McCabe
+        </div>
+      </div>
 
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-    
-    <div class="hidden name"><code>clean_settings_BRR.Rd</code></div>
-    </div>
-
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-    
-    <p>Cleans PEcAn settings file and prepares the settings to be saved in a reference run record in BETY</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>clean_settings_BRR</span>(<span class='no'>inputfile</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>inputfile</th>
-      <td><p>the PEcAn settings file to be used.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Cleans PEcAn settings file and prepares the settings to be saved
+              in a reference run record in BETY
+            </h1>
+
+            <div class="hidden name"><code>clean_settings_BRR.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Cleans PEcAn settings file and prepares the settings to be saved
+              in a reference run record in BETY
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>clean_settings_BRR</span>(<span class='no'>inputfile</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>inputfile</th>
+              <td><p>the PEcAn settings file to be used.</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/benchmark/docs/reference/create_BRR.html b/modules/benchmark/docs/reference/create_BRR.html
index 4492ffb..38d1c56 100644
--- a/modules/benchmark/docs/reference/create_BRR.html
+++ b/modules/benchmark/docs/reference/create_BRR.html
@@ -2,151 +2,191 @@
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+      Create benchmark reference run and ensemble — create_BRR • PEcAn.benchmark
+    </title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Create benchmark reference run and ensemble — create_BRR"
+    />
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+    />
+    <meta name="twitter:card" content="summary" />
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+            </div>
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+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create benchmark reference run and ensemble</h1>
-    
-    <div class="hidden name"><code>create_BRR.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>For each benchmark id, calculate metrics and update benchmarks_ensemble_scores</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>create_BRR</span>(<span class='no'>ens_wf</span>, <span class='no'>con</span>, <span class='kw'>user_id</span> <span class='kw'>=</span> <span class='st'>""</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ens_wf</th>
-      <td><p>table made from joining ensemble and workflow tables</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create benchmark reference run and ensemble</h1>
+
+            <div class="hidden name"><code>create_BRR.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              For each benchmark id, calculate metrics and update
+              benchmarks_ensemble_scores
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>create_BRR</span>(<span class='no'>ens_wf</span>, <span class='no'>con</span>, <span class='kw'>user_id</span> <span class='kw'>=</span> <span class='st'>""</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ens_wf</th>
+              <td>
+                <p>table made from joining ensemble and workflow tables</p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/benchmark/docs/reference/define_benchmark.html b/modules/benchmark/docs/reference/define_benchmark.html
index 996ea8e..6e03249 100644
--- a/modules/benchmark/docs/reference/define_benchmark.html
+++ b/modules/benchmark/docs/reference/define_benchmark.html
@@ -2,153 +2,196 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      Benchmark Definition: Retrieve or Create Bety Benchmarking Records —
+      define_benchmark • PEcAn.benchmark
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Benchmark Definition: Retrieve or Create Bety Benchmarking Records</h1>
-    
-    <div class="hidden name"><code>define_benchmark.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Creates records for benchmarks, benchmarks_benchmarks_reference_runs, benchmarks_metrics</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>define_benchmark</span>(<span class='no'>settings</span>, <span class='no'>bety</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bm.settings</th>
-      <td><p>settings list</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>updated settings list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Benchmark Definition: Retrieve or Create Bety Benchmarking Records
+            </h1>
+
+            <div class="hidden name"><code>define_benchmark.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Creates records for benchmarks,
+              benchmarks_benchmarks_reference_runs, benchmarks_metrics
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>define_benchmark</span>(<span class='no'>settings</span>, <span class='no'>bety</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bm.settings</th>
+              <td><p>settings list</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>updated settings list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Betsy Cowdery
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/benchmark/docs/reference/format_wide2long.html b/modules/benchmark/docs/reference/format_wide2long.html
index 3c441d0..bfca079 100644
--- a/modules/benchmark/docs/reference/format_wide2long.html
+++ b/modules/benchmark/docs/reference/format_wide2long.html
@@ -2,162 +2,190 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>format_wide2long — format_wide2long • PEcAn.benchmark</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="format_wide2long — format_wide2long" />
-
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-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>format_wide2long — format_wide2long • PEcAn.benchmark</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="format_wide2long — format_wide2long" />
+
+    <meta property="og:description" content="format_wide2long" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
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-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>format_wide2long</h1>
-    
-    <div class="hidden name"><code>format_wide2long.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>format_wide2long</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>format_wide2long</span>(<span class='no'>out</span>, <span class='no'>format</span>, <span class='no'>vars_used</span>, <span class='no'>time.row</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>out</th>
-      <td><p>wide format data</p></td>
-    </tr>
-    <tr>
-      <th>format</th>
-      <td><p>as returned by query.format.vars</p></td>
-    </tr>
-    <tr>
-      <th>vars_used</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list of updated values</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>format_wide2long</h1>
+
+            <div class="hidden name"><code>format_wide2long.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>format_wide2long</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>format_wide2long</span>(<span class='no'>out</span>, <span class='no'>format</span>, <span class='no'>vars_used</span>, <span class='no'>time.row</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>out</th>
+              <td><p>wide format data</p></td>
+            </tr>
+            <tr>
+              <th>format</th>
+              <td><p>as returned by query.format.vars</p></td>
+            </tr>
+            <tr>
+              <th>vars_used</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list of updated values</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
-Function to convert wide format to long format
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer Function to convert wide format to long format
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/benchmark/docs/reference/get_species_list_standard.html b/modules/benchmark/docs/reference/get_species_list_standard.html
index 2f7cbca..c11591e 100644
--- a/modules/benchmark/docs/reference/get_species_list_standard.html
+++ b/modules/benchmark/docs/reference/get_species_list_standard.html
@@ -2,168 +2,218 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>get_species_list_standard — get_species_list_standard • PEcAn.benchmark</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      get_species_list_standard — get_species_list_standard • PEcAn.benchmark
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
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+    <!-- clipboard.js -->
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+    />
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-<div class="row">
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-    <h1>get_species_list_standard</h1>
-    
-    <div class="hidden name"><code>get_species_list_standard.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>get_species_list_standard</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_species_list_standard</span>(<span class='no'>vars</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>observation_one</th>
-      <td><p>a vector of plant fucntional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>observation_two</th>
-      <td><p>anouther vector of plant fucntional types, or species</p></td>
-    </tr>
-    <tr>
-      <th>custom_table</th>
-      <td><p>a table that either maps two pft's to one another or maps custom species codes to bety id codes. 
-In the second case, must be passable to match_species_id.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>character</code> Returns "usda", "latin_name", "fia" or "custom"</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Returns the format type for convience of use with match_species_id</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get_species_list_standard</h1>
+
+            <div class="hidden name">
+              <code>get_species_list_standard.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>get_species_list_standard</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_species_list_standard</span>(<span class='no'>vars</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>observation_one</th>
+              <td><p>a vector of plant fucntional types, or species</p></td>
+            </tr>
+            <tr>
+              <th>observation_two</th>
+              <td>
+                <p>anouther vector of plant fucntional types, or species</p>
+              </td>
+            </tr>
+            <tr>
+              <th>custom_table</th>
+              <td>
+                <p>
+                  a table that either maps two pft's to one another or maps
+                  custom species codes to bety id codes. In the second case,
+                  must be passable to match_species_id.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            <code>character</code> Returns "usda", "latin_name", "fia" or
+            "custom"
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Returns the format type for convience of use with match_species_id
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Tempest McCabe
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Tempest McCabe
+        </div>
+      </div>
 
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+      <div class="row">
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-    <tbody>
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-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
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-        
-        <td>
-          <p><code><a href="add_workflow_info.html">add_workflow_info()</a></code> </p>
-        </td>
-        <td><p>Add workflow specific info to settings list for benchmarking</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="align_by_first_observation.html">align_by_first_observation()</a></code> </p>
-        </td>
-        <td><p>align_first_observation</p></td>
-      </tr><tr>
-        
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-          <p><code><a href="align_data.html">align_data()</a></code> </p>
-        </td>
-        <td><p>Align timeseries data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="align_data_to_data_pft.html">align_data_to_data_pft()</a></code> </p>
-        </td>
-        <td><p>align_data_to_data_pft</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="align_pft.html">align_pft()</a></code> </p>
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-        
-        <td>
-          <p><code><a href="bm_settings2pecan_settings.html">bm_settings2pecan_settings()</a></code> </p>
-        </td>
-        <td><p>Move benchmarking settings back in to original pecan settings object</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="calc_benchmark.html">calc_benchmark()</a></code> </p>
-        </td>
-        <td><p>Calculate benchmarking statistics</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="calc_metrics.html">calc_metrics()</a></code> </p>
-        </td>
-        <td><p>calc_metrics</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_BRR.html">check_BRR()</a></code> </p>
-        </td>
-        <td><p>Check whether a run has been registered as a reference run in BETY</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_if_legal_table.html">check_if_legal_table()</a></code> </p>
-        </td>
-        <td><p>check_if_legal_table</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_if_list_of_pfts.html">check_if_list_of_pfts()</a></code> </p>
-        </td>
-        <td><p>check_if_list_of_pfts</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_if_species_list.html">check_if_species_list()</a></code> </p>
-        </td>
-        <td><p>check_if_species_list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="clean_settings_BRR.html">clean_settings_BRR()</a></code> </p>
-        </td>
-        <td><p>Cleans PEcAn settings file and prepares the settings to be saved in a reference run record in BETY</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="create_BRR.html">create_BRR()</a></code> </p>
-        </td>
-        <td><p>Create benchmark reference run and ensemble</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="define_benchmark.html">define_benchmark()</a></code> </p>
-        </td>
-        <td><p>Benchmark Definition: Retrieve or Create Bety Benchmarking Records</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="format_wide2long.html">format_wide2long()</a></code> </p>
-        </td>
-        <td><p>format_wide2long</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_species_list_standard.html">get_species_list_standard()</a></code> </p>
-        </td>
-        <td><p>get_species_list_standard</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load_csv.html">load_csv()</a></code> </p>
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-        <td><p>load_csv</p></td>
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-        
-        <td>
-          <p><code><a href="load_data.html">load_data()</a></code> </p>
-        </td>
-        <td><p>load_data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load_rds.html">load_rds()</a></code> </p>
-        </td>
-        <td><p>load_rds</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load_tab_separated_values.html">load_tab_separated_values()</a></code> </p>
-        </td>
-        <td><p>load_tab_separated_values</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load_x_netcdf.html">load_x_netcdf()</a></code> </p>
-        </td>
-        <td><p>load_x_netcdf</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="match_timestep.html">match_timestep()</a></code> </p>
-        </td>
-        <td><p>Match time step</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="mean_over_larger_timestep.html">mean_over_larger_timestep()</a></code> </p>
-        </td>
-        <td><p>Calculate benchmarking statistics</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_AME.html">metric_AME()</a></code> </p>
-        </td>
-        <td><p>Absolute Maximum Error</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_Frechet.html">metric_Frechet()</a></code> </p>
-        </td>
-        <td><p>Frechet Distance</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_MAE.html">metric_MAE()</a></code> </p>
-        </td>
-        <td><p>Mean Absolute Error</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_MSE.html">metric_MSE()</a></code> </p>
-        </td>
-        <td><p>Mean Square Error</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_PPMC.html">metric_PPMC()</a></code> </p>
-        </td>
-        <td><p>Pearson Product Moment Correlation</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_R2.html">metric_R2()</a></code> </p>
-        </td>
-        <td><p>Coefficient of Determination (R2)</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_RAE.html">metric_RAE()</a></code> </p>
-        </td>
-        <td><p>Relative Absolute Error</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_RMSE.html">metric_RMSE()</a></code> </p>
-        </td>
-        <td><p>Root Mean Square Error</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_cor.html">metric_cor()</a></code> </p>
-        </td>
-        <td><p>Correlation Coefficient</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_lmDiag_plot.html">metric_lmDiag_plot()</a></code> </p>
-        </td>
-        <td><p>Linear Regression Diagnostic Plot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_residual_plot.html">metric_residual_plot()</a></code> </p>
-        </td>
-        <td><p>Residual Plot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_run.html">metric_run()</a></code> </p>
-        </td>
-        <td><p>Model Run Check</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_scatter_plot.html">metric_scatter_plot()</a></code> </p>
-        </td>
-        <td><p>Scatter Plot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metric_timeseries_plot.html">metric_timeseries_plot()</a></code> </p>
-        </td>
-        <td><p>Timeseries Plot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_settings_BRR.html">read_settings_BRR()</a></code> </p>
-        </td>
-        <td><p>Read settings from database using reference run id</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="add_workflow_info.html"
+                        >add_workflow_info()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Add workflow specific info to settings list for benchmarking
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="align_by_first_observation.html"
+                        >align_by_first_observation()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>align_first_observation</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="align_data.html">align_data()</a></code>
+                  </p>
+                </td>
+                <td><p>Align timeseries data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="align_data_to_data_pft.html"
+                        >align_data_to_data_pft()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>align_data_to_data_pft</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="align_pft.html">align_pft()</a></code>
+                  </p>
+                </td>
+                <td><p>align_pft</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="bm_settings2pecan_settings.html"
+                        >bm_settings2pecan_settings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Move benchmarking settings back in to original pecan
+                    settings object
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="calc_benchmark.html">calc_benchmark()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Calculate benchmarking statistics</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="calc_metrics.html">calc_metrics()</a></code>
+                  </p>
+                </td>
+                <td><p>calc_metrics</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="check_BRR.html">check_BRR()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Check whether a run has been registered as a reference run
+                    in BETY
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check_if_legal_table.html"
+                        >check_if_legal_table()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>check_if_legal_table</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check_if_list_of_pfts.html"
+                        >check_if_list_of_pfts()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>check_if_list_of_pfts</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check_if_species_list.html"
+                        >check_if_species_list()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>check_if_species_list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="clean_settings_BRR.html"
+                        >clean_settings_BRR()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Cleans PEcAn settings file and prepares the settings to be
+                    saved in a reference run record in BETY
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="create_BRR.html">create_BRR()</a></code>
+                  </p>
+                </td>
+                <td><p>Create benchmark reference run and ensemble</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="define_benchmark.html"
+                        >define_benchmark()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Benchmark Definition: Retrieve or Create Bety Benchmarking
+                    Records
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="format_wide2long.html"
+                        >format_wide2long()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>format_wide2long</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_species_list_standard.html"
+                        >get_species_list_standard()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>get_species_list_standard</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="load_csv.html">load_csv()</a></code>
+                  </p>
+                </td>
+                <td><p>load_csv</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="load_data.html">load_data()</a></code>
+                  </p>
+                </td>
+                <td><p>load_data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="load_rds.html">load_rds()</a></code>
+                  </p>
+                </td>
+                <td><p>load_rds</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="load_tab_separated_values.html"
+                        >load_tab_separated_values()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>load_tab_separated_values</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="load_x_netcdf.html">load_x_netcdf()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>load_x_netcdf</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="match_timestep.html">match_timestep()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Match time step</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="mean_over_larger_timestep.html"
+                        >mean_over_larger_timestep()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Calculate benchmarking statistics</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metric_AME.html">metric_AME()</a></code>
+                  </p>
+                </td>
+                <td><p>Absolute Maximum Error</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="metric_Frechet.html">metric_Frechet()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Frechet Distance</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metric_MAE.html">metric_MAE()</a></code>
+                  </p>
+                </td>
+                <td><p>Mean Absolute Error</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metric_MSE.html">metric_MSE()</a></code>
+                  </p>
+                </td>
+                <td><p>Mean Square Error</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metric_PPMC.html">metric_PPMC()</a></code>
+                  </p>
+                </td>
+                <td><p>Pearson Product Moment Correlation</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metric_R2.html">metric_R2()</a></code>
+                  </p>
+                </td>
+                <td><p>Coefficient of Determination (R2)</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metric_RAE.html">metric_RAE()</a></code>
+                  </p>
+                </td>
+                <td><p>Relative Absolute Error</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metric_RMSE.html">metric_RMSE()</a></code>
+                  </p>
+                </td>
+                <td><p>Root Mean Square Error</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metric_cor.html">metric_cor()</a></code>
+                  </p>
+                </td>
+                <td><p>Correlation Coefficient</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="metric_lmDiag_plot.html"
+                        >metric_lmDiag_plot()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Linear Regression Diagnostic Plot</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="metric_residual_plot.html"
+                        >metric_residual_plot()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Residual Plot</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metric_run.html">metric_run()</a></code>
+                  </p>
+                </td>
+                <td><p>Model Run Check</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="metric_scatter_plot.html"
+                        >metric_scatter_plot()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Scatter Plot</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="metric_timeseries_plot.html"
+                        >metric_timeseries_plot()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Timeseries Plot</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read_settings_BRR.html"
+                        >read_settings_BRR()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Read settings from database using reference run id</p>
+                </td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/benchmark/docs/reference/load_csv.html b/modules/benchmark/docs/reference/load_csv.html
index 47175ea..39b5a96 100644
--- a/modules/benchmark/docs/reference/load_csv.html
+++ b/modules/benchmark/docs/reference/load_csv.html
@@ -2,163 +2,190 @@
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 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-
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-
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-
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-
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-<link href="../pkgdown.css" rel="stylesheet">
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-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="load_csv — load_csv" />
+
+    <meta property="og:description" content="load_csv" />
+    <meta name="twitter:card" content="summary" />
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
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+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                    <span class="fa fa-home fa-lg"></span>
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>load_csv</h1>
-    
-    <div class="hidden name"><code>load_csv.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>load_csv</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>load_csv</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='no'>site</span>, <span class='kw'>vars</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data.path</th>
-      <td><p>character</p></td>
-    </tr>
-    <tr>
-      <th>format</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>site</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>start_year</th>
-      <td><p>numeric</p></td>
-    </tr>
-    <tr>
-      <th>end_year</th>
-      <td><p>numeric</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load_csv</h1>
+
+            <div class="hidden name"><code>load_csv.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>load_csv</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load_csv</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='no'>site</span>, <span class='kw'>vars</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data.path</th>
+              <td><p>character</p></td>
+            </tr>
+            <tr>
+              <th>format</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>site</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>start_year</th>
+              <td><p>numeric</p></td>
+            </tr>
+            <tr>
+              <th>end_year</th>
+              <td><p>numeric</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/benchmark/docs/reference/load_data.html b/modules/benchmark/docs/reference/load_data.html
index 538b575..a64f4a9 100644
--- a/modules/benchmark/docs/reference/load_data.html
+++ b/modules/benchmark/docs/reference/load_data.html
@@ -2,166 +2,192 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>load_data — load_data • PEcAn.benchmark</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>load_data — load_data • PEcAn.benchmark</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="load_data — load_data" />
+
+    <meta property="og:description" content="load_data" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-        <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
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-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>load_data</h1>
-    
-    <div class="hidden name"><code>load_data.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load_data</h1>
 
-    <div class="ref-description">
-    
-    <p>load_data</p>
-    
-    </div>
+            <div class="hidden name"><code>load_data.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>load_data</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='kw'>start_year</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>end_year</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
-  <span class='kw'>site</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>vars.used.index</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data.path</th>
-      <td><p>character</p></td>
-    </tr>
-    <tr>
-      <th>format</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>start_year</th>
-      <td><p>numeric</p></td>
-    </tr>
-    <tr>
-      <th>end_year</th>
-      <td><p>numeric</p></td>
-    </tr>
-    <tr>
-      <th>site</th>
-      <td><p>list</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery, Istem Fer, Joshua Mantooth
-Generic function to convert input files containing observational data to 
-a common PEcAn format.
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>load_data</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>load_data</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='kw'>start_year</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>end_year</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+  <span class='kw'>site</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>vars.used.index</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data.path</th>
+              <td><p>character</p></td>
+            </tr>
+            <tr>
+              <th>format</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>start_year</th>
+              <td><p>numeric</p></td>
+            </tr>
+            <tr>
+              <th>end_year</th>
+              <td><p>numeric</p></td>
+            </tr>
+            <tr>
+              <th>site</th>
+              <td><p>list</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery, Istem Fer, Joshua Mantooth Generic function to convert
+          input files containing observational data to a common PEcAn format.
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/benchmark/docs/reference/load_rds.html b/modules/benchmark/docs/reference/load_rds.html
index 9872298..8ee2083 100644
--- a/modules/benchmark/docs/reference/load_rds.html
+++ b/modules/benchmark/docs/reference/load_rds.html
@@ -2,159 +2,186 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>load_rds — load_rds • PEcAn.benchmark</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
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-<!-- clipboard.js -->
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-    <h1>load_rds</h1>
-    
-    <div class="hidden name"><code>load_rds.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>load_rds</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>load_rds</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='no'>site</span>, <span class='kw'>vars</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data.path</th>
-      <td><p>character</p></td>
-    </tr>
-    <tr>
-      <th>format</th>
-      <td><p>list, not used, for compatibility</p></td>
-    </tr>
-    <tr>
-      <th>site</th>
-      <td><p>not used, for compatibility</p></td>
-    </tr>
-    <tr>
-      <th>vars</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load_rds</h1>
+
+            <div class="hidden name"><code>load_rds.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>load_rds</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load_rds</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='no'>site</span>, <span class='kw'>vars</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data.path</th>
+              <td><p>character</p></td>
+            </tr>
+            <tr>
+              <th>format</th>
+              <td><p>list, not used, for compatibility</p></td>
+            </tr>
+            <tr>
+              <th>site</th>
+              <td><p>not used, for compatibility</p></td>
+            </tr>
+            <tr>
+              <th>vars</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
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diff --git a/modules/benchmark/docs/reference/load_tab_separated_values.html b/modules/benchmark/docs/reference/load_tab_separated_values.html
index 03078c8..9abac3e 100644
--- a/modules/benchmark/docs/reference/load_tab_separated_values.html
+++ b/modules/benchmark/docs/reference/load_tab_separated_values.html
@@ -2,163 +2,197 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      load_tab_separated_values — load_tab_separated_values • PEcAn.benchmark
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+    />
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+
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+    <script src="../pkgdown.js"></script>
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+    />
+
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+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>load_tab_separated_values</h1>
-    
-    <div class="hidden name"><code>load_tab_separated_values.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>load_tab_separated_values</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>load_tab_separated_values</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='kw'>site</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>vars</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data.path</th>
-      <td><p>character</p></td>
-    </tr>
-    <tr>
-      <th>format</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>site</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>start_year</th>
-      <td><p>numeric</p></td>
-    </tr>
-    <tr>
-      <th>end_year</th>
-      <td><p>numeric</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery, Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load_tab_separated_values</h1>
+
+            <div class="hidden name">
+              <code>load_tab_separated_values.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>load_tab_separated_values</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load_tab_separated_values</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='kw'>site</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>vars</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data.path</th>
+              <td><p>character</p></td>
+            </tr>
+            <tr>
+              <th>format</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>site</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>start_year</th>
+              <td><p>numeric</p></td>
+            </tr>
+            <tr>
+              <th>end_year</th>
+              <td><p>numeric</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery, Mike Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/benchmark/docs/reference/load_x_netcdf.html b/modules/benchmark/docs/reference/load_x_netcdf.html
index dda4178..1fcee2f 100644
--- a/modules/benchmark/docs/reference/load_x_netcdf.html
+++ b/modules/benchmark/docs/reference/load_x_netcdf.html
@@ -2,167 +2,194 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                  class="label label-default"
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>load_x_netcdf</h1>
-    
-    <div class="hidden name"><code>load_x_netcdf.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>load_x_netcdf</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>load_x_netcdf</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='no'>site</span>, <span class='kw'>vars</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data.path</th>
-      <td><p>character vector or list</p></td>
-    </tr>
-    <tr>
-      <th>format</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>site</th>
-      <td><p>list</p></td>
-    </tr>
-    <tr>
-      <th>vars</th>
-      <td><p>character</p></td>
-    </tr>
-    <tr>
-      <th>start_year</th>
-      <td><p>numeric</p></td>
-    </tr>
-    <tr>
-      <th>end_year</th>
-      <td><p>numeric</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load_x_netcdf</h1>
+
+            <div class="hidden name"><code>load_x_netcdf.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>load_x_netcdf</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load_x_netcdf</span>(<span class='no'>data.path</span>, <span class='no'>format</span>, <span class='no'>site</span>, <span class='kw'>vars</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data.path</th>
+              <td><p>character vector or list</p></td>
+            </tr>
+            <tr>
+              <th>format</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>site</th>
+              <td><p>list</p></td>
+            </tr>
+            <tr>
+              <th>vars</th>
+              <td><p>character</p></td>
+            </tr>
+            <tr>
+              <th>start_year</th>
+              <td><p>numeric</p></td>
+            </tr>
+            <tr>
+              <th>end_year</th>
+              <td><p>numeric</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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   </body>
 </html>
-
diff --git a/modules/benchmark/docs/reference/match_timestep.html b/modules/benchmark/docs/reference/match_timestep.html
index f0da2eb..88de7e4 100644
--- a/modules/benchmark/docs/reference/match_timestep.html
+++ b/modules/benchmark/docs/reference/match_timestep.html
@@ -2,155 +2,182 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
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-
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-
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+
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+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+    <![endif]-->
   </head>
 
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+          <div class="container">
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+                type="button"
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+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Match time step</h1>
-    
-    <div class="hidden name"><code>match_timestep.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Match time step</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>match_timestep</span>(<span class='no'>date.coarse</span>, <span class='no'>date.fine</span>, <span class='no'>data.fine</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>date.coarse</th>
-      <td><p>numeric</p></td>
-    </tr>
-    <tr>
-      <th>date.fine</th>
-      <td><p>numeric</p></td>
-    </tr>
-    <tr>
-      <th>data.fine</th>
-      <td><p>matrix</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Match time step</h1>
+
+            <div class="hidden name"><code>match_timestep.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Match time step</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>match_timestep</span>(<span class='no'>date.coarse</span>, <span class='no'>date.fine</span>, <span class='no'>data.fine</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>date.coarse</th>
+              <td><p>numeric</p></td>
+            </tr>
+            <tr>
+              <th>date.fine</th>
+              <td><p>numeric</p></td>
+            </tr>
+            <tr>
+              <th>data.fine</th>
+              <td><p>matrix</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/benchmark/docs/reference/mean_over_larger_timestep.html b/modules/benchmark/docs/reference/mean_over_larger_timestep.html
index e72d40d..ffd3f2f 100644
--- a/modules/benchmark/docs/reference/mean_over_larger_timestep.html
+++ b/modules/benchmark/docs/reference/mean_over_larger_timestep.html
@@ -2,155 +2,193 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      Calculate benchmarking statistics — mean_over_larger_timestep •
+      PEcAn.benchmark
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Calculate benchmarking statistics — mean_over_larger_timestep"
+    />
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+      property="og:description"
+      content="Calculate benchmarking statistics"
+    />
+    <meta name="twitter:card" content="summary" />
+
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-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate benchmarking statistics</h1>
-    
-    <div class="hidden name"><code>mean_over_larger_timestep.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate benchmarking statistics</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>mean_over_larger_timestep</span>(<span class='no'>date.coarse</span>, <span class='no'>date.fine</span>, <span class='no'>data.fine</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>date.coarse</th>
-      <td><p>numeric</p></td>
-    </tr>
-    <tr>
-      <th>date.fine</th>
-      <td><p>numeric</p></td>
-    </tr>
-    <tr>
-      <th>data.fine</th>
-      <td><p>data.frame</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery, Michael Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate benchmarking statistics</h1>
+
+            <div class="hidden name">
+              <code>mean_over_larger_timestep.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate benchmarking statistics</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>mean_over_larger_timestep</span>(<span class='no'>date.coarse</span>, <span class='no'>date.fine</span>, <span class='no'>data.fine</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>date.coarse</th>
+              <td><p>numeric</p></td>
+            </tr>
+            <tr>
+              <th>date.fine</th>
+              <td><p>numeric</p></td>
+            </tr>
+            <tr>
+              <th>data.fine</th>
+              <td><p>data.frame</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery, Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
-
diff --git a/modules/benchmark/docs/reference/metric_AME.html b/modules/benchmark/docs/reference/metric_AME.html
index 3bc1b61..c24f486 100644
--- a/modules/benchmark/docs/reference/metric_AME.html
+++ b/modules/benchmark/docs/reference/metric_AME.html
@@ -2,147 +2,174 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
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-
-<!-- clipboard.js -->
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
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+      crossorigin="anonymous"
+    ></script>
+
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Absolute Maximum Error</h1>
-    
-    <div class="hidden name"><code>metric_AME.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Absolute Maximum Error</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_AME</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>dataframe</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Absolute Maximum Error</h1>
+
+            <div class="hidden name"><code>metric_AME.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Absolute Maximum Error</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_AME</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td><p>dataframe</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/benchmark/docs/reference/metric_Frechet.html b/modules/benchmark/docs/reference/metric_Frechet.html
index be2879d..f2eb6f0 100644
--- a/modules/benchmark/docs/reference/metric_Frechet.html
+++ b/modules/benchmark/docs/reference/metric_Frechet.html
@@ -2,147 +2,174 @@
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 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <![endif]-->
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+                type="button"
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+                <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Frechet Distance</h1>
-    
-    <div class="hidden name"><code>metric_Frechet.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Frechet Distance</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_Frechet</span>(<span class='no'>metric_dat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>metric_dat</th>
-      <td><p>dataframe</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Frechet Distance</h1>
+
+            <div class="hidden name"><code>metric_Frechet.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Frechet Distance</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_Frechet</span>(<span class='no'>metric_dat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>metric_dat</th>
+              <td><p>dataframe</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/benchmark/docs/reference/metric_MAE.html b/modules/benchmark/docs/reference/metric_MAE.html
index 980910a..65599bd 100644
--- a/modules/benchmark/docs/reference/metric_MAE.html
+++ b/modules/benchmark/docs/reference/metric_MAE.html
@@ -2,147 +2,174 @@
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 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    />
+
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+    <script
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+                <span
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+                  >1.6.0</span
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+
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+                <li>
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Mean Absolute Error</h1>
-    
-    <div class="hidden name"><code>metric_MAE.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Mean Absolute Error</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_MAE</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>dataframe</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Mean Absolute Error</h1>
+
+            <div class="hidden name"><code>metric_MAE.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Mean Absolute Error</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_MAE</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td><p>dataframe</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
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-  <p>Developed by .</p>
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-</div>
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diff --git a/modules/benchmark/docs/reference/metric_MSE.html b/modules/benchmark/docs/reference/metric_MSE.html
index 7400d40..bc9dd91 100644
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@@ -2,147 +2,174 @@
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+                  >1.6.0</span
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Mean Square Error</h1>
-    
-    <div class="hidden name"><code>metric_MSE.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Mean Square Error</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_MSE</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>dataframe</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Mean Square Error</h1>
+
+            <div class="hidden name"><code>metric_MSE.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Mean Square Error</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_MSE</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td><p>dataframe</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/benchmark/docs/reference/metric_PPMC.html b/modules/benchmark/docs/reference/metric_PPMC.html
index 5fff306..45003c1 100644
--- a/modules/benchmark/docs/reference/metric_PPMC.html
+++ b/modules/benchmark/docs/reference/metric_PPMC.html
@@ -2,147 +2,182 @@
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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-<div class="row">
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-    <h1>Pearson Product Moment Correlation</h1>
-    
-    <div class="hidden name"><code>metric_PPMC.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Pearson Product Moment Correlation</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_PPMC</span>(<span class='no'>metric_dat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>metric_dat</th>
-      <td><p>dataframe</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Pearson Product Moment Correlation</h1>
+
+            <div class="hidden name"><code>metric_PPMC.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Pearson Product Moment Correlation</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_PPMC</span>(<span class='no'>metric_dat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>metric_dat</th>
+              <td><p>dataframe</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
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diff --git a/modules/benchmark/docs/reference/metric_R2.html b/modules/benchmark/docs/reference/metric_R2.html
index a4ad358..0cdf886 100644
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+
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+        <!--/.navbar -->
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Coefficient of Determination (R2)</h1>
-    
-    <div class="hidden name"><code>metric_R2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Coefficient of Determination (R2)</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_R2</span>(<span class='no'>metric_dat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>metric_dat</th>
-      <td><p>dataframe</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Coefficient of Determination (R2)</h1>
+
+            <div class="hidden name"><code>metric_R2.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Coefficient of Determination (R2)</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_R2</span>(<span class='no'>metric_dat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>metric_dat</th>
+              <td><p>dataframe</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/benchmark/docs/reference/metric_RAE.html b/modules/benchmark/docs/reference/metric_RAE.html
index d9adc7b..cf9e8aa 100644
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@@ -2,147 +2,174 @@
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-<div class="row">
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-    <h1>Relative Absolute Error</h1>
-    
-    <div class="hidden name"><code>metric_RAE.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Relative Absolute Error</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_RAE</span>(<span class='no'>metric_dat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>metric_dat</th>
-      <td><p>dataframe</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Relative Absolute Error</h1>
+
+            <div class="hidden name"><code>metric_RAE.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Relative Absolute Error</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_RAE</span>(<span class='no'>metric_dat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>metric_dat</th>
+              <td><p>dataframe</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
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+
+          Betsy Cowdery
+        </div>
+      </div>
 
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diff --git a/modules/benchmark/docs/reference/metric_RMSE.html b/modules/benchmark/docs/reference/metric_RMSE.html
index bbf8424..a6211c4 100644
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+    ></script>
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-<div class="row">
-  <div class="col-md-9 contents">
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-    <h1>Root Mean Square Error</h1>
-    
-    <div class="hidden name"><code>metric_RMSE.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Root Mean Square Error</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_RMSE</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>dataframe</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Root Mean Square Error</h1>
+
+            <div class="hidden name"><code>metric_RMSE.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Root Mean Square Error</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_RMSE</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td><p>dataframe</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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diff --git a/modules/benchmark/docs/reference/metric_cor.html b/modules/benchmark/docs/reference/metric_cor.html
index 82107eb..d677bca 100644
--- a/modules/benchmark/docs/reference/metric_cor.html
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@@ -2,147 +2,174 @@
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-<div class="row">
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-    <h1>Correlation Coefficient</h1>
-    
-    <div class="hidden name"><code>metric_cor.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Correlation Coefficient</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_cor</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>dataframe</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Correlation Coefficient</h1>
+
+            <div class="hidden name"><code>metric_cor.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Correlation Coefficient</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_cor</span>(<span class='no'>dat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td><p>dataframe</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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diff --git a/modules/benchmark/docs/reference/metric_lmDiag_plot.html b/modules/benchmark/docs/reference/metric_lmDiag_plot.html
index 4009339..1c98a48 100644
--- a/modules/benchmark/docs/reference/metric_lmDiag_plot.html
+++ b/modules/benchmark/docs/reference/metric_lmDiag_plot.html
@@ -2,147 +2,182 @@
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+
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Linear Regression Diagnostic Plot</h1>
-    
-    <div class="hidden name"><code>metric_lmDiag_plot.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Linear Regression Diagnostic Plot</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_lmDiag_plot</span>(<span class='no'>metric_dat</span>, <span class='no'>var</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>draw.plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>metric_dat</th>
-      <td><p>data.frame</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Linear Regression Diagnostic Plot</h1>
+
+            <div class="hidden name"><code>metric_lmDiag_plot.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Linear Regression Diagnostic Plot</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_lmDiag_plot</span>(<span class='no'>metric_dat</span>, <span class='no'>var</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>draw.plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>metric_dat</th>
+              <td><p>data.frame</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/benchmark/docs/reference/metric_residual_plot.html b/modules/benchmark/docs/reference/metric_residual_plot.html
index 84e8c0f..5145ed9 100644
--- a/modules/benchmark/docs/reference/metric_residual_plot.html
+++ b/modules/benchmark/docs/reference/metric_residual_plot.html
@@ -2,148 +2,175 @@
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+
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    <!-- clipboard.js -->
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Residual Plot</h1>
-    
-    <div class="hidden name"><code>metric_residual_plot.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Residual Plot</h1>
 
-    <div class="ref-description">
-    
-    <p>Residual Plot</p>
-    
-    </div>
+            <div class="hidden name"><code>metric_residual_plot.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>metric_residual_plot</span>(<span class='no'>metric_dat</span>, <span class='no'>var</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
-  <span class='kw'>draw.plot</span> <span class='kw'>=</span> <span class='fu'>is.na</span>(<span class='no'>filename</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>draw.plot</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Residual Plot</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>metric_residual_plot</span>(<span class='no'>metric_dat</span>, <span class='no'>var</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+  <span class='kw'>draw.plot</span> <span class='kw'>=</span> <span class='fu'>is.na</span>(<span class='no'>filename</span>))</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>draw.plot</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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+        <div class="copyright">
+          <p>Developed by .</p>
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diff --git a/modules/benchmark/docs/reference/metric_run.html b/modules/benchmark/docs/reference/metric_run.html
index 1f3fc1e..fa50427 100644
--- a/modules/benchmark/docs/reference/metric_run.html
+++ b/modules/benchmark/docs/reference/metric_run.html
@@ -2,147 +2,174 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+    />
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Model Run Check</h1>
-    
-    <div class="hidden name"><code>metric_run.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Model Run Check</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metric_run</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>list</p></td>
-    </tr>
-    </table>
-    
-
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Model Run Check</h1>
+
+            <div class="hidden name"><code>metric_run.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Model Run Check</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metric_run</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>list</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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 </html>
-
diff --git a/modules/benchmark/docs/reference/metric_scatter_plot.html b/modules/benchmark/docs/reference/metric_scatter_plot.html
index 16d6798..548fe14 100644
--- a/modules/benchmark/docs/reference/metric_scatter_plot.html
+++ b/modules/benchmark/docs/reference/metric_scatter_plot.html
@@ -2,148 +2,175 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
-<!-- clipboard.js -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Scatter Plot — metric_scatter_plot • PEcAn.benchmark</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Scatter Plot — metric_scatter_plot" />
+
+    <meta property="og:description" content="Scatter Plot" />
+    <meta name="twitter:card" content="summary" />
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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+                <span
+                  class="label label-default"
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+                  >1.6.0</span
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Scatter Plot</h1>
-    
-    <div class="hidden name"><code>metric_scatter_plot.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Scatter Plot</h1>
 
-    <div class="ref-description">
-    
-    <p>Scatter Plot</p>
-    
-    </div>
+            <div class="hidden name"><code>metric_scatter_plot.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>metric_scatter_plot</span>(<span class='no'>metric_dat</span>, <span class='no'>var</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
-  <span class='kw'>draw.plot</span> <span class='kw'>=</span> <span class='fu'>is.na</span>(<span class='no'>filename</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>draw.plot</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Scatter Plot</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>metric_scatter_plot</span>(<span class='no'>metric_dat</span>, <span class='no'>var</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+  <span class='kw'>draw.plot</span> <span class='kw'>=</span> <span class='fu'>is.na</span>(<span class='no'>filename</span>))</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>draw.plot</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/benchmark/docs/reference/metric_timeseries_plot.html b/modules/benchmark/docs/reference/metric_timeseries_plot.html
index 8d80d88..a48346a 100644
--- a/modules/benchmark/docs/reference/metric_timeseries_plot.html
+++ b/modules/benchmark/docs/reference/metric_timeseries_plot.html
@@ -2,138 +2,164 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Timeseries Plot — metric_timeseries_plot • PEcAn.benchmark</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Timeseries Plot — metric_timeseries_plot"
+    />
+
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+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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   <body>
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+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.benchmark</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Timeseries Plot</h1>
-    
-    <div class="hidden name"><code>metric_timeseries_plot.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Timeseries Plot</h1>
 
-    <div class="ref-description">
-    
-    <p>Timeseries Plot</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>metric_timeseries_plot.Rd</code>
+            </div>
+          </div>
 
-    <pre class="usage"><span class='fu'>metric_timeseries_plot</span>(<span class='no'>metric_dat</span>, <span class='no'>var</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
-  <span class='kw'>draw.plot</span> <span class='kw'>=</span> <span class='fu'>is.na</span>(<span class='no'>filename</span>))</pre>
-        
+          <div class="ref-description">
+            <p>Timeseries Plot</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>metric_timeseries_plot</span>(<span class='no'>metric_dat</span>, <span class='no'>var</span>, <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+  <span class='kw'>draw.plot</span> <span class='kw'>=</span> <span class='fu'>is.na</span>(<span class='no'>filename</span>))</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Betsy Cowdery
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
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-</div>
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+
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index 8d5f221..5b029e3 100644
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@@ -2,149 +2,187 @@
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+    />
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read settings from database using reference run id</h1>
-    
-    <div class="hidden name"><code>read_settings_BRR.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>For each benchmark entry in a (multi)settings object, get run settings using reference run id 
-and add to the settings object</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_settings_BRR</span>(<span class='no'>settings</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>settings or multisettings object</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read settings from database using reference run id</h1>
+
+            <div class="hidden name"><code>read_settings_BRR.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              For each benchmark entry in a (multi)settings object, get run
+              settings using reference run id and add to the settings object
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_settings_BRR</span>(<span class='no'>settings</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>settings or multisettings object</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
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-  <p>Developed by .</p>
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index ae6f899..688c42c 100644
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-<pre>University of Illinois/NCSA Open Source License
+          <pre>
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 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -142,27 +186,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
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+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
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+          <div class="page-header toc-ignore">
+            <h1>
+              PEcAn: Importing Met data from Bondville, IL Ameriflux station
+            </h1>
+            <h4 class="author">David LeBauer</h4>
 
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-      <h1>PEcAn: Importing Met data from Bondville, IL Ameriflux station</h1>
-                        <h4 class="author">David LeBauer</h4>
-            
             <h4 class="date">4/28/2015</h4>
-      
-      
-      <div class="hidden name"><code>ameriflux_demo.Rmd</code></div>
 
-    </div>
+            <div class="hidden name"><code>ameriflux_demo.Rmd</code></div>
+          </div>
 
-    
-    
-<div id="overview" class="section level1">
-<h1 class="hasAnchor">
-<a href="#overview" class="anchor"></a>Overview</h1>
-<p>This is a demonstration of the PEcAn utilities for downloading met data, converting it to the PEcAn-CF format (which is based on the Climate Forecasting conventions and similar to MsTMIP). These variables are defined in the <a href="https://pecanproject.github.io/pecan-documentation/master/met-data.html">PEcAn documentation</a>.</p>
-<p>In this example we will download 12 years of met data from the <a href="http://ameriflux.ornl.gov/fullsiteinfo.php?sid=44">Bondville Ameriflux site</a>. It has an Ameriflux <code>SITE_ID</code> of <code>US-Bo1</code></p>
-<p>The PEcAn.data.atmosphere source code is in <a href="https://github.com/PecanProject/pecan/tree/master/modules/data.atmosphere"><code>modules/data.atmosphere</code></a> and the documentation can be found with either <code>package?PEcAn.data.atmosphere</code> or in the <a href="https://pecanproject.github.io/pecan//modules/data.atmosphere/inst/web/index.html">data.atmosphere package documentation</a>.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(knitr)
+          <div id="overview" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#overview" class="anchor"></a>Overview
+            </h1>
+            <p>
+              This is a demonstration of the PEcAn utilities for downloading met
+              data, converting it to the PEcAn-CF format (which is based on the
+              Climate Forecasting conventions and similar to MsTMIP). These
+              variables are defined in the
+              <a
+                href="https://pecanproject.github.io/pecan-documentation/master/met-data.html"
+                >PEcAn documentation</a
+              >.
+            </p>
+            <p>
+              In this example we will download 12 years of met data from the
+              <a href="http://ameriflux.ornl.gov/fullsiteinfo.php?sid=44"
+                >Bondville Ameriflux site</a
+              >. It has an Ameriflux <code>SITE_ID</code> of <code>US-Bo1</code>
+            </p>
+            <p>
+              The PEcAn.data.atmosphere source code is in
+              <a
+                href="https://github.com/PecanProject/pecan/tree/master/modules/data.atmosphere"
+                ><code>modules/data.atmosphere</code></a
+              >
+              and the documentation can be found with either
+              <code>package?PEcAn.data.atmosphere</code> or in the
+              <a
+                href="https://pecanproject.github.io/pecan//modules/data.atmosphere/inst/web/index.html"
+                >data.atmosphere package documentation</a
+              >.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(knitr)
 <span class="kw">library</span>(ggplot2)
 <span class="kw">library</span>(ggthemes)
-<span class="kw">library</span>(PEcAn.data.atmosphere)</code></pre></div>
-<div id="download-ameriflux-data-for-bondville" class="section level2">
-<h2 class="hasAnchor">
-<a href="#download-ameriflux-data-for-bondville" class="anchor"></a>Download Ameriflux data for Bondville</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/download.Ameriflux.html">download.Ameriflux</a></span>(<span class="dt">sitename =</span> <span class="st">"US-Bo1"</span>, <span class="dt">outfolder =</span> <span class="st">"/tmp/"</span>, 
-                   <span class="dt">start_date =</span> <span class="st">"1996-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2008-04-10"</span>)</code></pre></div>
-</div>
-<div id="convert-to-pecan-cf-format" class="section level2">
-<h2 class="hasAnchor">
-<a href="#convert-to-pecan-cf-format" class="anchor"></a>Convert to PEcAn-CF format</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/met2CF.Ameriflux.html">met2CF.Ameriflux</a></span>(<span class="dt">in.path =</span> <span class="st">"/tmp/"</span>, <span class="dt">in.prefix =</span> <span class="st">"US-Bo1"</span>, <span class="dt">outfolder =</span> <span class="st">"/tmp/out/"</span>, 
-                 <span class="dt">start_date =</span> <span class="st">"1996-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2008-04-10"</span>)</code></pre></div>
-</div>
-<div id="concatenate-years" class="section level2">
-<h2 class="hasAnchor">
-<a href="#concatenate-years" class="anchor"></a>Concatenate years</h2>
-<p>NB: this is not required within PEcAn; used here for convenience. See documentation for <a href="http://research.jisao.washington.edu/data_sets/nco/#example8">NCO <code>ncrcat</code> function</a>.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">system</span>(<span class="st">"ncrcat -O -h /tmp/out/US-Bo1.199[6789].nc /tmp/out/US-Bo1.200[12348678].nc /tmp/out/US-Bo11996-2008.nc"</span>)</code></pre></div>
-</div>
-<div id="load" class="section level2">
-<h2 class="hasAnchor">
-<a href="#load" class="anchor"></a>Load</h2>
-<p>Using the <code>load.cfmet</code> convenience function. Ameriflux is provided at 30 min intervals. If needed at a finer resolution, see <code><a href="../reference/cfmet.downscale.time.html">?cfmet.downscale.time</a></code> (which works with subdaily and daily data). There is no <code>cfmet.upscale.time</code> function, but would be straightforward to implement if needed.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">bondville.nc &lt;-<span class="st"> </span><span class="kw">nc_open</span>(<span class="st">"/tmp/out/US-Bo11996-2008.nc"</span>)
-bondville.cfmet &lt;-<span class="st"> </span><span class="kw"><a href="../reference/load.cfmet.html">load.cfmet</a></span>(bondville.nc, <span class="dt">lat =</span> <span class="fl">40.0061988830566</span>, <span class="dt">lon =</span> <span class="op">-</span><span class="fl">88.290397644043</span>, <span class="dt">start.date =</span> <span class="st">"1996-08-25"</span>, <span class="dt">end.date =</span> <span class="st">"2008-04-10"</span>)[<span class="op">!</span><span class="kw">is.na</span>(air_pressure)]</code></pre></div>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/theme_get">theme_set</a></span>(<span class="kw">theme_tufte</span>())
+<span class="kw">library</span>(PEcAn.data.atmosphere)</code></pre>
+            </div>
+            <div
+              id="download-ameriflux-data-for-bondville"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#download-ameriflux-data-for-bondville"
+                  class="anchor"
+                ></a
+                >Download Ameriflux data for Bondville
+              </h2>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw"><a href="../reference/download.Ameriflux.html">download.Ameriflux</a></span>(<span class="dt">sitename =</span> <span class="st">"US-Bo1"</span>, <span class="dt">outfolder =</span> <span class="st">"/tmp/"</span>, 
+                   <span class="dt">start_date =</span> <span class="st">"1996-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2008-04-10"</span>)</code></pre>
+              </div>
+            </div>
+            <div id="convert-to-pecan-cf-format" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#convert-to-pecan-cf-format" class="anchor"></a>Convert
+                to PEcAn-CF format
+              </h2>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw"><a href="../reference/met2CF.Ameriflux.html">met2CF.Ameriflux</a></span>(<span class="dt">in.path =</span> <span class="st">"/tmp/"</span>, <span class="dt">in.prefix =</span> <span class="st">"US-Bo1"</span>, <span class="dt">outfolder =</span> <span class="st">"/tmp/out/"</span>, 
+                 <span class="dt">start_date =</span> <span class="st">"1996-01-01"</span>, <span class="dt">end_date =</span> <span class="st">"2008-04-10"</span>)</code></pre>
+              </div>
+            </div>
+            <div id="concatenate-years" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#concatenate-years" class="anchor"></a>Concatenate
+                years
+              </h2>
+              <p>
+                NB: this is not required within PEcAn; used here for
+                convenience. See documentation for
+                <a
+                  href="http://research.jisao.washington.edu/data_sets/nco/#example8"
+                  >NCO <code>ncrcat</code> function</a
+                >.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">system</span>(<span class="st">"ncrcat -O -h /tmp/out/US-Bo1.199[6789].nc /tmp/out/US-Bo1.200[12348678].nc /tmp/out/US-Bo11996-2008.nc"</span>)</code></pre>
+              </div>
+            </div>
+            <div id="load" class="section level2">
+              <h2 class="hasAnchor"><a href="#load" class="anchor"></a>Load</h2>
+              <p>
+                Using the <code>load.cfmet</code> convenience function.
+                Ameriflux is provided at 30 min intervals. If needed at a finer
+                resolution, see
+                <code
+                  ><a href="../reference/cfmet.downscale.time.html"
+                    >?cfmet.downscale.time</a
+                  ></code
+                >
+                (which works with subdaily and daily data). There is no
+                <code>cfmet.upscale.time</code> function, but would be
+                straightforward to implement if needed.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">bondville.nc &lt;-<span class="st"> </span><span class="kw">nc_open</span>(<span class="st">"/tmp/out/US-Bo11996-2008.nc"</span>)
+bondville.cfmet &lt;-<span class="st"> </span><span class="kw"><a href="../reference/load.cfmet.html">load.cfmet</a></span>(bondville.nc, <span class="dt">lat =</span> <span class="fl">40.0061988830566</span>, <span class="dt">lon =</span> <span class="op">-</span><span class="fl">88.290397644043</span>, <span class="dt">start.date =</span> <span class="st">"1996-08-25"</span>, <span class="dt">end.date =</span> <span class="st">"2008-04-10"</span>)[<span class="op">!</span><span class="kw">is.na</span>(air_pressure)]</code></pre>
+              </div>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/theme_get">theme_set</a></span>(<span class="kw">theme_tufte</span>())
 p1 &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_path">geom_line</a></span>(<span class="dt">data =</span> bondville.cfmet, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> date, <span class="dt">y =</span> surface_downwelling_shortwave_flux_in_air)) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/labs">ylab</a></span>(<span class="kw">paste</span>(bondville.nc<span class="op">$</span>var<span class="op">$</span>surface_downwelling_shortwave_flux_in_air<span class="op">$</span>longname, bondville.nc<span class="op">$</span>var<span class="op">$</span>surface_downwelling_shortwave_flux_in_air<span class="op">$</span>units))
 
 p2 &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_path">geom_line</a></span>(<span class="dt">data =</span> bondville.cfmet, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dt">x =</span> date, <span class="dt">y =</span> surface_downwelling_longwave_flux_in_air)) <span class="op">+</span><span class="st"> </span>
@@ -155,65 +306,98 @@ <h2 class="hasAnchor">
 <span class="st">   </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/labs">ylab</a></span>(<span class="kw">paste</span>(bondville.nc<span class="op">$</span>var<span class="op">$</span><span class="st"> </span>precipitation_flux<span class="op">$</span>longname, bondville.nc<span class="op">$</span>var<span class="op">$</span>precipitation_flux<span class="op">$</span>units))
 
 
-plots &lt;-<span class="st"> </span><span class="kw">list</span>(p1, p2, p3, p4, p5, p6, p7, p8, p9)</code></pre></div>
-</div>
-<div id="plot-entire-time-series" class="section level2">
-<h2 class="hasAnchor">
-<a href="#plot-entire-time-series" class="anchor"></a>Plot entire time series</h2>
-</div>
-<div id="plot-8-26-1996-to-10-14-1996" class="section level2">
-<h2 class="hasAnchor">
-<a href="#plot-8-26-1996-to-10-14-1996" class="anchor"></a>Plot 8-26-1996 to 10-14-1996</h2>
-</div>
-<div id="convert-to-biocro-model-format" class="section level2">
-<h2 class="hasAnchor">
-<a href="#convert-to-biocro-model-format" class="anchor"></a>Convert to BioCro Model format</h2>
-<p>To use the data, you can convert these to a model specific format</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAn.BIOCRO)
+plots &lt;-<span class="st"> </span><span class="kw">list</span>(p1, p2, p3, p4, p5, p6, p7, p8, p9)</code></pre>
+              </div>
+            </div>
+            <div id="plot-entire-time-series" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#plot-entire-time-series" class="anchor"></a>Plot
+                entire time series
+              </h2>
+            </div>
+            <div id="plot-8-26-1996-to-10-14-1996" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#plot-8-26-1996-to-10-14-1996" class="anchor"></a>Plot
+                8-26-1996 to 10-14-1996
+              </h2>
+            </div>
+            <div id="convert-to-biocro-model-format" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#convert-to-biocro-model-format" class="anchor"></a
+                >Convert to BioCro Model format
+              </h2>
+              <p>
+                To use the data, you can convert these to a model specific
+                format
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">library</span>(PEcAn.BIOCRO)
 <span class="co"># met2model.BioCro uses the following</span>
 bondville.biocromet &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/PEcAn.BIOCRO/topics/cf2biocro">cf2biocro</a></span>(bondville.cfmet, <span class="dt">longitude =</span> <span class="op">-</span><span class="fl">88.0</span>, <span class="dt">zulu2solarnoon =</span> <span class="ot">TRUE</span>)
 
 <span class="co"># write as csv for sharing </span>
-<span class="kw">write.csv</span>(bondville.biocromet, <span class="st">"../soy/data/bondville_1996-2008.csv"</span>, <span class="dt">row.names =</span> <span class="ot">FALSE</span>)</code></pre></div>
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-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li>
-<a href="#overview">Overview</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#download-ameriflux-data-for-bondville">Download Ameriflux data for Bondville</a></li>
-      <li><a href="#convert-to-pecan-cf-format">Convert to PEcAn-CF format</a></li>
-      <li><a href="#concatenate-years">Concatenate years</a></li>
-      <li><a href="#load">Load</a></li>
-      <li><a href="#plot-entire-time-series">Plot entire time series</a></li>
-      <li><a href="#plot-8-26-1996-to-10-14-1996">Plot 8-26-1996 to 10-14-1996</a></li>
-      <li><a href="#convert-to-biocro-model-format">Convert to BioCro Model format</a></li>
-      </ul>
-</li>
-      </ul>
-</div>
-      </div>
-
-</div>
+<span class="kw">write.csv</span>(bondville.biocromet, <span class="st">"../soy/data/bondville_1996-2008.csv"</span>, <span class="dt">row.names =</span> <span class="ot">FALSE</span>)</code></pre>
+              </div>
+            </div>
+          </div>
+        </div>
 
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#overview">Overview</a>
+                <ul class="nav nav-pills nav-stacked">
+                  <li>
+                    <a href="#download-ameriflux-data-for-bondville"
+                      >Download Ameriflux data for Bondville</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#convert-to-pecan-cf-format"
+                      >Convert to PEcAn-CF format</a
+                    >
+                  </li>
+                  <li><a href="#concatenate-years">Concatenate years</a></li>
+                  <li><a href="#load">Load</a></li>
+                  <li>
+                    <a href="#plot-entire-time-series"
+                      >Plot entire time series</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#plot-8-26-1996-to-10-14-1996"
+                      >Plot 8-26-1996 to 10-14-1996</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#convert-to-biocro-model-format"
+                      >Convert to BioCro Model format</a
+                    >
+                  </li>
+                </ul>
+              </li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
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index 95bf22b..0ade457 100644
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@@ -1,158 +1,246 @@
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+                  title="Released package"
+                  >1.6.0</span
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-    </div>
+            <div class="hidden name"><code>cfmet_downscaling.Rmd</code></div>
+          </div>
 
-    
-    
-<div id="met-downscaling" class="section level1">
-<h1 class="hasAnchor">
-<a href="#met-downscaling" class="anchor"></a>Met Downscaling</h1>
-<div id="subdaily-data" class="section level2">
-<h2 class="hasAnchor">
-<a href="#subdaily-data" class="anchor"></a>Subdaily Data</h2>
-<p>examples:</p>
-<ul>
-<li>NARR 3 hourly</li>
-<li>CRU-NCEP 6 hourly</li>
-</ul>
-<div id="extract" class="section level3">
-<h3 class="hasAnchor">
-<a href="#extract" class="anchor"></a>Extract</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAn.data.atmosphere)
+          <div id="met-downscaling" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#met-downscaling" class="anchor"></a>Met Downscaling
+            </h1>
+            <div id="subdaily-data" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#subdaily-data" class="anchor"></a>Subdaily Data
+              </h2>
+              <p>examples:</p>
+              <ul>
+                <li>NARR 3 hourly</li>
+                <li>CRU-NCEP 6 hourly</li>
+              </ul>
+              <div id="extract" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#extract" class="anchor"></a>Extract
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw">library</span>(PEcAn.data.atmosphere)
 subdaily.nc &lt;-<span class="st"> </span><span class="kw">nc_open</span>(<span class="kw">system.file</span>(<span class="st">"extdata/urbana_subdaily_test.nc"</span>, <span class="dt">package =</span> <span class="st">"PEcAn.data.atmosphere"</span>))
-subdaily.cf &lt;-<span class="st"> </span><span class="kw"><a href="../reference/load.cfmet.html">load.cfmet</a></span>(<span class="dt">met.nc =</span> subdaily.nc, <span class="dt">lat =</span> <span class="fl">39.75</span>, <span class="dt">lon =</span> <span class="op">-</span><span class="fl">87.25</span>, <span class="dt">start.date =</span> <span class="st">"1979-01-01"</span>, <span class="dt">end.date =</span> <span class="st">"1979-06-30"</span>)</code></pre></div>
-</div>
-<div id="downscale" class="section level3">
-<h3 class="hasAnchor">
-<a href="#downscale" class="anchor"></a>Downscale</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">hourly.cf &lt;-<span class="st"> </span><span class="kw"><a href="../reference/cfmet.downscale.time.html">cfmet.downscale.time</a></span>(<span class="dt">cfmet =</span> subdaily.cf)</code></pre></div>
-</div>
-<div id="convert-to-model-specific-format" class="section level3">
-<h3 class="hasAnchor">
-<a href="#convert-to-model-specific-format" class="anchor"></a>Convert to model-specific format</h3>
-</div>
-</div>
-<div id="daily-what-to-do-with-isimip---only-daily-average-rh" class="section level2">
-<h2 class="hasAnchor">
-<a href="#daily-what-to-do-with-isimip---only-daily-average-rh" class="anchor"></a>Daily: what to do with ISIMIP - only daily average RH</h2>
-</div>
-</div>
-  </div>
+subdaily.cf &lt;-<span class="st"> </span><span class="kw"><a href="../reference/load.cfmet.html">load.cfmet</a></span>(<span class="dt">met.nc =</span> subdaily.nc, <span class="dt">lat =</span> <span class="fl">39.75</span>, <span class="dt">lon =</span> <span class="op">-</span><span class="fl">87.25</span>, <span class="dt">start.date =</span> <span class="st">"1979-01-01"</span>, <span class="dt">end.date =</span> <span class="st">"1979-06-30"</span>)</code></pre>
+                </div>
+              </div>
+              <div id="downscale" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#downscale" class="anchor"></a>Downscale
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">hourly.cf &lt;-<span class="st"> </span><span class="kw"><a href="../reference/cfmet.downscale.time.html">cfmet.downscale.time</a></span>(<span class="dt">cfmet =</span> subdaily.cf)</code></pre>
+                </div>
+              </div>
+              <div id="convert-to-model-specific-format" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#convert-to-model-specific-format" class="anchor"></a
+                  >Convert to model-specific format
+                </h3>
+              </div>
+            </div>
+            <div
+              id="daily-what-to-do-with-isimip---only-daily-average-rh"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#daily-what-to-do-with-isimip---only-daily-average-rh"
+                  class="anchor"
+                ></a
+                >Daily: what to do with ISIMIP - only daily average RH
+              </h2>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li>
-<a href="#met-downscaling">Met Downscaling</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#subdaily-data">Subdaily Data</a></li>
-      <li><a href="#daily-what-to-do-with-isimip---only-daily-average-rh">Daily: what to do with ISIMIP - only daily average RH</a></li>
-      </ul>
-</li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#met-downscaling">Met Downscaling</a>
+                <ul class="nav nav-pills nav-stacked">
+                  <li><a href="#subdaily-data">Subdaily Data</a></li>
+                  <li>
+                    <a
+                      href="#daily-what-to-do-with-isimip---only-daily-average-rh"
+                      >Daily: what to do with ISIMIP - only daily average RH</a
+                    >
+                  </li>
+                </ul>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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diff --git a/modules/data.atmosphere/docs/articles/compare_narr_cruncep_met.html b/modules/data.atmosphere/docs/articles/compare_narr_cruncep_met.html
index 2c76410..af192dc 100644
--- a/modules/data.atmosphere/docs/articles/compare_narr_cruncep_met.html
+++ b/modules/data.atmosphere/docs/articles/compare_narr_cruncep_met.html
@@ -1,150 +1,266 @@
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    <!-- clipboard.js -->
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
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-
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-    Articles
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-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
-    </li>
-    <li>
-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="../articles/compare_narr_cruncep_met.html">UNKNOWN TITLE</a>
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-      
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-  <div class="col-md-9 contents">
-    <div class="page-header toc-ignore">
-      <h1></h1>
-            
-      
-      
-      <div class="hidden name"><code>compare_narr_cruncep_met.Rmd</code></div>
-
-    </div>
-
-    
-    
-<div id="comparing-met-data-from-various-sources" class="section level1">
-<h1 class="hasAnchor">
-<a href="#comparing-met-data-from-various-sources" class="anchor"></a>Comparing met data from various sources</h1>
-<div id="sources" class="section level2">
-<h2 class="hasAnchor">
-<a href="#sources" class="anchor"></a>Sources:</h2>
-<ul>
-<li>
-<code>ebifarm</code> local met station <em>Data</em>
-</li>
-<li>point location (40.08<span class="math inline">\(^o\)</span> N, -88.2<span class="math inline">\(^o\)</span> W), energy farm, Urbana, IL</li>
-<li>
-<code>narr</code> <a href="http://www.esrl.noaa.gov/psd/data/gridded/data.narr.html">NARR daily</a>
-</li>
-<li>0.3<span class="math inline">\(^o\)</span> grid daily 1979-2013</li>
-<li>
-<code>narr3h</code> NARR from MsTMIP</li>
-<li>0.25<span class="math inline">\(^o\)</span> grid 3-hourly 1979-2010</li>
-<li>
-<code>cruncep</code> CRU-NCEP from MsTMIP</li>
-<li>0.5<span class="math inline">\(^o\)</span> grid 6 hourly 1901-2010</li>
-<li>input record in BETYdb: <a href="https://www.betydb.org/inputs/280" class="uri">https://www.betydb.org/inputs/280</a>
-</li>
-</ul>
-</div>
-<div id="variables" class="section level2">
-<h2 class="hasAnchor">
-<a href="#variables" class="anchor"></a>Variables</h2>
-<ul>
-<li>RH / Relative Humidity (%)</li>
-<li>PAR / Solar Radiation (umol/h/m2)</li>
-<li>Temperature (C)</li>
-<li>Wind Speed (m/s)</li>
-<li>Precipitation (mm/h)</li>
-</ul>
-<p><em>Note</em> there is obviously an error in the downscaling method used to generate hourly NARR from daily. This is an obsolete method (since we now have sub-daily, and if we are going to correct this, it should be in the version of weachDT currently in PEcAn.data.atmosphere)</p>
-<p>Comparing ‘data’ (ebifarm) with gridded products</p>
-<p>TODO: clean up figure titles, labels, write explanations</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAn.data.atmosphere)
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header toc-ignore">
+            <h1></h1>
+
+            <div class="hidden name">
+              <code>compare_narr_cruncep_met.Rmd</code>
+            </div>
+          </div>
+
+          <div
+            id="comparing-met-data-from-various-sources"
+            class="section level1"
+          >
+            <h1 class="hasAnchor">
+              <a
+                href="#comparing-met-data-from-various-sources"
+                class="anchor"
+              ></a
+              >Comparing met data from various sources
+            </h1>
+            <div id="sources" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#sources" class="anchor"></a>Sources:
+              </h2>
+              <ul>
+                <li><code>ebifarm</code> local met station <em>Data</em></li>
+                <li>
+                  point location (40.08<span class="math inline">\(^o\)</span>
+                  N, -88.2<span class="math inline">\(^o\)</span> W), energy
+                  farm, Urbana, IL
+                </li>
+                <li>
+                  <code>narr</code>
+                  <a
+                    href="http://www.esrl.noaa.gov/psd/data/gridded/data.narr.html"
+                    >NARR daily</a
+                  >
+                </li>
+                <li>
+                  0.3<span class="math inline">\(^o\)</span> grid daily
+                  1979-2013
+                </li>
+                <li><code>narr3h</code> NARR from MsTMIP</li>
+                <li>
+                  0.25<span class="math inline">\(^o\)</span> grid 3-hourly
+                  1979-2010
+                </li>
+                <li><code>cruncep</code> CRU-NCEP from MsTMIP</li>
+                <li>
+                  0.5<span class="math inline">\(^o\)</span> grid 6 hourly
+                  1901-2010
+                </li>
+                <li>
+                  input record in BETYdb:
+                  <a href="https://www.betydb.org/inputs/280" class="uri"
+                    >https://www.betydb.org/inputs/280</a
+                  >
+                </li>
+              </ul>
+            </div>
+            <div id="variables" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#variables" class="anchor"></a>Variables
+              </h2>
+              <ul>
+                <li>RH / Relative Humidity (%)</li>
+                <li>PAR / Solar Radiation (umol/h/m2)</li>
+                <li>Temperature (C)</li>
+                <li>Wind Speed (m/s)</li>
+                <li>Precipitation (mm/h)</li>
+              </ul>
+              <p>
+                <em>Note</em> there is obviously an error in the downscaling
+                method used to generate hourly NARR from daily. This is an
+                obsolete method (since we now have sub-daily, and if we are
+                going to correct this, it should be in the version of weachDT
+                currently in PEcAn.data.atmosphere)
+              </p>
+              <p>Comparing ‘data’ (ebifarm) with gridded products</p>
+              <p>TODO: clean up figure titles, labels, write explanations</p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">library</span>(PEcAn.data.atmosphere)
 <span class="kw">library</span>(data.table)
 <span class="kw">library</span>(ggplot2)
 <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/theme_get">theme_set</a></span>(<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggtheme">theme_bw</a></span>())
 <span class="kw">data</span>(narr_cruncep_ebifarm)
 
 knitr<span class="op">::</span>opts_chunk<span class="op">$</span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/assign">set</a></span>(<span class="dt">echo=</span><span class="ot">FALSE</span>, <span class="dt">cache =</span> <span class="ot">TRUE</span>, <span class="dt">comment=</span><span class="ot">NA</span>, <span class="dt">tidy=</span><span class="ot">TRUE</span>, <span class="dt">warning=</span><span class="ot">FALSE</span>, <span class="dt">results =</span> <span class="st">'hide'</span>, 
-                      <span class="dt">fig.width =</span> <span class="dv">10</span>, <span class="dt">fig.height =</span> <span class="dv">4</span>)</code></pre></div>
-<div id="extracting-data" class="section level3">
-<h3 class="hasAnchor">
-<a href="#extracting-data" class="anchor"></a>Extracting data</h3>
-<p>These data are on biocluster.igb.illinois.edu, most 10-100s GB. Scripts used to download and convert these data to PEcAn CF format, optimized for time series extraction, are on <a href="https://github.com/ebimodeling/model-drivers">GitHub ebimodeling/model-drivers</a>.</p>
-<div class="sourceCode"><pre class="sourceCode sh"><code class="sourceCode bash"><span class="fu">mkdir</span> ~/testmet/
+                      <span class="dt">fig.width =</span> <span class="dv">10</span>, <span class="dt">fig.height =</span> <span class="dv">4</span>)</code></pre>
+              </div>
+              <div id="extracting-data" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#extracting-data" class="anchor"></a>Extracting data
+                </h3>
+                <p>
+                  These data are on biocluster.igb.illinois.edu, most 10-100s
+                  GB. Scripts used to download and convert these data to PEcAn
+                  CF format, optimized for time series extraction, are on
+                  <a href="https://github.com/ebimodeling/model-drivers"
+                    >GitHub ebimodeling/model-drivers</a
+                  >.
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode sh"
+                  ><code class="sourceCode bash"><span class="fu">mkdir</span> ~/testmet/
 <span class="ex">ncks</span> -O -d lon,-76.75,-76.25 -d lat,2.75,3.25 /home/groups/ebimodeling/met/narr/threehourly_32km/1979_2013.nc ~/testmet/narr32km_champaign.nc
 
 <span class="ex">ncks</span> -O -d lon,-76.75,-76.25 -d lat,2.75,3.25 /home/groups/ebimodeling/met/narr/threehourly/all.nc ~/testmet/narr_champaign.nc
 
-<span class="ex">ncks</span> -O -d lon,-76.75,-76.25 -d lat,2.75,3.25 /home/groups/ebimodeling/met/cruncep/all.nc ~/testmet/cruncep_champaign.nc</code></pre></div>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">Lat &lt;-<span class="st"> </span><span class="fl">40.08</span>
+<span class="ex">ncks</span> -O -d lon,-76.75,-76.25 -d lat,2.75,3.25 /home/groups/ebimodeling/met/cruncep/all.nc ~/testmet/cruncep_champaign.nc</code></pre>
+                </div>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">Lat &lt;-<span class="st"> </span><span class="fl">40.08</span>
 Lon &lt;-<span class="st"> </span><span class="op">-</span><span class="fl">88.2</span>
  
 
@@ -183,51 +299,90 @@ <h3 class="hasAnchor">
 cruncep<span class="op">$</span>source &lt;-<span class="st"> "cruncep"</span>
 narr<span class="op">$</span>source &lt;-<span class="st"> "narr"</span>
 narr3h<span class="op">$</span>source &lt;-<span class="st"> "narr3h"</span>
-ebifarm<span class="op">$</span>source &lt;-<span class="st"> "ebifarm"</span></code></pre></div>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">met &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/rbindlist">rbind</a></span>(cruncep[,<span class="kw">list</span>(source, date, <span class="dt">temp =</span> DailyTemp.C, RH, <span class="dt">wind =</span> WindSpeed, precip, <span class="dt">solar =</span> solarR)],
+ebifarm<span class="op">$</span>source &lt;-<span class="st"> "ebifarm"</span></code></pre>
+                </div>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">met &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/rbindlist">rbind</a></span>(cruncep[,<span class="kw">list</span>(source, date, <span class="dt">temp =</span> DailyTemp.C, RH, <span class="dt">wind =</span> WindSpeed, precip, <span class="dt">solar =</span> solarR)],
              narr[,<span class="kw">list</span>(source, date, <span class="dt">temp =</span> Temp, RH, <span class="dt">wind =</span> WS, precip, <span class="dt">solar =</span> SolarR)],
              narr3h[,<span class="kw">list</span>(source, date, <span class="dt">temp =</span> DailyTemp.C, RH, <span class="dt">wind =</span> WindSpeed, precip, <span class="dt">solar =</span> solarR)],
              ebifarm[,<span class="kw">list</span>(source, date, <span class="dt">temp =</span> Temp, <span class="dt">RH =</span> RH<span class="op">/</span><span class="dv">100</span>, wind, precip, <span class="dt">solar =</span> solar)])
 
 met<span class="op">$</span>source &lt;-<span class="st"> </span><span class="kw">factor</span>(met<span class="op">$</span>source,
-         <span class="dt">levels =</span> <span class="kw">c</span>(<span class="st">"ebifarm"</span>, <span class="st">"narr3h"</span>, <span class="st">"narr"</span>, <span class="st">"cruncep"</span>))</code></pre></div>
-</div>
-<div id="solar-radiation-par-vs-temp" class="section level3">
-<h3 class="hasAnchor">
-<a href="#solar-radiation-par-vs-temp" class="anchor"></a>Solar Radiation (PAR) vs Temp</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> met, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(solar, temp, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.1</span>) <span class="op">+</span><span class="st"> </span>
+         <span class="dt">levels =</span> <span class="kw">c</span>(<span class="st">"ebifarm"</span>, <span class="st">"narr3h"</span>, <span class="st">"narr"</span>, <span class="st">"cruncep"</span>))</code></pre>
+                </div>
+              </div>
+              <div id="solar-radiation-par-vs-temp" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#solar-radiation-par-vs-temp" class="anchor"></a
+                  >Solar Radiation (PAR) vs Temp
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> met, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(solar, temp, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.1</span>) <span class="op">+</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap">facet_wrap</a></span>(<span class="op">~</span>source, <span class="dt">nrow=</span><span class="dv">1</span>) <span class="op">+</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_gradient">scale_color_gradientn</a></span>(<span class="dt">colours =</span> <span class="kw">c</span>(<span class="st">"Red"</span>, <span class="st">"Orange"</span>, <span class="st">"Yellow"</span>, <span class="st">"Green"</span>, <span class="st">"Blue"</span>))
 
-## ggplot() + geom_point(data = met, aes(solar, temp, color = hour(date)), alpha = 0.1) + facet_wrap(~source, nrow=1) + scale_color_gradientn(colours = c("Red", "Orange", "Yellow", "Green", "Blue"))</code></pre></div>
-</div>
-<div id="rh-vs-temp" class="section level3">
-<h3 class="hasAnchor">
-<a href="#rh-vs-temp" class="anchor"></a>RH vs Temp</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> met, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(RH, temp, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.1</span>) <span class="op">+</span><span class="st"> </span>
+## ggplot() + geom_point(data = met, aes(solar, temp, color = hour(date)), alpha = 0.1) + facet_wrap(~source, nrow=1) + scale_color_gradientn(colours = c("Red", "Orange", "Yellow", "Green", "Blue"))</code></pre>
+                </div>
+              </div>
+              <div id="rh-vs-temp" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#rh-vs-temp" class="anchor"></a>RH vs Temp
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> met, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(RH, temp, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.1</span>) <span class="op">+</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap">facet_wrap</a></span>(<span class="op">~</span>source, <span class="dt">nrow=</span><span class="dv">1</span>) <span class="op">+</span><span class="st"> </span>
-<span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_gradient">scale_color_gradientn</a></span>(<span class="dt">colours =</span> <span class="kw">c</span>(<span class="st">"Red"</span>, <span class="st">"Orange"</span>, <span class="st">"Yellow"</span>, <span class="st">"Green"</span>, <span class="st">"Blue"</span>))</code></pre></div>
-</div>
-<div id="solar-radiation-and-precipitation-narr-daily-vs-3-hourly" class="section level3">
-<h3 class="hasAnchor">
-<a href="#solar-radiation-and-precipitation-narr-daily-vs-3-hourly" class="anchor"></a>Solar Radiation and Precipitation: NARR daily vs 3 hourly</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> met[solar <span class="op">&gt;</span><span class="st"> </span><span class="dv">1</span> <span class="op">&amp;</span><span class="st"> </span>precip <span class="op">&gt;</span><span class="st"> </span><span class="fl">0.1</span>], <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(solar, precip, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.1</span>) <span class="op">+</span><span class="st"> </span>
+<span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_gradient">scale_color_gradientn</a></span>(<span class="dt">colours =</span> <span class="kw">c</span>(<span class="st">"Red"</span>, <span class="st">"Orange"</span>, <span class="st">"Yellow"</span>, <span class="st">"Green"</span>, <span class="st">"Blue"</span>))</code></pre>
+                </div>
+              </div>
+              <div
+                id="solar-radiation-and-precipitation-narr-daily-vs-3-hourly"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#solar-radiation-and-precipitation-narr-daily-vs-3-hourly"
+                    class="anchor"
+                  ></a
+                  >Solar Radiation and Precipitation: NARR daily vs 3 hourly
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> met[solar <span class="op">&gt;</span><span class="st"> </span><span class="dv">1</span> <span class="op">&amp;</span><span class="st"> </span>precip <span class="op">&gt;</span><span class="st"> </span><span class="fl">0.1</span>], <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(solar, precip, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.1</span>) <span class="op">+</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap">facet_wrap</a></span>(<span class="op">~</span>source, <span class="dt">nrow=</span><span class="dv">1</span>) <span class="op">+</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_gradient">scale_color_gradientn</a></span>(<span class="dt">colours =</span> <span class="kw">c</span>(<span class="st">"Red"</span>, <span class="st">"Orange"</span>, <span class="st">"Yellow"</span>, <span class="st">"Green"</span>, <span class="st">"Blue"</span>)) <span class="op">+</span><span class="st"> </span>
-<span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous">scale_x_log10</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous">scale_y_log10</a></span>()</code></pre></div>
-</div>
-<div id="precipitation-v-temperature" class="section level3">
-<h3 class="hasAnchor">
-<a href="#precipitation-v-temperature" class="anchor"></a>Precipitation v Temperature</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> met, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(precip, temp, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.1</span>) <span class="op">+</span><span class="st"> </span>
+<span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous">scale_x_log10</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous">scale_y_log10</a></span>()</code></pre>
+                </div>
+              </div>
+              <div id="precipitation-v-temperature" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#precipitation-v-temperature" class="anchor"></a
+                  >Precipitation v Temperature
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> met, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(precip, temp, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.1</span>) <span class="op">+</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap">facet_wrap</a></span>(<span class="op">~</span>source, <span class="dt">nrow=</span><span class="dv">1</span>) <span class="op">+</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_gradient">scale_color_gradientn</a></span>(<span class="dt">colours =</span> <span class="kw">c</span>(<span class="st">"Red"</span>, <span class="st">"Orange"</span>, <span class="st">"Yellow"</span>, <span class="st">"Green"</span>, <span class="st">"Blue"</span>)) <span class="op">+</span><span class="st"> </span>
-<span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous">scale_x_log10</a></span>()</code></pre></div>
-</div>
-<div id="compare-solar-radiation" class="section level3">
-<h3 class="hasAnchor">
-<a href="#compare-solar-radiation" class="anchor"></a>Compare Solar Radiation</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">s &lt;-<span class="st"> </span>met[,<span class="kw">list</span>(date, <span class="dt">day =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">yday</a></span>(date), solar, source )]
+<span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous">scale_x_log10</a></span>()</code></pre>
+                </div>
+              </div>
+              <div id="compare-solar-radiation" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#compare-solar-radiation" class="anchor"></a>Compare
+                  Solar Radiation
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">s &lt;-<span class="st"> </span>met[,<span class="kw">list</span>(date, <span class="dt">day =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">yday</a></span>(date), solar, source )]
 s &lt;-<span class="st"> </span>s[,<span class="kw">list</span>(<span class="dt">date =</span> <span class="kw">min</span>(date), <span class="dt">solar =</span> <span class="kw">max</span>(solar)), by =<span class="st"> 'day,source'</span>]
 
 
@@ -241,20 +396,44 @@ <h3 class="hasAnchor">
 <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> met[<span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date) <span class="op">&gt;</span><span class="dv">5</span> <span class="op">&amp;</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)<span class="op">&lt;</span><span class="dv">9</span> <span class="op">&amp;</span><span class="st"> </span>solar <span class="op">&gt;</span><span class="st"> </span><span class="dv">100</span>], <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(date, solar, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">hour</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.1</span>) <span class="op">+</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/facet_wrap">facet_wrap</a></span>(<span class="op">~</span>source, <span class="dt">nrow=</span><span class="dv">1</span>) <span class="op">+</span><span class="st"> </span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_gradient">scale_color_gradientn</a></span>(<span class="dt">colours =</span> <span class="kw">c</span>(<span class="st">"Red"</span>, <span class="st">"Orange"</span>, <span class="st">"Yellow"</span>, <span class="st">"Green"</span>, <span class="st">"Blue"</span>)) <span class="op">+</span><span class="st"> </span>
-<span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous">scale_y_log10</a></span>()</code></pre></div>
-</div>
-<div id="max-solar-radiation-for-june-1-aug31-2010" class="section level3">
-<h3 class="hasAnchor">
-<a href="#max-solar-radiation-for-june-1-aug31-2010" class="anchor"></a>Max Solar Radiation for June 1-Aug31 2010</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">maxsolarplot &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span>
+<span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_continuous">scale_y_log10</a></span>()</code></pre>
+                </div>
+              </div>
+              <div
+                id="max-solar-radiation-for-june-1-aug31-2010"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#max-solar-radiation-for-june-1-aug31-2010"
+                    class="anchor"
+                  ></a
+                  >Max Solar Radiation for June 1-Aug31 2010
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">maxsolarplot &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span>
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_path">geom_line</a></span>(<span class="dt">data =</span> s, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(date, solar, <span class="dt">color =</span> source)) <span class="op">+</span>
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/lims">xlim</a></span>(<span class="kw">ymd</span>(<span class="st">"2010-06-01"</span>), <span class="kw">ymd</span>(<span class="st">"2010-08-31"</span>)) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Max Daily PAR"</span>)
-<span class="kw">print</span>(maxsolarplot)</code></pre></div>
-</div>
-<div id="max-solar-radiation-par-model-v-obs" class="section level3">
-<h3 class="hasAnchor">
-<a href="#max-solar-radiation-par-model-v-obs" class="anchor"></a>Max Solar Radiation (PAR) Model v OBS</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">maxsolar &lt;-<span class="st"> </span>allsolar[,<span class="kw">list</span>(<span class="dt">obs=</span><span class="kw">max</span>(obs),<span class="dt">cruncep=</span><span class="kw">max</span>(cruncep), <span class="dt">narr =</span> <span class="kw">max</span>(narr), <span class="dt">narr3h=</span><span class="kw">max</span>(narr3h), <span class="dt">date =</span> <span class="kw">min</span>(date)), by =<span class="st"> </span>day]
+<span class="kw">print</span>(maxsolarplot)</code></pre>
+                </div>
+              </div>
+              <div
+                id="max-solar-radiation-par-model-v-obs"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#max-solar-radiation-par-model-v-obs"
+                    class="anchor"
+                  ></a
+                  >Max Solar Radiation (PAR) Model v OBS
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">maxsolar &lt;-<span class="st"> </span>allsolar[,<span class="kw">list</span>(<span class="dt">obs=</span><span class="kw">max</span>(obs),<span class="dt">cruncep=</span><span class="kw">max</span>(cruncep), <span class="dt">narr =</span> <span class="kw">max</span>(narr), <span class="dt">narr3h=</span><span class="kw">max</span>(narr3h), <span class="dt">date =</span> <span class="kw">min</span>(date)), by =<span class="st"> </span>day]
 
 narrsolar &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="dt">data =</span> maxsolar, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(obs, narr, <span class="dt">color =</span> <span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">month</a></span>(date)), <span class="dt">alpha =</span> <span class="fl">0.3</span>)<span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/scale_gradient">scale_color_gradientn</a></span>(<span class="dt">colours =</span> <span class="kw">c</span>(<span class="st">"Red"</span>, <span class="st">"Orange"</span>, <span class="st">"Yellow"</span>, <span class="st">"Green"</span>, <span class="st">"Blue"</span>))<span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_path">geom_line</a></span>(<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(<span class="dv">0</span><span class="op">:</span><span class="dv">2000</span>, <span class="dv">0</span><span class="op">:</span><span class="dv">2000</span>)) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/lims">xlim</a></span>(<span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">2100</span>)) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/lims">ylim</a></span>(<span class="kw">c</span>(<span class="dv">0</span>,<span class="dv">2100</span>))
 
@@ -270,12 +449,18 @@ <h3 class="hasAnchor">
   narrsolar,
   narr3hsolar, 
   cruncepsolar,
-  <span class="dt">ncol =</span> <span class="dv">3</span>)</code></pre></div>
-</div>
-<div id="par-residuals-model---obs" class="section level3">
-<h3 class="hasAnchor">
-<a href="#par-residuals-model---obs" class="anchor"></a>PAR residuals (model - obs)</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">solarresiduals &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(<span class="dt">data=</span>allsolar[narr<span class="op">+</span>obs<span class="op">&gt;</span><span class="dv">100</span>]) <span class="op">+</span>
+  <span class="dt">ncol =</span> <span class="dv">3</span>)</code></pre>
+                </div>
+              </div>
+              <div id="par-residuals-model---obs" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#par-residuals-model---obs" class="anchor"></a>PAR
+                  residuals (model - obs)
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">solarresiduals &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>(<span class="dt">data=</span>allsolar[narr<span class="op">+</span>obs<span class="op">&gt;</span><span class="dv">100</span>]) <span class="op">+</span>
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(date, narr <span class="op">-</span><span class="st"> </span>obs), <span class="dt">alpha =</span> <span class="fl">0.1</span>, <span class="dt">color =</span> <span class="st">"blue"</span>) <span class="op">+</span>
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(date, narr3h <span class="op">-</span><span class="st"> </span>obs), <span class="dt">alpha =</span> <span class="fl">0.1</span>, <span class="dt">color =</span> <span class="st">"red"</span>) <span class="op">+</span>
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_point">geom_point</a></span>(<span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(date, cruncep <span class="op">-</span><span class="st"> </span>obs), <span class="dt">alpha =</span> <span class="fl">0.1</span>, <span class="dt">color =</span> <span class="st">"green"</span>) <span class="op">+</span>
@@ -287,23 +472,53 @@ <h3 class="hasAnchor">
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"observed vs. modeled solar radiation:</span><span class="ch">\n</span><span class="st"> daily narr / weach (blue), cruncep 6 hourly (green), narr 3hourly (red)"</span>) <span class="op">+</span>
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/labs">ylab</a></span>(<span class="st">"Modeled - Observed Solar Radiation (umol / h )"</span>)
 
-<span class="kw">print</span>(solarresiduals)</code></pre></div>
-</div>
-<div id="correlations-of-daily-max-solar-radiation" class="section level3">
-<h3 class="hasAnchor">
-<a href="#correlations-of-daily-max-solar-radiation" class="anchor"></a>Correlations of daily max solar radiation</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(GGally)
-<span class="kw">ggpairs</span>(maxsolar[,<span class="kw">list</span>(obs, narr3h, narr, cruncep)])</code></pre></div>
-</div>
-<div id="compare-daily-and-3hourly-downscaled-narr" class="section level3">
-<h3 class="hasAnchor">
-<a href="#compare-daily-and-3hourly-downscaled-narr" class="anchor"></a>Compare daily and 3hourly downscaled NARR</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">weachnarr_narr3h</code></pre></div>
-</div>
-<div id="multiple-variables" class="section level3">
-<h3 class="hasAnchor">
-<a href="#multiple-variables" class="anchor"></a>Multiple variables</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">### Generate some plots to compare August 
+<span class="kw">print</span>(solarresiduals)</code></pre>
+                </div>
+              </div>
+              <div
+                id="correlations-of-daily-max-solar-radiation"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#correlations-of-daily-max-solar-radiation"
+                    class="anchor"
+                  ></a
+                  >Correlations of daily max solar radiation
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw">library</span>(GGally)
+<span class="kw">ggpairs</span>(maxsolar[,<span class="kw">list</span>(obs, narr3h, narr, cruncep)])</code></pre>
+                </div>
+              </div>
+              <div
+                id="compare-daily-and-3hourly-downscaled-narr"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#compare-daily-and-3hourly-downscaled-narr"
+                    class="anchor"
+                  ></a
+                  >Compare daily and 3hourly downscaled NARR
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">weachnarr_narr3h</code></pre>
+                </div>
+              </div>
+              <div id="multiple-variables" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#multiple-variables" class="anchor"></a>Multiple
+                  variables
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">### Generate some plots to compare August 
 
 rh &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/ggplot">ggplot</a></span>() <span class="op">+</span>
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_path">geom_line</a></span>(<span class="dt">data =</span> met, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(date, RH, <span class="dt">color =</span> source)) <span class="op">+</span>
@@ -324,31 +539,51 @@ <h3 class="hasAnchor">
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_path">geom_line</a></span>(<span class="dt">data =</span> met, <span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/aes">aes</a></span>(date, solar, <span class="dt">color =</span> source)) <span class="op">+</span>
 <span class="st">    </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/lims">xlim</a></span>(<span class="kw">ymd</span>(<span class="st">"2010-08-01"</span>), <span class="kw">ymd</span>(<span class="st">"2010-08-31"</span>)) <span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"PAR"</span>)
 
-<span class="kw">print</span>(gridExtra<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/gridExtra/topics/arrangeGrob">grid.arrange</a></span>(rh, precip, temp, wind, solar, <span class="dt">ncol =</span> <span class="dv">1</span>))</code></pre></div>
-</div>
-<div id="some-sanity-checks-on-variables" class="section level3">
-<h3 class="hasAnchor">
-<a href="#some-sanity-checks-on-variables" class="anchor"></a>Some sanity checks on variables</h3>
-<ul>
-<li>Temperature:</li>
-</ul>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">kable</span>(met[,<span class="kw">list</span>(<span class="dt">min =</span> <span class="kw">min</span>(temp), <span class="dt">mean =</span> <span class="kw">mean</span>(temp), <span class="dt">max =</span> <span class="kw">max</span>(temp)), <span class="dt">by =</span> source])</code></pre></div>
-<ul>
-<li>RH</li>
-</ul>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">kable</span>(met[,<span class="kw">list</span>(<span class="dt">min =</span> <span class="kw">min</span>(RH<span class="op">*</span><span class="dv">100</span>), <span class="dt">mean =</span> <span class="kw">mean</span>(RH<span class="op">*</span><span class="dv">100</span>), <span class="dt">max =</span> <span class="kw">max</span>(RH<span class="op">*</span><span class="dv">100</span>)), <span class="dt">by =</span> source])</code></pre></div>
-<ul>
-<li>Total Precip</li>
-</ul>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">kable</span>(met[,<span class="kw">list</span>(<span class="dt">total=</span><span class="kw">sum</span>(precip)), <span class="dt">by =</span> source])</code></pre></div>
-</div>
-<div id="more-diagnostic-plots" class="section level3">
-<h3 class="hasAnchor">
-<a href="#more-diagnostic-plots" class="anchor"></a>More diagnostic plots</h3>
-<ul>
-<li>need to print each one …</li>
-</ul>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">obs &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/merge">merge</a></span>(met[<span class="op">!</span>source <span class="op">==</span><span class="st"> "ebifarm"</span>], met[source <span class="op">==</span><span class="st"> "ebifarm"</span>], <span class="dt">by =</span> <span class="st">"date"</span>)
+<span class="kw">print</span>(gridExtra<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/gridExtra/topics/arrangeGrob">grid.arrange</a></span>(rh, precip, temp, wind, solar, <span class="dt">ncol =</span> <span class="dv">1</span>))</code></pre>
+                </div>
+              </div>
+              <div id="some-sanity-checks-on-variables" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#some-sanity-checks-on-variables" class="anchor"></a
+                  >Some sanity checks on variables
+                </h3>
+                <ul>
+                  <li>Temperature:</li>
+                </ul>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw">kable</span>(met[,<span class="kw">list</span>(<span class="dt">min =</span> <span class="kw">min</span>(temp), <span class="dt">mean =</span> <span class="kw">mean</span>(temp), <span class="dt">max =</span> <span class="kw">max</span>(temp)), <span class="dt">by =</span> source])</code></pre>
+                </div>
+                <ul>
+                  <li>RH</li>
+                </ul>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw">kable</span>(met[,<span class="kw">list</span>(<span class="dt">min =</span> <span class="kw">min</span>(RH<span class="op">*</span><span class="dv">100</span>), <span class="dt">mean =</span> <span class="kw">mean</span>(RH<span class="op">*</span><span class="dv">100</span>), <span class="dt">max =</span> <span class="kw">max</span>(RH<span class="op">*</span><span class="dv">100</span>)), <span class="dt">by =</span> source])</code></pre>
+                </div>
+                <ul>
+                  <li>Total Precip</li>
+                </ul>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw">kable</span>(met[,<span class="kw">list</span>(<span class="dt">total=</span><span class="kw">sum</span>(precip)), <span class="dt">by =</span> source])</code></pre>
+                </div>
+              </div>
+              <div id="more-diagnostic-plots" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#more-diagnostic-plots" class="anchor"></a>More
+                  diagnostic plots
+                </h3>
+                <ul>
+                  <li>need to print each one …</li>
+                </ul>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">obs &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/merge">merge</a></span>(met[<span class="op">!</span>source <span class="op">==</span><span class="st"> "ebifarm"</span>], met[source <span class="op">==</span><span class="st"> "ebifarm"</span>], <span class="dt">by =</span> <span class="st">"date"</span>)
 obs<span class="op">$</span>yday &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/data.table/topics/IDateTime">yday</a></span>(obs<span class="op">$</span>date)
 dailyprecip &lt;-<span class="st"> </span>obs[,<span class="kw">list</span>(<span class="dt">precip.x =</span> <span class="kw">mean</span>(precip.x), <span class="dt">precip.y =</span> <span class="kw">mean</span>(precip.y)), by =<span class="st"> 'source.x,yday'</span>]
 
@@ -398,42 +633,44 @@ <h3 class="hasAnchor">
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/geom_smooth">geom_smooth</a></span>()<span class="op">+</span>
 <span class="st">  </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/lims">ylim</a></span>(<span class="kw">c</span>(<span class="op">-</span><span class="fl">0.5</span>,<span class="fl">0.5</span>))<span class="op">+</span><span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/ggplot2/topics/labs">ggtitle</a></span>(<span class="st">"Precip (daily average)"</span>),
 <span class="dt">ncol =</span> <span class="dv">1</span>
-)</code></pre></div>
-</div>
-</div>
-</div>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li>
-<a href="#comparing-met-data-from-various-sources">Comparing met data from various sources</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#sources">Sources:</a></li>
-      <li><a href="#variables">Variables</a></li>
-      </ul>
-</li>
-      </ul>
-</div>
+)</code></pre>
+                </div>
+              </div>
+            </div>
+          </div>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#comparing-met-data-from-various-sources"
+                  >Comparing met data from various sources</a
+                >
+                <ul class="nav nav-pills nav-stacked">
+                  <li><a href="#sources">Sources:</a></li>
+                  <li><a href="#variables">Variables</a></li>
+                </ul>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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diff --git a/modules/data.atmosphere/docs/articles/index.html b/modules/data.atmosphere/docs/articles/index.html
index 1124eb1..4d605c1 100644
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+++ b/modules/data.atmosphere/docs/articles/index.html
@@ -2,145 +2,192 @@
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+            <p class="section-desc"></p>
+
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+              <li>
+                <a href="ameriflux_demo.html"
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+                  station</a
+                >
+              </li>
+              <li><a href="cfmet_downscaling.html">UNKNOWN TITLE</a></li>
+              <li><a href="compare_narr_cruncep_met.html">UNKNOWN TITLE</a></li>
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diff --git a/modules/data.atmosphere/docs/articles/tdm_downscaling.html b/modules/data.atmosphere/docs/articles/tdm_downscaling.html
index 1e02af4..069e6c9 100644
--- a/modules/data.atmosphere/docs/articles/tdm_downscaling.html
+++ b/modules/data.atmosphere/docs/articles/tdm_downscaling.html
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-    
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-<div id="subdaily-training-data" class="section level3">
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-<a href="#subdaily-training-data" class="anchor"></a>Subdaily Training Data</h3>
-<p>Examples:</p>
-<ul>
-<li>Fluxnet2015 30-minute/hourly</li>
-<li>Ameriflux 30-minute/hourly</li>
-</ul>
-</div>
-<div id="extract-training-data-and-merge-all-years-into-1-file" class="section level3">
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-<a href="#extract-training-data-and-merge-all-years-into-1-file" class="anchor"></a>Extract Training Data and Merge All Years Into 1 File</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAn.data.atmosphere)
+          <div id="temporally-downscale-meteorology" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#temporally-downscale-meteorology" class="anchor"></a
+              >Temporally Downscale Meteorology
+            </h1>
+            <div id="subdaily-training-data" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#subdaily-training-data" class="anchor"></a>Subdaily
+                Training Data
+              </h3>
+              <p>Examples:</p>
+              <ul>
+                <li>Fluxnet2015 30-minute/hourly</li>
+                <li>Ameriflux 30-minute/hourly</li>
+              </ul>
+            </div>
+            <div
+              id="extract-training-data-and-merge-all-years-into-1-file"
+              class="section level3"
+            >
+              <h3 class="hasAnchor">
+                <a
+                  href="#extract-training-data-and-merge-all-years-into-1-file"
+                  class="anchor"
+                ></a
+                >Extract Training Data and Merge All Years Into 1 File
+              </h3>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">library</span>(PEcAn.data.atmosphere)
 <span class="kw">library</span>(PEcAn.DB)
 
 <span class="co"># Download the Fluxnet2015 file</span>
@@ -125,75 +202,113 @@ <h3 class="hasAnchor">
 <span class="kw"><a href="../reference/metgapfill.html">metgapfill</a></span>(<span class="dt">lst =</span> <span class="op">-</span><span class="dv">7</span>, <span class="dt">in.path =</span> <span class="kw">file.path</span>(outfolder, <span class="st">"CF"</span>), in.prefix, <span class="dt">outfolder =</span> <span class="kw">file.path</span>(outfolder, <span class="st">"gapfill"</span>), start_date, end_date)
 
 <span class="co"># Merge the individual years of the gapfilled NC files together </span>
-<span class="kw"><a href="../reference/nc.merge.html">nc.merge</a></span>(<span class="dt">outfolder =</span> <span class="kw">file.path</span>(outfolder, <span class="st">"training_data"</span>), <span class="dt">in.path =</span> <span class="kw">file.path</span>(outfolder, <span class="st">"gapfill"</span>), in.prefix, start_date, end_date, <span class="dt">upscale =</span> <span class="st">"hour"</span>)</code></pre></div>
-</div>
-<div id="generate-linear-regression-models-from-training-data" class="section level3">
-<h3 class="hasAnchor">
-<a href="#generate-linear-regression-models-from-training-data" class="anchor"></a>Generate Linear Regression Models From Training Data</h3>
-<p>Note: This requires ~ 120 GB of space if using the entire training dataset</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">in.prefix      &lt;-<span class="st"> "US-NR1"</span>
+<span class="kw"><a href="../reference/nc.merge.html">nc.merge</a></span>(<span class="dt">outfolder =</span> <span class="kw">file.path</span>(outfolder, <span class="st">"training_data"</span>), <span class="dt">in.path =</span> <span class="kw">file.path</span>(outfolder, <span class="st">"gapfill"</span>), in.prefix, start_date, end_date, <span class="dt">upscale =</span> <span class="st">"hour"</span>)</code></pre>
+              </div>
+            </div>
+            <div
+              id="generate-linear-regression-models-from-training-data"
+              class="section level3"
+            >
+              <h3 class="hasAnchor">
+                <a
+                  href="#generate-linear-regression-models-from-training-data"
+                  class="anchor"
+                ></a
+                >Generate Linear Regression Models From Training Data
+              </h3>
+              <p>
+                Note: This requires ~ 120 GB of space if using the entire
+                training dataset
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">in.prefix      &lt;-<span class="st"> "US-NR1"</span>
 dat.train.file &lt;-<span class="st"> "~/Example/training_data/FLX_US-NR1_FLUXNET2015_SUBSET_HH_1998-2014_1-3_dat.train.nc"</span> 
 n.beta         &lt;-<span class="st"> </span><span class="dv">10</span> <span class="co"># Number of betas for the linear regression model to create, we'll choose 10 for time's sake</span>
 day.window     &lt;-<span class="st"> </span><span class="dv">5</span>  <span class="co"># Number of days around a specific timestamp to gather statistics from (at the same timestamp)</span>
-<span class="kw"><a href="../reference/gen.subdaily.models.html">gen.subdaily.models</a></span>(<span class="dt">outfolder =</span> <span class="kw">dir.create</span>(outfolder, <span class="st">"lm_models_base"</span>), dat.train.file, in.prefix, n.beta, day.window)</code></pre></div>
-</div>
-<div id="coarse-data-to-downscale" class="section level3">
-<h3 class="hasAnchor">
-<a href="#coarse-data-to-downscale" class="anchor"></a>Coarse Data to Downscale</h3>
-<p>Examples:</p>
-<ul>
-<li>MACA daily</li>
-<li>CRU-NCEP 6 hourly</li>
-</ul>
-</div>
-<div id="extract-data-we-want-to-downscale" class="section level3">
-<h3 class="hasAnchor">
-<a href="#extract-data-we-want-to-downscale" class="anchor"></a>Extract Data We Want To Downscale</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">start_date      &lt;-<span class="st"> "2020-01-01"</span>
+<span class="kw"><a href="../reference/gen.subdaily.models.html">gen.subdaily.models</a></span>(<span class="dt">outfolder =</span> <span class="kw">dir.create</span>(outfolder, <span class="st">"lm_models_base"</span>), dat.train.file, in.prefix, n.beta, day.window)</code></pre>
+              </div>
+            </div>
+            <div id="coarse-data-to-downscale" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#coarse-data-to-downscale" class="anchor"></a>Coarse
+                Data to Downscale
+              </h3>
+              <p>Examples:</p>
+              <ul>
+                <li>MACA daily</li>
+                <li>CRU-NCEP 6 hourly</li>
+              </ul>
+            </div>
+            <div id="extract-data-we-want-to-downscale" class="section level3">
+              <h3 class="hasAnchor">
+                <a href="#extract-data-we-want-to-downscale" class="anchor"></a
+                >Extract Data We Want To Downscale
+              </h3>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">start_date      &lt;-<span class="st"> "2020-01-01"</span>
 end_date        &lt;-<span class="st"> "2020-12-31"</span>
 site_id         &lt;-<span class="st"> </span><span class="dv">772</span>
 model           &lt;-<span class="st"> "BNU-ESM"</span>
 scenario        &lt;-<span class="st"> "rcp85"</span>
 ensemble_member &lt;-<span class="st"> "r1i1p1"</span>
-<span class="kw"><a href="../reference/download.MACA.html">download.MACA</a></span>(outfolder, start_date, end_date, site_id, model, scenario, ensemble_member)</code></pre></div>
-</div>
-<div id="predict-subdaily-data-using-statistics-from-training-data" class="section level3">
-<h3 class="hasAnchor">
-<a href="#predict-subdaily-data-using-statistics-from-training-data" class="anchor"></a>Predict Subdaily Data Using Statistics From Training Data</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">in.path        &lt;-<span class="st"> "~/Example/MACA_site_0-772"</span>
+<span class="kw"><a href="../reference/download.MACA.html">download.MACA</a></span>(outfolder, start_date, end_date, site_id, model, scenario, ensemble_member)</code></pre>
+              </div>
+            </div>
+            <div
+              id="predict-subdaily-data-using-statistics-from-training-data"
+              class="section level3"
+            >
+              <h3 class="hasAnchor">
+                <a
+                  href="#predict-subdaily-data-using-statistics-from-training-data"
+                  class="anchor"
+                ></a
+                >Predict Subdaily Data Using Statistics From Training Data
+              </h3>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">in.path        &lt;-<span class="st"> "~/Example/MACA_site_0-772"</span>
 in.prefix      &lt;-<span class="st"> "MACA.BNU-ESM.rcp85.r1i1p1"</span> <span class="co"># this is the data we are going to downscale</span>
 lm.models.base &lt;-<span class="st"> "~/Example/lm_model_output"</span> <span class="co"># where we stored the lm models</span>
 n.ens          &lt;-<span class="st"> </span><span class="dv">3</span> <span class="co"># number of ensemble members we want to generate</span>
-<span class="kw"><a href="../reference/predict_subdaily_met.html">predict_subdaily_met</a></span>(<span class="dt">outfolder =</span> <span class="kw">file.path</span>(outfolder, <span class="st">"downscaled_data"</span>), in.path, in.prefix, lm.models.base, n.ens, start_date, end_date)</code></pre></div>
-</div>
-</div>
-  </div>
+<span class="kw"><a href="../reference/predict_subdaily_met.html">predict_subdaily_met</a></span>(<span class="dt">outfolder =</span> <span class="kw">file.path</span>(outfolder, <span class="st">"downscaled_data"</span>), in.path, in.prefix, lm.models.base, n.ens, start_date, end_date)</code></pre>
+              </div>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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-      <h2 class="hasAnchor">
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-      <ul class="nav nav-pills nav-stacked">
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+            </h2>
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+              <li>
+                <a href="#temporally-downscale-meteorology"
+                  >Temporally Downscale Meteorology</a
+                >
+              </li>
+            </ul>
+          </div>
+        </div>
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+        </div>
 
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index 4c383e4..385de2c 100644
--- a/modules/data.atmosphere/docs/authors.html
+++ b/modules/data.atmosphere/docs/authors.html
@@ -2,163 +2,194 @@
 <!DOCTYPE html>
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+                  >1.6.0</span
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+                      <a href="articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
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 </html>
-
diff --git a/modules/data.atmosphere/docs/docsearch.css b/modules/data.atmosphere/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/data.atmosphere/docs/docsearch.css
+++ b/modules/data.atmosphere/docs/docsearch.css
@@ -8,106 +8,110 @@
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   -webkit-box-flex: 1;
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-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
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   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
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 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
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+  display: none;
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-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
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-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/data.atmosphere/docs/docsearch.js b/modules/data.atmosphere/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/data.atmosphere/docs/docsearch.js
+++ b/modules/data.atmosphere/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/data.atmosphere/docs/index.html b/modules/data.atmosphere/docs/index.html
index 0fe0a56..2afcc3d 100644
--- a/modules/data.atmosphere/docs/index.html
+++ b/modules/data.atmosphere/docs/index.html
@@ -1,411 +1,597 @@
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-<title>PEcAn functions used for managing climate driver data • PEcAn.data.atmosphere</title>
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-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for managing climate driver data">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for managing climate driver data •
+      PEcAn.data.atmosphere
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for managing climate driver data"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The PECAn.data.atmosphere
     package converts climate driver data into a standard format for models
     integrated into PEcAn. As a standalone package, it provides an interface to
-    access diverse climate data sets.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    access diverse climate data sets."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
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+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
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-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
-    </li>
-    <li>
-      <a href="articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/compare_narr_cruncep_met.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="articles/tdm_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    <div id="pecan-functions-for-processing-meteorological-data" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#pecan-functions-for-processing-meteorological-data" class="anchor"></a>PEcAn functions for processing meteorological data</h1></div>
-<p>Converts meteorological products to PEcAn-CF formated netCDF files.</p>
-<div id="supported-formats" class="section level2">
-<h2 class="hasAnchor">
-<a href="#supported-formats" class="anchor"></a>Supported Formats</h2>
-<p>Current list of input meteorological formats supported, functions are named <code>download.&lt;source&gt;</code> and <code>met2CF.&lt;source&gt;</code>.</p>
-<ul>
-<li>NCEP</li>
-<li>NARR</li>
-<li>Ameriflux</li>
-<li>FACE</li>
-<li>ALMA</li>
-<li>NOAA GEFS</li>
-<li>arbitrary csv files</li>
-</ul>
-</div>
-<div id="installation" class="section level2">
-<h2 class="hasAnchor">
-<a href="#installation" class="anchor"></a>Installation</h2>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools)
-<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan/modules/data.atmosphere"</span>)</code></pre></div>
-<p>The PEcAn.data.atmosphere package is ‘standalone’.</p>
-</div>
-<div id="documentation" class="section level2">
-<h2 class="hasAnchor">
-<a href="#documentation" class="anchor"></a>Documentation</h2>
-<ul>
-<li><a href="https://pecanproject.github.io/pecan//modules/data.atmosphere/inst/web/index.html">Package Documentation</a></li>
-<li>Vignettes</li>
-</ul>
-</div>
-<div id="pecan-variable-names" class="section level2">
-<h2 class="hasAnchor">
-<a href="#pecan-variable-names" class="anchor"></a>PEcAn variable names</h2>
-<p>See <a href="https://pecanproject.github.io/pecan-documentation/master/met-data.html" class="uri">https://pecanproject.github.io/pecan-documentation/master/met-data.html</a></p>
-<p>General Note: dates in the database should be datatime (preferably with timezone), and datetime passed around in PEcAn should be of type POSIXlt.</p>
-</div>
-<div id="met-data" class="section level2">
-<h2 class="hasAnchor">
-<a href="#met-data" class="anchor"></a>Met Data</h2>
-<p>The standard met data inputs should be of the form:</p>
-<p>Converters from a raw to standard format go in <code>/modules/data.atmosphere/R</code>; converters from standard to model-specific go in <code>models/&lt;mymodel&gt;/R</code>.</p>
-<ul>
-<li>For a number of common gridded products (NARR, CRUNCEP, ISIMIP), there are bash scripts for converting and rechunking in this repository: <a href="https://github.com/ebimodeling/model-drivers" class="uri">https://github.com/ebimodeling/model-drivers</a>; these are not generalized, but may be merged into PEcAn at some point.</li>
-</ul>
-<p>Examples:</p>
-<ul>
-<li>NARR:</li>
-<li>CRUNCEP:</li>
-<li>ISIMIP:</li>
-</ul>
-<p>Names should be <code>met2CF.&lt;sourcename&gt;</code> and <code>met2model.&lt;modelname&gt;</code>.</p>
-</div>
-<div id="dimensions" class="section level2">
-<h2 class="hasAnchor">
-<a href="#dimensions" class="anchor"></a>Dimensions:</h2>
-<table class="table">
-<thead><tr class="header">
-<th align="left">CF standard-name</th>
-<th align="left">units</th>
-</tr></thead>
-<tbody>
-<tr class="odd">
-<td align="left">time</td>
-<td align="left">days since 1700-01-01 00:00:00 UTC</td>
-</tr>
-<tr class="even">
-<td align="left">longitude</td>
-<td align="left">degrees_east</td>
-</tr>
-<tr class="odd">
-<td align="left">latitude</td>
-<td align="left">degrees_north</td>
-</tr>
-</tbody>
-</table>
-</div>
-<div id="the-variable-names-should-be-standard_name" class="section level2">
-<h2 class="hasAnchor">
-<a href="#the-variable-names-should-be-standard_name" class="anchor"></a>The variable names should be <code>standard_name</code>
-</h2>
-<table style="width:100%;" class="table">
-<colgroup>
-<col width="39%">
-<col width="7%">
-<col width="13%">
-<col width="13%">
-<col width="8%">
-<col width="7%">
-<col width="10%">
-</colgroup>
-<thead><tr class="header">
-<th align="left">CF standard-name</th>
-<th align="left">units</th>
-<th align="left">bety</th>
-<th align="left">isimip</th>
-<th align="left">cruncep</th>
-<th align="left">narr</th>
-<th align="left">ameriflux</th>
-</tr></thead>
-<tbody>
-<tr class="odd">
-<td align="left"><strong>air_temperature</strong></td>
-<td align="left">K</td>
-<td align="left">airT</td>
-<td align="left">tasAdjust</td>
-<td align="left">tair</td>
-<td align="left">air</td>
-<td align="left">TA (C)</td>
-</tr>
-<tr class="even">
-<td align="left">air_temperature_max</td>
-<td align="left">K</td>
-<td align="left"></td>
-<td align="left">tasmaxAdjust</td>
-<td align="left">NA</td>
-<td align="left">tmax</td>
-<td align="left"></td>
-</tr>
-<tr class="odd">
-<td align="left">air_temperature_min</td>
-<td align="left">K</td>
-<td align="left"></td>
-<td align="left">tasminAdjust</td>
-<td align="left">NA</td>
-<td align="left">tmin</td>
-<td align="left"></td>
-</tr>
-<tr class="even">
-<td align="left"><strong>air_pressure</strong></td>
-<td align="left">Pa</td>
-<td align="left">air_pressure</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">PRESS (KPa)</td>
-</tr>
-<tr class="odd">
-<td align="left">mole_fraction_of_carbon_dioxide_in_air</td>
-<td align="left">mol/mol</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">CO2</td>
-</tr>
-<tr class="even">
-<td align="left">moisture_content_of_soil_layer</td>
-<td align="left">kg m-2</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-</tr>
-<tr class="odd">
-<td align="left">soil_temperature</td>
-<td align="left">K</td>
-<td align="left">soilT</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">TS1 <em>(NOT DONE)</em>
-</td>
-</tr>
-<tr class="even">
-<td align="left">relative_humidity</td>
-<td align="left">%</td>
-<td align="left">relative_humidity</td>
-<td align="left">rhurs</td>
-<td align="left">NA</td>
-<td align="left">rhum</td>
-<td align="left">RH</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong>specific_humidity</strong></td>
-<td align="left">1</td>
-<td align="left">specific_humidity</td>
-<td align="left">NA</td>
-<td align="left">qair</td>
-<td align="left">shum</td>
-<td align="left">CALC(RH)</td>
-</tr>
-<tr class="even">
-<td align="left">water_vapor_saturation_deficit</td>
-<td align="left">Pa</td>
-<td align="left">VPD</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">VPD <em>(NOT DONE)</em>
-</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong>surface_downwelling_longwave_flux_in_air</strong></td>
-<td align="left">W m-2</td>
-<td align="left">same</td>
-<td align="left">rldsAdjust</td>
-<td align="left">lwdown</td>
-<td align="left">dlwrf</td>
-<td align="left">Rgl</td>
-</tr>
-<tr class="even">
-<td align="left"><strong>surface_downwelling_shortwave_flux_in_air</strong></td>
-<td align="left">W m-2</td>
-<td align="left">solar_radiation</td>
-<td align="left">rsdsAdjust</td>
-<td align="left">swdown</td>
-<td align="left">dswrf</td>
-<td align="left">Rg</td>
-</tr>
-<tr class="odd">
-<td align="left">surface_downwelling_photosynthetic_photon_flux_in_air</td>
-<td align="left">mol m-2 s-1</td>
-<td align="left">PAR</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">PAR <em>(NOT DONE)</em>
-</td>
-</tr>
-<tr class="even">
-<td align="left"><strong>precipitation_flux</strong></td>
-<td align="left">kg m-2 s-1</td>
-<td align="left">cccc</td>
-<td align="left">prAdjust</td>
-<td align="left">rain</td>
-<td align="left">acpc</td>
-<td align="left">PREC (mm/s)</td>
-</tr>
-<tr class="odd">
-<td align="left"></td>
-<td align="left">degrees</td>
-<td align="left">wind_direction</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">WD</td>
-</tr>
-<tr class="even">
-<td align="left">wind_speed</td>
-<td align="left">m/s</td>
-<td align="left">Wspd</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">WS</td>
-</tr>
-<tr class="odd">
-<td align="left"><strong>eastward_wind</strong></td>
-<td align="left">m/s</td>
-<td align="left">eastward_wind</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">CALC(WS+WD)</td>
-</tr>
-<tr class="even">
-<td align="left"><strong>northward_wind</strong></td>
-<td align="left">m/s</td>
-<td align="left">northward_wind</td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left"></td>
-<td align="left">CALC(WS+WD)</td>
-</tr>
-</tbody>
-</table>
-<ul>
-<li>preferred variables indicated in bold</li>
-<li>wind_direction has no CF equivalent and should not be converted, instead the met2CF functions should convert wind_direction and wind_speed to eastward_wind and northward_wind</li>
-<li>variable names are from <a href="http://nacp.ornl.gov/MsTMIP_variables.shtml">MsTMIP</a>, but lowercase to be consistent with the MsTMIP drivers.</li>
-<li>standard_name is CF-convention standard names</li>
-<li>units can be converted by udunits, so these can vary (e.g. the time denominator may change with time frequency of inputs)</li>
-<li>soil moisture for the full column, rather than a layer, is soil_moisture_content</li>
-</ul>
-<p>For the standardized files, we are using CF standard names as variable names.</p>
-<p>For example, in the <a href="https://www.betydb.org/inputs/280">MsTMIP-CRUNCEP</a> data, the variable <code>rain</code> should be <code>precipitation_rate</code>. We want to standardize the units as well as part of the <code>met2CF.&lt;product&gt;</code> step. I believe we want to use the CF “canonical” units but retain the MsTMIP units any time CF is ambiguous about the units.</p>
-<p>The key is to process each type of met data (site, reanalysis, forecast, climate scenario, etc) to the exact same standard. This way every operation after that (extract, gap fill, downscale, convert to a model, etc) will always have the exact same inputs. This will make everything else much simpler to code and allow us to avoid a lot of unnecessary data checking, tests, etc being repeated in every downstream function.</p>
-</div>
-</div>
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
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-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
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-<div class="developers">
-<h2>Developers</h2>
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-<li><a href="authors.html">All authors...</a></li>
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+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="articles/tdm_downscaling.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div
+            id="pecan-functions-for-processing-meteorological-data"
+            class="section level1"
+          >
+            <div class="page-header">
+              <h1 class="hasAnchor">
+                <a
+                  href="#pecan-functions-for-processing-meteorological-data"
+                  class="anchor"
+                ></a
+                >PEcAn functions for processing meteorological data
+              </h1>
+            </div>
+            <p>
+              Converts meteorological products to PEcAn-CF formated netCDF
+              files.
+            </p>
+            <div id="supported-formats" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#supported-formats" class="anchor"></a>Supported
+                Formats
+              </h2>
+              <p>
+                Current list of input meteorological formats supported,
+                functions are named <code>download.&lt;source&gt;</code> and
+                <code>met2CF.&lt;source&gt;</code>.
+              </p>
+              <ul>
+                <li>NCEP</li>
+                <li>NARR</li>
+                <li>Ameriflux</li>
+                <li>FACE</li>
+                <li>ALMA</li>
+                <li>NOAA GEFS</li>
+                <li>arbitrary csv files</li>
+              </ul>
+            </div>
+            <div id="installation" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#installation" class="anchor"></a>Installation
+              </h2>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">library</span>(devtools)
+<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan/modules/data.atmosphere"</span>)</code></pre>
+              </div>
+              <p>The PEcAn.data.atmosphere package is ‘standalone’.</p>
+            </div>
+            <div id="documentation" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#documentation" class="anchor"></a>Documentation
+              </h2>
+              <ul>
+                <li>
+                  <a
+                    href="https://pecanproject.github.io/pecan//modules/data.atmosphere/inst/web/index.html"
+                    >Package Documentation</a
+                  >
+                </li>
+                <li>Vignettes</li>
+              </ul>
+            </div>
+            <div id="pecan-variable-names" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#pecan-variable-names" class="anchor"></a>PEcAn
+                variable names
+              </h2>
+              <p>
+                See
+                <a
+                  href="https://pecanproject.github.io/pecan-documentation/master/met-data.html"
+                  class="uri"
+                  >https://pecanproject.github.io/pecan-documentation/master/met-data.html</a
+                >
+              </p>
+              <p>
+                General Note: dates in the database should be datatime
+                (preferably with timezone), and datetime passed around in PEcAn
+                should be of type POSIXlt.
+              </p>
+            </div>
+            <div id="met-data" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#met-data" class="anchor"></a>Met Data
+              </h2>
+              <p>The standard met data inputs should be of the form:</p>
+              <p>
+                Converters from a raw to standard format go in
+                <code>/modules/data.atmosphere/R</code>; converters from
+                standard to model-specific go in
+                <code>models/&lt;mymodel&gt;/R</code>.
+              </p>
+              <ul>
+                <li>
+                  For a number of common gridded products (NARR, CRUNCEP,
+                  ISIMIP), there are bash scripts for converting and rechunking
+                  in this repository:
+                  <a
+                    href="https://github.com/ebimodeling/model-drivers"
+                    class="uri"
+                    >https://github.com/ebimodeling/model-drivers</a
+                  >; these are not generalized, but may be merged into PEcAn at
+                  some point.
+                </li>
+              </ul>
+              <p>Examples:</p>
+              <ul>
+                <li>NARR:</li>
+                <li>CRUNCEP:</li>
+                <li>ISIMIP:</li>
+              </ul>
+              <p>
+                Names should be <code>met2CF.&lt;sourcename&gt;</code> and
+                <code>met2model.&lt;modelname&gt;</code>.
+              </p>
+            </div>
+            <div id="dimensions" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#dimensions" class="anchor"></a>Dimensions:
+              </h2>
+              <table class="table">
+                <thead>
+                  <tr class="header">
+                    <th align="left">CF standard-name</th>
+                    <th align="left">units</th>
+                  </tr>
+                </thead>
+                <tbody>
+                  <tr class="odd">
+                    <td align="left">time</td>
+                    <td align="left">days since 1700-01-01 00:00:00 UTC</td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left">longitude</td>
+                    <td align="left">degrees_east</td>
+                  </tr>
+                  <tr class="odd">
+                    <td align="left">latitude</td>
+                    <td align="left">degrees_north</td>
+                  </tr>
+                </tbody>
+              </table>
+            </div>
+            <div
+              id="the-variable-names-should-be-standard_name"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#the-variable-names-should-be-standard_name"
+                  class="anchor"
+                ></a
+                >The variable names should be <code>standard_name</code>
+              </h2>
+              <table style="width:100%;" class="table">
+                <colgroup>
+                  <col width="39%" />
+                  <col width="7%" />
+                  <col width="13%" />
+                  <col width="13%" />
+                  <col width="8%" />
+                  <col width="7%" />
+                  <col width="10%" />
+                </colgroup>
+                <thead>
+                  <tr class="header">
+                    <th align="left">CF standard-name</th>
+                    <th align="left">units</th>
+                    <th align="left">bety</th>
+                    <th align="left">isimip</th>
+                    <th align="left">cruncep</th>
+                    <th align="left">narr</th>
+                    <th align="left">ameriflux</th>
+                  </tr>
+                </thead>
+                <tbody>
+                  <tr class="odd">
+                    <td align="left"><strong>air_temperature</strong></td>
+                    <td align="left">K</td>
+                    <td align="left">airT</td>
+                    <td align="left">tasAdjust</td>
+                    <td align="left">tair</td>
+                    <td align="left">air</td>
+                    <td align="left">TA (C)</td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left">air_temperature_max</td>
+                    <td align="left">K</td>
+                    <td align="left"></td>
+                    <td align="left">tasmaxAdjust</td>
+                    <td align="left">NA</td>
+                    <td align="left">tmax</td>
+                    <td align="left"></td>
+                  </tr>
+                  <tr class="odd">
+                    <td align="left">air_temperature_min</td>
+                    <td align="left">K</td>
+                    <td align="left"></td>
+                    <td align="left">tasminAdjust</td>
+                    <td align="left">NA</td>
+                    <td align="left">tmin</td>
+                    <td align="left"></td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left"><strong>air_pressure</strong></td>
+                    <td align="left">Pa</td>
+                    <td align="left">air_pressure</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left">PRESS (KPa)</td>
+                  </tr>
+                  <tr class="odd">
+                    <td align="left">mole_fraction_of_carbon_dioxide_in_air</td>
+                    <td align="left">mol/mol</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left">CO2</td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left">moisture_content_of_soil_layer</td>
+                    <td align="left">kg m-2</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                  </tr>
+                  <tr class="odd">
+                    <td align="left">soil_temperature</td>
+                    <td align="left">K</td>
+                    <td align="left">soilT</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left">TS1 <em>(NOT DONE)</em></td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left">relative_humidity</td>
+                    <td align="left">%</td>
+                    <td align="left">relative_humidity</td>
+                    <td align="left">rhurs</td>
+                    <td align="left">NA</td>
+                    <td align="left">rhum</td>
+                    <td align="left">RH</td>
+                  </tr>
+                  <tr class="odd">
+                    <td align="left"><strong>specific_humidity</strong></td>
+                    <td align="left">1</td>
+                    <td align="left">specific_humidity</td>
+                    <td align="left">NA</td>
+                    <td align="left">qair</td>
+                    <td align="left">shum</td>
+                    <td align="left">CALC(RH)</td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left">water_vapor_saturation_deficit</td>
+                    <td align="left">Pa</td>
+                    <td align="left">VPD</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left">VPD <em>(NOT DONE)</em></td>
+                  </tr>
+                  <tr class="odd">
+                    <td align="left">
+                      <strong>surface_downwelling_longwave_flux_in_air</strong>
+                    </td>
+                    <td align="left">W m-2</td>
+                    <td align="left">same</td>
+                    <td align="left">rldsAdjust</td>
+                    <td align="left">lwdown</td>
+                    <td align="left">dlwrf</td>
+                    <td align="left">Rgl</td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left">
+                      <strong>surface_downwelling_shortwave_flux_in_air</strong>
+                    </td>
+                    <td align="left">W m-2</td>
+                    <td align="left">solar_radiation</td>
+                    <td align="left">rsdsAdjust</td>
+                    <td align="left">swdown</td>
+                    <td align="left">dswrf</td>
+                    <td align="left">Rg</td>
+                  </tr>
+                  <tr class="odd">
+                    <td align="left">
+                      surface_downwelling_photosynthetic_photon_flux_in_air
+                    </td>
+                    <td align="left">mol m-2 s-1</td>
+                    <td align="left">PAR</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left">PAR <em>(NOT DONE)</em></td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left"><strong>precipitation_flux</strong></td>
+                    <td align="left">kg m-2 s-1</td>
+                    <td align="left">cccc</td>
+                    <td align="left">prAdjust</td>
+                    <td align="left">rain</td>
+                    <td align="left">acpc</td>
+                    <td align="left">PREC (mm/s)</td>
+                  </tr>
+                  <tr class="odd">
+                    <td align="left"></td>
+                    <td align="left">degrees</td>
+                    <td align="left">wind_direction</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left">WD</td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left">wind_speed</td>
+                    <td align="left">m/s</td>
+                    <td align="left">Wspd</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left">WS</td>
+                  </tr>
+                  <tr class="odd">
+                    <td align="left"><strong>eastward_wind</strong></td>
+                    <td align="left">m/s</td>
+                    <td align="left">eastward_wind</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left">CALC(WS+WD)</td>
+                  </tr>
+                  <tr class="even">
+                    <td align="left"><strong>northward_wind</strong></td>
+                    <td align="left">m/s</td>
+                    <td align="left">northward_wind</td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left"></td>
+                    <td align="left">CALC(WS+WD)</td>
+                  </tr>
+                </tbody>
+              </table>
+              <ul>
+                <li>preferred variables indicated in bold</li>
+                <li>
+                  wind_direction has no CF equivalent and should not be
+                  converted, instead the met2CF functions should convert
+                  wind_direction and wind_speed to eastward_wind and
+                  northward_wind
+                </li>
+                <li>
+                  variable names are from
+                  <a href="http://nacp.ornl.gov/MsTMIP_variables.shtml"
+                    >MsTMIP</a
+                  >, but lowercase to be consistent with the MsTMIP drivers.
+                </li>
+                <li>standard_name is CF-convention standard names</li>
+                <li>
+                  units can be converted by udunits, so these can vary (e.g. the
+                  time denominator may change with time frequency of inputs)
+                </li>
+                <li>
+                  soil moisture for the full column, rather than a layer, is
+                  soil_moisture_content
+                </li>
+              </ul>
+              <p>
+                For the standardized files, we are using CF standard names as
+                variable names.
+              </p>
+              <p>
+                For example, in the
+                <a href="https://www.betydb.org/inputs/280">MsTMIP-CRUNCEP</a>
+                data, the variable <code>rain</code> should be
+                <code>precipitation_rate</code>. We want to standardize the
+                units as well as part of the
+                <code>met2CF.&lt;product&gt;</code> step. I believe we want to
+                use the CF “canonical” units but retain the MsTMIP units any
+                time CF is ambiguous about the units.
+              </p>
+              <p>
+                The key is to process each type of met data (site, reanalysis,
+                forecast, climate scenario, etc) to the exact same standard.
+                This way every operation after that (extract, gap fill,
+                downscale, convert to a model, etc) will always have the exact
+                same inputs. This will make everything else much simpler to code
+                and allow us to avoid a lot of unnecessary data checking, tests,
+                etc being repeated in every downstream function.
+              </p>
+            </div>
+          </div>
+        </div>
 
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-  <p>Developed by .</p>
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diff --git a/modules/data.atmosphere/docs/pkgdown.css b/modules/data.atmosphere/docs/pkgdown.css
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diff --git a/modules/data.atmosphere/docs/reference/AirDens.html b/modules/data.atmosphere/docs/reference/AirDens.html
index 19136ca..7881a64 100644
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+    />
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     <div class="container template-reference-topic">
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+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
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+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Air Density</h1>
-    
-    <div class="hidden name"><code>AirDens.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>estimate air density from pressure, temperature, and humidity</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>AirDens</span>(<span class='no'>pres</span>, <span class='no'>T</span>, <span class='no'>rv</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pres</th>
-      <td><p>air pressure (pascals)</p></td>
-    </tr>
-    <tr>
-      <th>T</th>
-      <td><p>air temperature (Kelvin)</p></td>
-    </tr>
-    <tr>
-      <th>rv</th>
-      <td><p>humidity</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Air Density</h1>
+
+            <div class="hidden name"><code>AirDens.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>estimate air density from pressure, temperature, and humidity</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>AirDens</span>(<span class='no'>pres</span>, <span class='no'>T</span>, <span class='no'>rv</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pres</th>
+              <td><p>air pressure (pascals)</p></td>
+            </tr>
+            <tr>
+              <th>T</th>
+              <td><p>air temperature (Kelvin)</p></td>
+            </tr>
+            <tr>
+              <th>rv</th>
+              <td><p>humidity</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
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index f5e6369..8608a2e 100644
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+
+    <meta
+      property="og:description"
+      content="This script aligns meteorology datasets in at temporal resolution for debiasing &amp;amp; 
              temporal downscaling.  
              Note: The output here is stored in memory!  
              Note: can probably at borrow from or adapt align_data.R in Benchmarking module, but 
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+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                    <li>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>align.met</h1>
-    
-    <div class="hidden name"><code>align.met.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This script aligns meteorology datasets in at temporal resolution for debiasing &amp; 
-             temporal downscaling.  
-             Note: The output here is stored in memory!  
-             Note: can probably at borrow from or adapt align_data.R in Benchmarking module, but 
-             it's too much of a black box at the moment.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>align.met</span>(<span class='no'>train.path</span>, <span class='no'>source.path</span>, <span class='kw'>yrs.train</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>yrs.source</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>align.met</h1>
+
+            <div class="hidden name"><code>align.met.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This script aligns meteorology datasets in at temporal resolution
+              for debiasing &amp; temporal downscaling. Note: The output here is
+              stored in memory! Note: can probably at borrow from or adapt
+              align_data.R in Benchmarking module, but it's too much of a black
+              box at the moment.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>align.met</span>(<span class='no'>train.path</span>, <span class='no'>source.path</span>, <span class='kw'>yrs.train</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>yrs.source</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>n.ens</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>pair.mems</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>mems.train</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fu'>Sys.Date</span>(), <span class='kw'>print.progress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>train.path</th>
-      <td><p>- path to the dataset to be used to downscale the data</p></td>
-    </tr>
-    <tr>
-      <th>source.path</th>
-      <td><p>- data to be bias-corrected aligned with training data (from align.met)</p></td>
-    </tr>
-    <tr>
-      <th>yrs.train</th>
-      <td><p>- (optional) specify a specific years to be loaded for the training data; 
-prevents needing to load the entire dataset.  If NULL, all available years 
-will be loaded. If not null, should be a vector of numbers (so you can skip
-problematic years)</p></td>
-    </tr>
-    <tr>
-      <th>yrs.source</th>
-      <td><p>- (optional) specify a specific years to be loaded for the source data;
-prevents needing to load the entire dataset.  If NULL, all available years 
-will be loaded. If not null, should be a vector of numbers (so you can skip
-problematic years)</p></td>
-    </tr>
-    <tr>
-      <th>n.ens</th>
-      <td><p>- number of ensemble members to generate and save</p></td>
-    </tr>
-    <tr>
-      <th>pair.mems</th>
-      <td><p>- logical stating whether ensemble members should be paired in 
-the case where ensembles are being read in in both the training and source data</p></td>
-    </tr>
-    <tr>
-      <th>mems.train</th>
-      <td><p>- (optional) string of ensemble identifiers that ensure the training data is read 
-in a specific order to ensure consistent time series &amp; proper error propagation.
-If null, members of the training data ensemble will be randomly selected and 
-ordered.  Specifying the ensemble members IDs (e.g. CCSM_001, CCSM_002) will 
-ensure ensemble members are properly identified and combined.</p></td>
-    </tr>
-    <tr>
-      <th>seed</th>
-      <td><p>- specify seed so that random draws can be reproduced</p></td>
-    </tr>
-    <tr>
-      <th>print.progress</th>
-      <td><p>- if TRUE, prints progress bar</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>2-layered list (stored in memory) containing the training and source data that are now matched
-        in temporal resolution have the specified number of ensemble members
-         - dat.train (training dataset) and dat.source (source data to be downscaled or bias-corrected)
-           are both lists that contain separate data frames for time indices and all available met 
-           variables with ensemble members in columns</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Align meteorology datasets for debiasing</p>
-<p>1. Assumes that both the training and source data are in *at least* daily resolution 
-            and each dataset is in a consistent temporal resolution being read from a single file 
-            (CF/Pecan format).  For example, CMIP5 historical/p1000 runs where radiation drivers 
-            are in monthly resolution and temperature is in daily will need to be reconciled using
-            one of the "met2CF" or "download" or "extract" functions
-         2. Default file structure: Ensembles members for a given site or set of simes are housed 
-            in a common folder with the site ID.  Right now everything is based off of Christy's 
-            PalEON ensemble ID scheme where the site ID is a character string (e.g. HARVARD) followed
-            the SOURCE data family (i.e. GCM) as a string and then the ensemble member ID as a number 
-            (e.g. 001).  For example, the file path for a single daily ensemble member for PalEON is:
-            "~/Desktop/Research/met_ensembles/data/met_ensembles/HARVARD/day/ensembles/bcc-csm1-1_004"
-            with each year in a separate netcdf file inside of it.  "bcc-csm1-1_004" is an example of
-            an ensemnle member ID that might be used if you are specifying mems.train.</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other debias - Debias &amp; Align Meteorology Datasets into continuous time series: <code><a href='debias.met.regression.html'>debias.met.regression</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
 
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>train.path</th>
+              <td>
+                <p>- path to the dataset to be used to downscale the data</p>
+              </td>
+            </tr>
+            <tr>
+              <th>source.path</th>
+              <td>
+                <p>
+                  - data to be bias-corrected aligned with training data (from
+                  align.met)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>yrs.train</th>
+              <td>
+                <p>
+                  - (optional) specify a specific years to be loaded for the
+                  training data; prevents needing to load the entire dataset. If
+                  NULL, all available years will be loaded. If not null, should
+                  be a vector of numbers (so you can skip problematic years)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>yrs.source</th>
+              <td>
+                <p>
+                  - (optional) specify a specific years to be loaded for the
+                  source data; prevents needing to load the entire dataset. If
+                  NULL, all available years will be loaded. If not null, should
+                  be a vector of numbers (so you can skip problematic years)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.ens</th>
+              <td><p>- number of ensemble members to generate and save</p></td>
+            </tr>
+            <tr>
+              <th>pair.mems</th>
+              <td>
+                <p>
+                  - logical stating whether ensemble members should be paired in
+                  the case where ensembles are being read in in both the
+                  training and source data
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>mems.train</th>
+              <td>
+                <p>
+                  - (optional) string of ensemble identifiers that ensure the
+                  training data is read in a specific order to ensure consistent
+                  time series &amp; proper error propagation. If null, members
+                  of the training data ensemble will be randomly selected and
+                  ordered. Specifying the ensemble members IDs (e.g. CCSM_001,
+                  CCSM_002) will ensure ensemble members are properly identified
+                  and combined.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>seed</th>
+              <td>
+                <p>- specify seed so that random draws can be reproduced</p>
+              </td>
+            </tr>
+            <tr>
+              <th>print.progress</th>
+              <td><p>- if TRUE, prints progress bar</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            2-layered list (stored in memory) containing the training and source
+            data that are now matched in temporal resolution have the specified
+            number of ensemble members - dat.train (training dataset) and
+            dat.source (source data to be downscaled or bias-corrected) are both
+            lists that contain separate data frames for time indices and all
+            available met variables with ensemble members in columns
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Align meteorology datasets for debiasing</p>
+          <p>
+            1. Assumes that both the training and source data are in *at least*
+            daily resolution and each dataset is in a consistent temporal
+            resolution being read from a single file (CF/Pecan format). For
+            example, CMIP5 historical/p1000 runs where radiation drivers are in
+            monthly resolution and temperature is in daily will need to be
+            reconciled using one of the "met2CF" or "download" or "extract"
+            functions 2. Default file structure: Ensembles members for a given
+            site or set of simes are housed in a common folder with the site ID.
+            Right now everything is based off of Christy's PalEON ensemble ID
+            scheme where the site ID is a character string (e.g. HARVARD)
+            followed the SOURCE data family (i.e. GCM) as a string and then the
+            ensemble member ID as a number (e.g. 001). For example, the file
+            path for a single daily ensemble member for PalEON is:
+            "~/Desktop/Research/met_ensembles/data/met_ensembles/HARVARD/day/ensembles/bcc-csm1-1_004"
+            with each year in a separate netcdf file inside of it.
+            "bcc-csm1-1_004" is an example of an ensemnle member ID that might
+            be used if you are specifying mems.train.
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other debias - Debias &amp; Align Meteorology Datasets into
+              continuous time series:
+              <code
+                ><a href="debias.met.regression.html"
+                  >debias.met.regression</a
+                ></code
+              >
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/browndog.met.html b/modules/data.atmosphere/docs/reference/browndog.met.html
index 8842fe1..7e35d2b 100644
--- a/modules/data.atmosphere/docs/reference/browndog.met.html
+++ b/modules/data.atmosphere/docs/reference/browndog.met.html
@@ -2,201 +2,269 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>get met data from browndog — browndog.met • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="get met data from browndog — browndog.met" />
-
-<meta property="og:description" content="Use browndog to get the met data for a specific model" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      get met data from browndog — browndog.met • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="get met data from browndog — browndog.met"
+    />
+
+    <meta
+      property="og:description"
+      content="Use browndog to get the met data for a specific model"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
-    </li>
-    <li>
-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="../articles/compare_narr_cruncep_met.html">UNKNOWN TITLE</a>
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-      <a href="../articles/tdm_downscaling.html">UNKNOWN TITLE</a>
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-  </ul>
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-      
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-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get met data from browndog</h1>
-    
-    <div class="hidden name"><code>browndog.met.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get met data from browndog</h1>
 
-    <div class="ref-description">
-    
-    <p>Use browndog to get the met data for a specific model</p>
-    
-    </div>
+            <div class="hidden name"><code>browndog.met.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>browndog.met</span>(<span class='no'>browndog</span>, <span class='no'>source</span>, <span class='no'>site</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>model</span>, <span class='no'>dir</span>,
-  <span class='no'>username</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>browndog, </th>
-      <td><p>list with url, username and password to connect to browndog</p></td>
-    </tr>
-    <tr>
-      <th>source, </th>
-      <td><p>the source of the met data, currently only NARR an Ameriflux is supported</p></td>
-    </tr>
-    <tr>
-      <th>site, </th>
-      <td><p>site information should have id, lat, lon and name (ameriflux id)</p></td>
-    </tr>
-    <tr>
-      <th>start_date, </th>
-      <td><p>start date for result</p></td>
-    </tr>
-    <tr>
-      <th>end_date, </th>
-      <td><p>end date for result</p></td>
-    </tr>
-    <tr>
-      <th>model, </th>
-      <td><p>model to convert the met data to</p></td>
-    </tr>
-    <tr>
-      <th>dir, </th>
-      <td><p>folder where results are stored (in subfolder)</p></td>
-    </tr>
-    <tr>
-      <th>username, </th>
-      <td><p>used when downloading data from Ameriflux like sites</p></td>
-    </tr>
-    <tr>
-      <th>con, </th>
-      <td><p>database connection</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Rob Kooper
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Use browndog to get the met data for a specific model</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>browndog.met</span>(<span class='no'>browndog</span>, <span class='no'>source</span>, <span class='no'>site</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>model</span>, <span class='no'>dir</span>,
+  <span class='no'>username</span>, <span class='no'>con</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>browndog,</th>
+              <td>
+                <p>
+                  list with url, username and password to connect to browndog
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>source,</th>
+              <td>
+                <p>
+                  the source of the met data, currently only NARR an Ameriflux
+                  is supported
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>site,</th>
+              <td>
+                <p>
+                  site information should have id, lat, lon and name (ameriflux
+                  id)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>start_date,</th>
+              <td><p>start date for result</p></td>
+            </tr>
+            <tr>
+              <th>end_date,</th>
+              <td><p>end date for result</p></td>
+            </tr>
+            <tr>
+              <th>model,</th>
+              <td><p>model to convert the met data to</p></td>
+            </tr>
+            <tr>
+              <th>dir,</th>
+              <td><p>folder where results are stored (in subfolder)</p></td>
+            </tr>
+            <tr>
+              <th>username,</th>
+              <td>
+                <p>used when downloading data from Ameriflux like sites</p>
+              </td>
+            </tr>
+            <tr>
+              <th>con,</th>
+              <td><p>database connection</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/build_cf_variables_table_url.html b/modules/data.atmosphere/docs/reference/build_cf_variables_table_url.html
index cd9e687..476b46a 100644
--- a/modules/data.atmosphere/docs/reference/build_cf_variables_table_url.html
+++ b/modules/data.atmosphere/docs/reference/build_cf_variables_table_url.html
@@ -2,183 +2,251 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Construct a URL to a specific version of the CF variables table XML — build_cf_variables_table_url • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Construct a URL to a specific version of the CF variables table XML — build_cf_variables_table_url" />
-
-<meta property="og:description" content="This uses sprintf to construct the URL with the version number as
-the first argument." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Construct a URL to a specific version of the CF variables table XML —
+      build_cf_variables_table_url • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
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+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Construct a URL to a specific version of the CF variables table XML — build_cf_variables_table_url"
+    />
+
+    <meta
+      property="og:description"
+      content="This uses sprintf to construct the URL with the version number as
+the first argument."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
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+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Construct a URL to a specific version of the CF variables table XML</h1>
-    
-    <div class="hidden name"><code>build_cf_variables_table_url.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This uses sprintf to construct the URL with the version number as
-the first argument.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>build_cf_variables_table_url</span>(<span class='no'>version</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Construct a URL to a specific version of the CF variables table
+              XML
+            </h1>
+
+            <div class="hidden name">
+              <code>build_cf_variables_table_url.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This uses sprintf to construct the URL with the version number as
+              the first argument.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>build_cf_variables_table_url</span>(<span class='no'>version</span>,
   <span class='kw'>url_format_string</span> <span class='kw'>=</span> <span class='st'>"http://cfconventions.org/Data/cf-standard-names/%d/src/src-cf-standard-name-table.xml"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>version</th>
-      <td><p>CF variables table version number (integer/numeric)</p></td>
-    </tr>
-    <tr>
-      <th>url_format_string</th>
-      <td><p>A format string passed to sprintf. This
-should contain the entire target URL with the version number
-replaced by <code>"%d"</code>, and <em>no other string substitutions</em>.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Complete URL, as a string</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>version</th>
+              <td>
+                <p>CF variables table version number (integer/numeric)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>url_format_string</th>
+              <td>
+                <p>
+                  A format string passed to sprintf. This should contain the
+                  entire target URL with the version number replaced by
+                  <code>"%d"</code>, and <em>no other string substitutions</em>.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Complete URL, as a string</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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diff --git a/modules/data.atmosphere/docs/reference/cfmet.downscale.daily.html b/modules/data.atmosphere/docs/reference/cfmet.downscale.daily.html
index 89eaa05..d5ac7b0 100644
--- a/modules/data.atmosphere/docs/reference/cfmet.downscale.daily.html
+++ b/modules/data.atmosphere/docs/reference/cfmet.downscale.daily.html
@@ -2,191 +2,250 @@
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+      PEcAn.data.atmosphere
+    </title>
+
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+      crossorigin="anonymous"
+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+                type="button"
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+                data-toggle="collapse"
+                data-target="#navbar"
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+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>daily to subdaily downscaling</h1>
-    
-    <div class="hidden name"><code>cfmet.downscale.daily.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Simple, Fast Daily to Hourly Climate Downscaling</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>cfmet.downscale.daily</span>(<span class='no'>dailymet</span>, <span class='kw'>output.dt</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>lat</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dailymet</th>
-      <td><p>data table with climate variables</p></td>
-    </tr>
-    <tr>
-      <th>output.dt</th>
-      <td><p>output timestep</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>latitude (for calculating solar radiation)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>weather file with subdaily timesteps</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Based on weach family of functions but 5x faster than weachNEW,
-and requiring metric units (temperature in celsius, windspeed in kph,
-precip in mm, relative humidity as fraction).
-Derived from the weachDT function in the BioCro package.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>daily to subdaily downscaling</h1>
+
+            <div class="hidden name"><code>cfmet.downscale.daily.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Simple, Fast Daily to Hourly Climate Downscaling</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>cfmet.downscale.daily</span>(<span class='no'>dailymet</span>, <span class='kw'>output.dt</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>lat</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dailymet</th>
+              <td><p>data table with climate variables</p></td>
+            </tr>
+            <tr>
+              <th>output.dt</th>
+              <td><p>output timestep</p></td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>latitude (for calculating solar radiation)</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>weather file with subdaily timesteps</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Based on weach family of functions but 5x faster than weachNEW, and
+            requiring metric units (temperature in celsius, windspeed in kph,
+            precip in mm, relative humidity as fraction). Derived from the
+            weachDT function in the BioCro package.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/data.atmosphere/docs/reference/cfmet.downscale.subdaily.html b/modules/data.atmosphere/docs/reference/cfmet.downscale.subdaily.html
index 85dd675..c12b346 100644
--- a/modules/data.atmosphere/docs/reference/cfmet.downscale.subdaily.html
+++ b/modules/data.atmosphere/docs/reference/cfmet.downscale.subdaily.html
@@ -2,185 +2,255 @@
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+
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+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="subdaily downscaling — cfmet.downscale.subdaily"
+    />
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+    <meta
+      property="og:description"
+      content="Subdaily to hourly (or less) downscaling"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
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+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
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+                    <li>
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+                        >UNKNOWN TITLE</a
+                      >
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+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>subdaily downscaling</h1>
-    
-    <div class="hidden name"><code>cfmet.downscale.subdaily.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Subdaily to hourly (or less) downscaling</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>cfmet.downscale.subdaily</span>(<span class='no'>subdailymet</span>, <span class='kw'>output.dt</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>subdailymet</th>
-      <td><p>data table with climate variables queried from <code><a href='load.cfmet.html'>load.cfmet</a></code></p></td>
-    </tr>
-    <tr>
-      <th>output.dt</th>
-      <td><p>output timestep. default is one hour</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>weather file with subdaily met variables rescaled to output time step</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Uses simple spline to interpolate variables with diurnal variability, otherwise uses averaging or repeating
-for variables with no clear diurnal pattern. For all variables except temperature, negative values are set to zero.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>subdaily downscaling</h1>
+
+            <div class="hidden name">
+              <code>cfmet.downscale.subdaily.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Subdaily to hourly (or less) downscaling</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>cfmet.downscale.subdaily</span>(<span class='no'>subdailymet</span>, <span class='kw'>output.dt</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>subdailymet</th>
+              <td>
+                <p>
+                  data table with climate variables queried from
+                  <code><a href="load.cfmet.html">load.cfmet</a></code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>output.dt</th>
+              <td><p>output timestep. default is one hour</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            weather file with subdaily met variables rescaled to output time
+            step
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Uses simple spline to interpolate variables with diurnal
+            variability, otherwise uses averaging or repeating for variables
+            with no clear diurnal pattern. For all variables except temperature,
+            negative values are set to zero.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
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-
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diff --git a/modules/data.atmosphere/docs/reference/cfmet.downscale.time.html b/modules/data.atmosphere/docs/reference/cfmet.downscale.time.html
index c48ec45..2a5bf00 100644
--- a/modules/data.atmosphere/docs/reference/cfmet.downscale.time.html
+++ b/modules/data.atmosphere/docs/reference/cfmet.downscale.time.html
@@ -2,178 +2,237 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<![endif]-->
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+    <!-- sticky kit -->
+    <script
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+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Downscale CF met data</h1>
-    
-    <div class="hidden name"><code>cfmet.downscale.time.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Temporal downscaling of daily or subdaily met data</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>cfmet.downscale.time</span>(<span class='no'>cfmet</span>, <span class='kw'>output.dt</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>lat</span> <span class='kw'>=</span> <span class='no'>lat</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>cfmet</th>
-      <td><p>data.table with CF variables generated by <code><a href='load.cfmet.html'>load.cfmet</a></code></p></td>
-    </tr>
-    <tr>
-      <th>output.dt</th>
-      <td><p>time step (hours) for output</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>downscaled result</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Downscale CF met data</h1>
+
+            <div class="hidden name"><code>cfmet.downscale.time.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Temporal downscaling of daily or subdaily met data</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>cfmet.downscale.time</span>(<span class='no'>cfmet</span>, <span class='kw'>output.dt</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>lat</span> <span class='kw'>=</span> <span class='no'>lat</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>cfmet</th>
+              <td>
+                <p>
+                  data.table with CF variables generated by
+                  <code><a href="load.cfmet.html">load.cfmet</a></code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>output.dt</th>
+              <td><p>time step (hours) for output</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>downscaled result</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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index 5a38a42..87393b4 100644
--- a/modules/data.atmosphere/docs/reference/check_met_input_file.html
+++ b/modules/data.atmosphere/docs/reference/check_met_input_file.html
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+    </title>
+
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+                  >PEcAn.data.atmosphere</a
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+                        station</a
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+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check a meteorology data file for compliance with the PEcAn standard</h1>
-    
-    <div class="hidden name"><code>check_met_input_file.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check a meteorology data file for compliance with the PEcAn standard</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check_met_input_file</span>(<span class='no'>metfile</span>, <span class='kw'>variable_table</span> <span class='kw'>=</span> <span class='no'>pecan_standard_met_table</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Check a meteorology data file for compliance with the PEcAn
+              standard
+            </h1>
+
+            <div class="hidden name"><code>check_met_input_file.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Check a meteorology data file for compliance with the PEcAn
+              standard
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_met_input_file</span>(<span class='no'>metfile</span>, <span class='kw'>variable_table</span> <span class='kw'>=</span> <span class='no'>pecan_standard_met_table</span>,
   <span class='kw'>required_vars</span> <span class='kw'>=</span> <span class='no'>variable_table</span> <span class='kw'>%&gt;%</span> <span class='kw pkg'>dplyr</span><span class='kw ns'>::</span><span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>is_required</span>) <span class='kw'>%&gt;%</span>
   <span class='kw pkg'>dplyr</span><span class='kw ns'>::</span><span class='fu'><a href='http://dplyr.tidyverse.org/reference/pull.html'>pull</a></span>(<span class='no'>cf_standard_name</span>), <span class='kw'>warn_unknown</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>metfile</th>
-      <td><p>Path of met file to check, as a scalar character.</p></td>
-    </tr>
-    <tr>
-      <th>variable_table</th>
-      <td><p>`data.frame` linking standard names to their
-units. Must contain columns "cf_standard_name" and "units".
-Default is [pecan_standard_met_table].</p></td>
-    </tr>
-    <tr>
-      <th>required_vars</th>
-      <td><p>Character vector of required variables.
-Defaults to variables marked as required in `variable_table`.</p></td>
-    </tr>
-    <tr>
-      <th>warn_unknown</th>
-      <td><p>Logical. If `TRUE` (default), throw a warning
-for variables not in `variable_table`. Otherwise, ignore unknown
-variables.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`data.frame` summarizing the results of the tests.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>metfile</th>
+              <td><p>Path of met file to check, as a scalar character.</p></td>
+            </tr>
+            <tr>
+              <th>variable_table</th>
+              <td>
+                <p>
+                  `data.frame` linking standard names to their units. Must
+                  contain columns "cf_standard_name" and "units". Default is
+                  [pecan_standard_met_table].
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>required_vars</th>
+              <td>
+                <p>
+                  Character vector of required variables. Defaults to variables
+                  marked as required in `variable_table`.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>warn_unknown</th>
+              <td>
+                <p>
+                  Logical. If `TRUE` (default), throw a warning for variables
+                  not in `variable_table`. Otherwise, ignore unknown variables.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>`data.frame` summarizing the results of the tests.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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-  
-
+    </div>
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 </html>
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diff --git a/modules/data.atmosphere/docs/reference/check_unit.html b/modules/data.atmosphere/docs/reference/check_unit.html
index bbda19c..75c3ddd 100644
--- a/modules/data.atmosphere/docs/reference/check_unit.html
+++ b/modules/data.atmosphere/docs/reference/check_unit.html
@@ -2,195 +2,263 @@
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+      Check that the unit of a variable in a NetCDF file is equivalent to the
+      expected unit. — check_unit • PEcAn.data.atmosphere
+    </title>
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    <script src="../pkgdown.js"></script>
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+the expected unit. — check_unit"
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+the expected unit."
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+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+            </div>
+
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+              <ul class="nav navbar-nav">
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+                    <span class="fa fa-home fa-lg"></span>
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check that the unit of a variable in a NetCDF file is equivalent to
-the expected unit.</h1>
-    
-    <div class="hidden name"><code>check_unit.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check that the unit of a variable in a NetCDF file is equivalent to
-the expected unit.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check_unit</span>(<span class='no'>variable</span>, <span class='no'>nc</span>, <span class='no'>variable_table</span>, <span class='kw'>warn_unknown</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>variable</th>
-      <td><p>Name of target variable, as a length 1 character</p></td>
-    </tr>
-    <tr>
-      <th>nc</th>
-      <td><p>NetCDF object containing target variable</p></td>
-    </tr>
-    <tr>
-      <th>variable_table</th>
-      <td><p>`data.frame` linking standard names to their
-units. Must contain columns "cf_standard_name" and "units".
-Default is [pecan_standard_met_table].</p></td>
-    </tr>
-    <tr>
-      <th>warn_unknown</th>
-      <td><p>Logical. If `TRUE` (default), throw a warning
-for variables not in `variable_table`. Otherwise, ignore unknown
-variables.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`TRUE` if unit is correct, or `try-error` object if there is a mismatch.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Check that the unit of a variable in a NetCDF file is equivalent
+              to the expected unit.
+            </h1>
+
+            <div class="hidden name"><code>check_unit.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Check that the unit of a variable in a NetCDF file is equivalent
+              to the expected unit.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check_unit</span>(<span class='no'>variable</span>, <span class='no'>nc</span>, <span class='no'>variable_table</span>, <span class='kw'>warn_unknown</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>variable</th>
+              <td><p>Name of target variable, as a length 1 character</p></td>
+            </tr>
+            <tr>
+              <th>nc</th>
+              <td><p>NetCDF object containing target variable</p></td>
+            </tr>
+            <tr>
+              <th>variable_table</th>
+              <td>
+                <p>
+                  `data.frame` linking standard names to their units. Must
+                  contain columns "cf_standard_name" and "units". Default is
+                  [pecan_standard_met_table].
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>warn_unknown</th>
+              <td>
+                <p>
+                  Logical. If `TRUE` (default), throw a warning for variables
+                  not in `variable_table`. Otherwise, ignore unknown variables.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            `TRUE` if unit is correct, or `try-error` object if there is a
+            mismatch.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/closest_xy.html b/modules/data.atmosphere/docs/reference/closest_xy.html
index e425b77..f65afef 100644
--- a/modules/data.atmosphere/docs/reference/closest_xy.html
+++ b/modules/data.atmosphere/docs/reference/closest_xy.html
@@ -2,158 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>closest_xy</h1>
-    
-    <div class="hidden name"><code>closest_xy.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>closest_xy</h1>
 
-    <div class="ref-description">
-    
-    <p>Given latitude and longitude coordinates, find NARR x and y indices</p>
-    
-    </div>
+            <div class="hidden name"><code>closest_xy.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>closest_xy</span>(<span class='no'>slat</span>, <span class='no'>slon</span>, <span class='no'>infolder</span>, <span class='no'>infile</span>)</pre>
-        
+          <div class="ref-description">
+            <p>
+              Given latitude and longitude coordinates, find NARR x and y
+              indices
+            </p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>closest_xy</span>(<span class='no'>slat</span>, <span class='no'>slon</span>, <span class='no'>infolder</span>, <span class='no'>infile</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Betsy Cowdery
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Betsy Cowdery
+        </div>
+      </div>
 
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diff --git a/modules/data.atmosphere/docs/reference/col2ncvar.html b/modules/data.atmosphere/docs/reference/col2ncvar.html
index 23cc28c..ab8e156 100644
--- a/modules/data.atmosphere/docs/reference/col2ncvar.html
+++ b/modules/data.atmosphere/docs/reference/col2ncvar.html
@@ -2,175 +2,234 @@
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+                    </li>
+                  </ul>
+                </li>
+              </ul>
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+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create `ncvar` object from variable name</h1>
-    
-    <div class="hidden name"><code>col2ncvar.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Create `ncvar` object from variable name</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>col2ncvar</span>(<span class='no'>variable</span>, <span class='no'>dims</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>variable</th>
-      <td><p>CF variable name</p></td>
-    </tr>
-    <tr>
-      <th>dims</th>
-      <td><p>List of NetCDF dimension objects (passed to 
-`ncdf4::ncvar_def(..., dim)`)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`ncvar` object (from `ncvar_def`)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create `ncvar` object from variable name</h1>
+
+            <div class="hidden name"><code>col2ncvar.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Create `ncvar` object from variable name</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>col2ncvar</span>(<span class='no'>variable</span>, <span class='no'>dims</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>variable</th>
+              <td><p>CF variable name</p></td>
+            </tr>
+            <tr>
+              <th>dims</th>
+              <td>
+                <p>
+                  List of NetCDF dimension objects (passed to
+                  `ncdf4::ncvar_def(..., dim)`)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>`ncvar` object (from `ncvar_def`)</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/data.atmosphere/docs/reference/cos_solar_zenith_angle.html b/modules/data.atmosphere/docs/reference/cos_solar_zenith_angle.html
index 74a7990..b2f4318 100644
--- a/modules/data.atmosphere/docs/reference/cos_solar_zenith_angle.html
+++ b/modules/data.atmosphere/docs/reference/cos_solar_zenith_angle.html
@@ -2,190 +2,250 @@
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+      Cosine of solar zenith angle — cos_solar_zenith_angle •
+      PEcAn.data.atmosphere
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+
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+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Cosine of solar zenith angle</h1>
-    
-    <div class="hidden name"><code>cos_solar_zenith_angle.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>For explanations of formulae, see http://www.itacanet.org/the-sun-as-a-source-of-energy/part-3-calculating-solar-angles/</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>cos_solar_zenith_angle</span>(<span class='no'>doy</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>dt</span>, <span class='no'>hr</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>doy</th>
-      <td><p>Day of year</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>Latitude</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>Longitude</p></td>
-    </tr>
-    <tr>
-      <th>dt</th>
-      <td><p>Timestep</p></td>
-    </tr>
-    <tr>
-      <th>hr</th>
-      <td><p>Hours timestep</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`numeric(1)` of cosine of solar zenith angle</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Cosine of solar zenith angle</h1>
+
+            <div class="hidden name">
+              <code>cos_solar_zenith_angle.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              For explanations of formulae, see
+              http://www.itacanet.org/the-sun-as-a-source-of-energy/part-3-calculating-solar-angles/
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>cos_solar_zenith_angle</span>(<span class='no'>doy</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>dt</span>, <span class='no'>hr</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>doy</th>
+              <td><p>Day of year</p></td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>Latitude</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>Longitude</p></td>
+            </tr>
+            <tr>
+              <th>dt</th>
+              <td><p>Timestep</p></td>
+            </tr>
+            <tr>
+              <th>hr</th>
+              <td><p>Hours timestep</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>`numeric(1)` of cosine of solar zenith angle</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/data.atmosphere/docs/reference/daygroup.html b/modules/data.atmosphere/docs/reference/daygroup.html
index 2121ff5..bce5a40 100644
--- a/modules/data.atmosphere/docs/reference/daygroup.html
+++ b/modules/data.atmosphere/docs/reference/daygroup.html
@@ -2,154 +2,200 @@
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+
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+      crossorigin="anonymous"
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+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+
+    <!-- clipboard.js -->
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+                  >PEcAn.data.atmosphere</a
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+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
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+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Assign daygroup tag for a given date</h1>
-    
-    <div class="hidden name"><code>daygroup.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Assign daygroup tag for a given date</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Assign daygroup tag for a given date</h1>
 
-    <pre class="usage"><span class='fu'>daygroup</span>(<span class='no'>date</span>, <span class='no'>flx</span>)</pre>
-        
+            <div class="hidden name"><code>daygroup.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Assign daygroup tag for a given date</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>daygroup</span>(<span class='no'>date</span>, <span class='no'>flx</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
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+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/data.atmosphere/docs/reference/db.site.lat.lon.html b/modules/data.atmosphere/docs/reference/db.site.lat.lon.html
index 4e5e1f5..d31e047 100644
--- a/modules/data.atmosphere/docs/reference/db.site.lat.lon.html
+++ b/modules/data.atmosphere/docs/reference/db.site.lat.lon.html
@@ -2,158 +2,196 @@
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 <html>
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-  <meta charset="utf-8">
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
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+
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
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+                  title="Released package"
+                  >1.6.0</span
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>db.site.lat.lon</h1>
-    
-    <div class="hidden name"><code>db.site.lat.lon.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>db.site.lat.lon</h1>
 
-    <div class="ref-description">
-    
-    <p>db.site.lat.lon</p>
-    
-    </div>
+            <div class="hidden name"><code>db.site.lat.lon.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>db.site.lat.lon</span>(<span class='no'>site.id</span>, <span class='no'>con</span>)</pre>
-        
+          <div class="ref-description">
+            <p>db.site.lat.lon</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>db.site.lat.lon</span>(<span class='no'>site.id</span>, <span class='no'>con</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Betsy Cowdery
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>debias.met.regression</h1>
-    
-    <div class="hidden name"><code>debias.met.regression.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This script debiases one dataset (e.g. GCM, re-analysis product) given another higher 
-             resolution product or empirical observations. It assumes input are in annual CF standard 
-             files that are generate from the pecan extract or download funcitons.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>debias.met.regression</span>(<span class='no'>train.data</span>, <span class='no'>source.data</span>, <span class='no'>n.ens</span>, <span class='kw'>vars.debias</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>debias.met.regression</h1>
+
+            <div class="hidden name"><code>debias.met.regression.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This script debiases one dataset (e.g. GCM, re-analysis product)
+              given another higher resolution product or empirical observations.
+              It assumes input are in annual CF standard files that are generate
+              from the pecan extract or download funcitons.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>debias.met.regression</span>(<span class='no'>train.data</span>, <span class='no'>source.data</span>, <span class='no'>n.ens</span>, <span class='kw'>vars.debias</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>CRUNCEP</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>pair.anoms</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>pair.ens</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>uncert.prop</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>resids</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fu'>Sys.Date</span>(), <span class='no'>outfolder</span>,
   <span class='kw'>yrs.save</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>ens.name</span>, <span class='kw'>ens.mems</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>force.sanity</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>sanity.tries</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>, <span class='kw'>save.diagnostics</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>path.diagnostics</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>parallel</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>n.cores</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>train.data</th>
-      <td><p>- training data coming out of align.met</p></td>
-    </tr>
-    <tr>
-      <th>source.data</th>
-      <td><p>- data to be bias-corrected aligned with training data (from align.met)</p></td>
-    </tr>
-    <tr>
-      <th>n.ens</th>
-      <td><p>- number of ensemble members to generate and save for EACH source ensemble member</p></td>
-    </tr>
-    <tr>
-      <th>vars.debias</th>
-      <td><p>- which met variables should be debiased? if NULL, all variables in train.data</p></td>
-    </tr>
-    <tr>
-      <th>CRUNCEP</th>
-      <td><p>- flag for if the dataset being downscaled is CRUNCEP; if TRUE, special cases triggered for 
-met variables that have been naively gapfilled for certain time periods</p></td>
-    </tr>
-    <tr>
-      <th>pair.anoms</th>
-      <td><p>- logical stating whether anomalies from the same year should be matched or not</p></td>
-    </tr>
-    <tr>
-      <th>pair.ens</th>
-      <td><p>- logical stating whether ensembles from train and source data need to be paired together 
-(for uncertainty propogation)</p></td>
-    </tr>
-    <tr>
-      <th>uncert.prop</th>
-      <td><p>- method for error propogation if only 1 ensemble member; options=c(random, mean); *Not Implemented yet</p></td>
-    </tr>
-    <tr>
-      <th>resids</th>
-      <td><p>- logical stating whether to pass on residual data or not *Not implemented yet</p></td>
-    </tr>
-    <tr>
-      <th>seed</th>
-      <td><p>- specify seed so that random draws can be reproduced</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>- directory where the data should go</p></td>
-    </tr>
-    <tr>
-      <th>yrs.save</th>
-      <td><p>- what years from the source data should be saved; if NULL all years of the source data will be saved</p></td>
-    </tr>
-    <tr>
-      <th>ens.name</th>
-      <td><p>- what is the name that should be attached to the debiased ensemble</p></td>
-    </tr>
-    <tr>
-      <th>ens.mems</th>
-      <td><p>- what labels/numbers to attach to the ensemble members so we can gradually build bigger ensembles 
-without having to do do giant runs at once; if NULL will be numbered 1:n.ens</p></td>
-    </tr>
-    <tr>
-      <th>force.sanity</th>
-      <td><p>- (logical) do we force the data to meet sanity checks?</p></td>
-    </tr>
-    <tr>
-      <th>sanity.tries</th>
-      <td><p>- how many time should we try to predict a reasonable value before giving up?  We don't want to end up in an infinite loop</p></td>
-    </tr>
-    <tr>
-      <th>lat.in</th>
-      <td><p>- latitude of site</p></td>
-    </tr>
-    <tr>
-      <th>lon.in</th>
-      <td><p>- longitude of site</p></td>
-    </tr>
-    <tr>
-      <th>save.diagnostics</th>
-      <td><p>- logical; save diagnostic plots of output?</p></td>
-    </tr>
-    <tr>
-      <th>path.diagnostics</th>
-      <td><p>- path to where the diagnostic graphs should be saved</p></td>
-    </tr>
-    <tr>
-      <th>parallel</th>
-      <td><p>- (experimental) logical stating whether to run temporal_downscale_functions.R in parallel *Not Implemented yet</p></td>
-    </tr>
-    <tr>
-      <th>n.cores</th>
-      <td><p>- (experimental) how many cores to use in parallelization *Not implemented yet</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>- overwrite existing files? Currently ignored</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical: should <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package'>ncdf4</a></code>
-functions print debugging information as they run?</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Debias Meteorology using Multiple Linear Regression
-Statistically debias met datasets and generate ensembles based on the observed uncertainty</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p>Other debias - Debias &amp; Align Meteorology Datasets into continuous time series: <code><a href='align.met.html'>align.met</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>train.data</th>
+              <td><p>- training data coming out of align.met</p></td>
+            </tr>
+            <tr>
+              <th>source.data</th>
+              <td>
+                <p>
+                  - data to be bias-corrected aligned with training data (from
+                  align.met)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.ens</th>
+              <td>
+                <p>
+                  - number of ensemble members to generate and save for EACH
+                  source ensemble member
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>vars.debias</th>
+              <td>
+                <p>
+                  - which met variables should be debiased? if NULL, all
+                  variables in train.data
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>CRUNCEP</th>
+              <td>
+                <p>
+                  - flag for if the dataset being downscaled is CRUNCEP; if
+                  TRUE, special cases triggered for met variables that have been
+                  naively gapfilled for certain time periods
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pair.anoms</th>
+              <td>
+                <p>
+                  - logical stating whether anomalies from the same year should
+                  be matched or not
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pair.ens</th>
+              <td>
+                <p>
+                  - logical stating whether ensembles from train and source data
+                  need to be paired together (for uncertainty propogation)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>uncert.prop</th>
+              <td>
+                <p>
+                  - method for error propogation if only 1 ensemble member;
+                  options=c(random, mean); *Not Implemented yet
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>resids</th>
+              <td>
+                <p>
+                  - logical stating whether to pass on residual data or not *Not
+                  implemented yet
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>seed</th>
+              <td>
+                <p>- specify seed so that random draws can be reproduced</p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>- directory where the data should go</p></td>
+            </tr>
+            <tr>
+              <th>yrs.save</th>
+              <td>
+                <p>
+                  - what years from the source data should be saved; if NULL all
+                  years of the source data will be saved
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ens.name</th>
+              <td>
+                <p>
+                  - what is the name that should be attached to the debiased
+                  ensemble
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ens.mems</th>
+              <td>
+                <p>
+                  - what labels/numbers to attach to the ensemble members so we
+                  can gradually build bigger ensembles without having to do do
+                  giant runs at once; if NULL will be numbered 1:n.ens
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>force.sanity</th>
+              <td>
+                <p>- (logical) do we force the data to meet sanity checks?</p>
+              </td>
+            </tr>
+            <tr>
+              <th>sanity.tries</th>
+              <td>
+                <p>
+                  - how many time should we try to predict a reasonable value
+                  before giving up? We don't want to end up in an infinite loop
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lat.in</th>
+              <td><p>- latitude of site</p></td>
+            </tr>
+            <tr>
+              <th>lon.in</th>
+              <td><p>- longitude of site</p></td>
+            </tr>
+            <tr>
+              <th>save.diagnostics</th>
+              <td><p>- logical; save diagnostic plots of output?</p></td>
+            </tr>
+            <tr>
+              <th>path.diagnostics</th>
+              <td>
+                <p>- path to where the diagnostic graphs should be saved</p>
+              </td>
+            </tr>
+            <tr>
+              <th>parallel</th>
+              <td>
+                <p>
+                  - (experimental) logical stating whether to run
+                  temporal_downscale_functions.R in parallel *Not Implemented
+                  yet
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.cores</th>
+              <td>
+                <p>
+                  - (experimental) how many cores to use in parallelization *Not
+                  implemented yet
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>- overwrite existing files? Currently ignored</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical: should
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package"
+                      >ncdf4</a
+                    ></code
+                  >
+                  functions print debugging information as they run?
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Debias Meteorology using Multiple Linear Regression Statistically
+            debias met datasets and generate ensembles based on the observed
+            uncertainty
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other debias - Debias &amp; Align Meteorology Datasets into
+              continuous time series:
+              <code><a href="align.met.html">align.met</a></code>
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
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index 2a51303..21fa3bb 100644
--- a/modules/data.atmosphere/docs/reference/debias_met.html
+++ b/modules/data.atmosphere/docs/reference/debias_met.html
@@ -2,186 +2,266 @@
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+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>debias_met</h1>
-    
-    <div class="hidden name"><code>debias_met.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>debias_met</h1>
 
-    <div class="ref-description">
-    
-    <p>debias.met takes input_met and debiases it based on statistics from a train_met dataset</p>
-    
-    </div>
+            <div class="hidden name"><code>debias_met.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>debias.met</span>(<span class='no'>outfolder</span>, <span class='no'>input_met</span>, <span class='no'>train_met</span>, <span class='no'>site_id</span>,
-  <span class='kw'>de_method</span> <span class='kw'>=</span> <span class='st'>"linear"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>input_met</th>
-      <td><p>- the source_met dataset that will be altered by the training dataset in NC format.</p></td>
-    </tr>
-    <tr>
-      <th>train_met</th>
-      <td><p>- the observed dataset that will be used to train the modeled dataset in NC format</p></td>
-    </tr>
-    <tr>
-      <th>de_method</th>
-      <td><p>- select which debias method you would like to use, options are 'normal', 'linear regression'</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: replace output file if it already exists? Currently ignored.</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical: should <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package'>ncdf4</a></code>
-functions print debugging information as they run?</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-James Simkins
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              debias.met takes input_met and debiases it based on statistics
+              from a train_met dataset
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>debias.met</span>(<span class='no'>outfolder</span>, <span class='no'>input_met</span>, <span class='no'>train_met</span>, <span class='no'>site_id</span>,
+  <span class='kw'>de_method</span> <span class='kw'>=</span> <span class='st'>"linear"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>input_met</th>
+              <td>
+                <p>
+                  - the source_met dataset that will be altered by the training
+                  dataset in NC format.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>train_met</th>
+              <td>
+                <p>
+                  - the observed dataset that will be used to train the modeled
+                  dataset in NC format
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>de_method</th>
+              <td>
+                <p>
+                  - select which debias method you would like to use, options
+                  are 'normal', 'linear regression'
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>
+                  logical: replace output file if it already exists? Currently
+                  ignored.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical: should
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package"
+                      >ncdf4</a
+                    ></code
+                  >
+                  functions print debugging information as they run?
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          James Simkins
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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diff --git a/modules/data.atmosphere/docs/reference/download.Ameriflux.html b/modules/data.atmosphere/docs/reference/download.Ameriflux.html
index 0b5a26a..4ef8b1f 100644
--- a/modules/data.atmosphere/docs/reference/download.Ameriflux.html
+++ b/modules/data.atmosphere/docs/reference/download.Ameriflux.html
@@ -2,190 +2,259 @@
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 <html>
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
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+                        >UNKNOWN TITLE</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.Ameriflux</h1>
-    
-    <div class="hidden name"><code>download.Ameriflux.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.Ameriflux</h1>
 
-    <div class="ref-description">
-    
-    <p>Download Ameriflux L2 netCDF files</p>
-    
-    </div>
+            <div class="hidden name"><code>download.Ameriflux.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.Ameriflux</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sitename</th>
-      <td><p>the FLUXNET ID of the site to be downloaded, used as file name prefix. 
-The 'SITE_ID' field in <a href='http://ameriflux.lbl.gov/sites/site-list-and-pages/'>list of Ameriflux sites</a></p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Josh Mantooth, Rob Kooper, Ankur Desai
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Download Ameriflux L2 netCDF files</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>download.Ameriflux</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sitename</th>
+              <td>
+                <p>
+                  the FLUXNET ID of the site to be downloaded, used as file name
+                  prefix. The 'SITE_ID' field in
+                  <a href="http://ameriflux.lbl.gov/sites/site-list-and-pages/"
+                    >list of Ameriflux sites</a
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Josh Mantooth, Rob Kooper, Ankur Desai
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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 </html>
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diff --git a/modules/data.atmosphere/docs/reference/download.AmerifluxLBL.html b/modules/data.atmosphere/docs/reference/download.AmerifluxLBL.html
index f00141a..8b86ada 100644
--- a/modules/data.atmosphere/docs/reference/download.AmerifluxLBL.html
+++ b/modules/data.atmosphere/docs/reference/download.AmerifluxLBL.html
@@ -2,213 +2,294 @@
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+      Download Ameriflux LBL CSV files — download.AmerifluxLBL •
+      PEcAn.data.atmosphere
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+    />
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+    <meta name="twitter:card" content="summary" />
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+                type="button"
+                class="navbar-toggle collapsed"
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+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download Ameriflux LBL CSV files</h1>
-    
-    <div class="hidden name"><code>download.AmerifluxLBL.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download Ameriflux LBL CSV files</h1>
 
-    <div class="ref-description">
-    
-    <p>download.AmerifluxLBL</p>
-    
-    </div>
+            <div class="hidden name"><code>download.AmerifluxLBL.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>download.AmerifluxLBL</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.AmerifluxLBL</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>download.AmerifluxLBL</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>username</span> <span class='kw'>=</span> <span class='st'>"pecan"</span>, <span class='no'>method</span>,
   <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sitename</th>
-      <td><p>the Ameriflux ID of the site to be downloaded, used as file name prefix. 
-The 'SITE_ID' field in <a href='http://ameriflux.lbl.gov/sites/site-list-and-pages/'>list of Ameriflux sites</a></p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    <tr>
-      <th>username</th>
-      <td><p>Ameriflux username</p></td>
-    </tr>
-    <tr>
-      <th>method</th>
-      <td><p>Optional. download.file() function option.  Use this to set custom programs such as ncftp</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Uses Ameirflux LBL JSON API to download met data from Ameriflux towers in CSV format</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sitename</th>
+              <td>
+                <p>
+                  the Ameriflux ID of the site to be downloaded, used as file
+                  name prefix. The 'SITE_ID' field in
+                  <a href="http://ameriflux.lbl.gov/sites/site-list-and-pages/"
+                    >list of Ameriflux sites</a
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+            <tr>
+              <th>username</th>
+              <td><p>Ameriflux username</p></td>
+            </tr>
+            <tr>
+              <th>method</th>
+              <td>
+                <p>
+                  Optional. download.file() function option. Use this to set
+                  custom programs such as ncftp
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Uses Ameirflux LBL JSON API to download met data from Ameriflux
+            towers in CSV format
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>result</span> <span class='kw'>&lt;-</span> <span class='fu'>download.AmerifluxLBL</span>(<span class='st'>"US-Akn"</span>,<span class='st'>"~/"</span>,<span class='st'>"2011-01-01"</span>,<span class='st'>"2011-12-31"</span>,<span class='kw'>overwrite</span><span class='kw'>=</span><span class='fl'>TRUE</span>)
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Ankur Desai, based on download.Ameriflux.R by Josh Mantooth, Rob Kooper, Shawn Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Ankur Desai, based on download.Ameriflux.R by Josh Mantooth, Rob
+          Kooper, Shawn Serbin
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.CRUNCEP.html b/modules/data.atmosphere/docs/reference/download.CRUNCEP.html
index 3a40791..3bb3e70 100644
--- a/modules/data.atmosphere/docs/reference/download.CRUNCEP.html
+++ b/modules/data.atmosphere/docs/reference/download.CRUNCEP.html
@@ -2,208 +2,299 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
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-
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-<meta property="og:title" content="Download CRUNCEP data — download.CRUNCEP" />
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Download CRUNCEP data — download.CRUNCEP • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Download CRUNCEP data — download.CRUNCEP"
+    />
+
+    <meta
+      property="og:description"
+      content="Download and convert to CF CRUNCEP single grid point from MSTIMIP server using OPENDAP interface"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
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-    <span class="fa fa-home fa-lg"></span>
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-<li>
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-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download CRUNCEP data</h1>
-    
-    <div class="hidden name"><code>download.CRUNCEP.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download CRUNCEP data</h1>
 
-    <div class="ref-description">
-    
-    <p>Download and convert to CF CRUNCEP single grid point from MSTIMIP server using OPENDAP interface</p>
-    
-    </div>
+            <div class="hidden name"><code>download.CRUNCEP.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Download and convert to CF CRUNCEP single grid point from MSTIMIP
+              server using OPENDAP interface
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.CRUNCEP</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>download.CRUNCEP</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>maxErrors</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>sleep</span> <span class='kw'>=</span> <span class='fl'>2</span>,
   <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>Directory where results should be written</p></td>
-    </tr>
-    <tr>
-      <th>start_date, end_date</th>
-      <td><p>Range of years to retrieve. Format is YYYY-MM-DD,
-but only the year portion is used and the resulting files always contain a full year of data.</p></td>
-    </tr>
-    <tr>
-      <th>site_id</th>
-      <td><p>numeric. Currently ignored</p></td>
-    </tr>
-    <tr>
-      <th>lat.in</th>
-      <td><p>site latitude in decimal degrees</p></td>
-    </tr>
-    <tr>
-      <th>lon.in</th>
-      <td><p>site longitude in decimal degrees</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical. Download a fresh version even if a local file with the same name already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical. Passed on to <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncvar_def'>ncvar_def</a></code> and <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/nc_create'>nc_create</a></code>
-to control printing of debug info</p></td>
-    </tr>
-    <tr>
-      <th>maxErrors</th>
-      <td><p>Maximum times to re-try folloing an error accessing netCDF data through THREDDS</p></td>
-    </tr>
-    <tr>
-      <th>sleep</th>
-      <td><p>Wait time between attempts following a THREDDS or other error</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Other arguments, currently ignored</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-James Simkins, Mike Dietze
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>Directory where results should be written</p></td>
+            </tr>
+            <tr>
+              <th>start_date, end_date</th>
+              <td>
+                <p>
+                  Range of years to retrieve. Format is YYYY-MM-DD, but only the
+                  year portion is used and the resulting files always contain a
+                  full year of data.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>site_id</th>
+              <td><p>numeric. Currently ignored</p></td>
+            </tr>
+            <tr>
+              <th>lat.in</th>
+              <td><p>site latitude in decimal degrees</p></td>
+            </tr>
+            <tr>
+              <th>lon.in</th>
+              <td><p>site longitude in decimal degrees</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>
+                  logical. Download a fresh version even if a local file with
+                  the same name already exists?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical. Passed on to
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncvar_def"
+                      >ncvar_def</a
+                    ></code
+                  >
+                  and
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/nc_create"
+                      >nc_create</a
+                    ></code
+                  >
+                  to control printing of debug info
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>maxErrors</th>
+              <td>
+                <p>
+                  Maximum times to re-try folloing an error accessing netCDF
+                  data through THREDDS
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sleep</th>
+              <td>
+                <p>
+                  Wait time between attempts following a THREDDS or other error
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>Other arguments, currently ignored</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          James Simkins, Mike Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.FACE.html b/modules/data.atmosphere/docs/reference/download.FACE.html
index 58c8b7e..bde8cb8 100644
--- a/modules/data.atmosphere/docs/reference/download.FACE.html
+++ b/modules/data.atmosphere/docs/reference/download.FACE.html
@@ -2,170 +2,222 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>download.FACE — download.FACE • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="download.FACE — download.FACE" />
-
-<meta property="og:description" content="Download Raw FACE data from the internet" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>download.FACE — download.FACE • PEcAn.data.atmosphere</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="download.FACE — download.FACE" />
+
+    <meta
+      property="og:description"
+      content="Download Raw FACE data from the internet"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
-    </li>
-    <li>
-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="../articles/compare_narr_cruncep_met.html">UNKNOWN TITLE</a>
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-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.FACE</h1>
-    
-    <div class="hidden name"><code>download.FACE.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.FACE</h1>
 
-    <div class="ref-description">
-    
-    <p>Download Raw FACE data from the internet</p>
-    
-    </div>
+            <div class="hidden name"><code>download.FACE.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.FACE</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>method</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>method</th>
-      <td><p>Optional. Passed to download.file() function.  Use this to set custom programs such as ncftp to use when
-downloading files from FTP sites</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Download Raw FACE data from the internet</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>download.FACE</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>method</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>method</th>
+              <td>
+                <p>
+                  Optional. Passed to download.file() function. Use this to set
+                  custom programs such as ncftp to use when downloading files
+                  from FTP sites
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.Fluxnet2015.html b/modules/data.atmosphere/docs/reference/download.Fluxnet2015.html
index e6eb717..3868699 100644
--- a/modules/data.atmosphere/docs/reference/download.Fluxnet2015.html
+++ b/modules/data.atmosphere/docs/reference/download.Fluxnet2015.html
@@ -2,190 +2,258 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>download.Fluxnet2015 — download.Fluxnet2015 • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="download.Fluxnet2015 — download.Fluxnet2015" />
-
-<meta property="og:description" content="Download Fluxnet 2015 CSV files" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
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+    <meta property="og:description" content="Download Fluxnet 2015 CSV files" />
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+                  title="Released package"
+                  >1.6.0</span
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+                    role="button"
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+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
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+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.Fluxnet2015</h1>
-    
-    <div class="hidden name"><code>download.Fluxnet2015.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.Fluxnet2015</h1>
 
-    <div class="ref-description">
-    
-    <p>Download Fluxnet 2015 CSV files</p>
-    
-    </div>
+            <div class="hidden name"><code>download.Fluxnet2015.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.Fluxnet2015</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>username</span> <span class='kw'>=</span> <span class='st'>"pecan"</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sitename</th>
-      <td><p>the FLUXNET ID of the site to be downloaded, used as file name prefix. 
-The 'SITE_ID' field in <a href='http://fluxnet.fluxdata.org//sites/site-list-and-pages/'>list of Ameriflux sites</a></p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Ankur Desai, based on download.Ameriflux.R by Josh Mantooth, Rob Kooper
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Download Fluxnet 2015 CSV files</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>download.Fluxnet2015</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>username</span> <span class='kw'>=</span> <span class='st'>"pecan"</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sitename</th>
+              <td>
+                <p>
+                  the FLUXNET ID of the site to be downloaded, used as file name
+                  prefix. The 'SITE_ID' field in
+                  <a
+                    href="http://fluxnet.fluxdata.org//sites/site-list-and-pages/"
+                    >list of Ameriflux sites</a
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Ankur Desai, based on download.Ameriflux.R by Josh Mantooth, Rob
+          Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.FluxnetLaThuile.html b/modules/data.atmosphere/docs/reference/download.FluxnetLaThuile.html
index cc087c7..436dd60 100644
--- a/modules/data.atmosphere/docs/reference/download.FluxnetLaThuile.html
+++ b/modules/data.atmosphere/docs/reference/download.FluxnetLaThuile.html
@@ -2,194 +2,272 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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+      download.FluxnetLaThuile — download.FluxnetLaThuile •
+      PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      content="download.FluxnetLaThuile — download.FluxnetLaThuile"
+    />
+
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+      property="og:description"
+      content="Download Flxunet LaThuile CSV files"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.FluxnetLaThuile</h1>
-    
-    <div class="hidden name"><code>download.FluxnetLaThuile.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.FluxnetLaThuile</h1>
 
-    <div class="ref-description">
-    
-    <p>Download Flxunet LaThuile CSV files</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>download.FluxnetLaThuile.Rd</code>
+            </div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.FluxnetLaThuile</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>username</span> <span class='kw'>=</span> <span class='st'>"pecan"</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sitename</th>
-      <td><p>the FLUXNET ID of the site to be downloaded, used as file name prefix.
-The 'SITE_ID' field in <a href='http://www.fluxdata.org/DataInfo/Dataset%20Doc%20Lib/SynthDataSummary.aspx'>list of Fluxnet LaThuile sites</a></p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    <tr>
-      <th>username</th>
-      <td><p>should be the registered Fluxnet username, else defaults to pecan</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Ankur Desai
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Download Flxunet LaThuile CSV files</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>download.FluxnetLaThuile</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>username</span> <span class='kw'>=</span> <span class='st'>"pecan"</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sitename</th>
+              <td>
+                <p>
+                  the FLUXNET ID of the site to be downloaded, used as file name
+                  prefix. The 'SITE_ID' field in
+                  <a
+                    href="http://www.fluxdata.org/DataInfo/Dataset%20Doc%20Lib/SynthDataSummary.aspx"
+                    >list of Fluxnet LaThuile sites</a
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+            <tr>
+              <th>username</th>
+              <td>
+                <p>
+                  should be the registered Fluxnet username, else defaults to
+                  pecan
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Ankur Desai
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.GFDL.html b/modules/data.atmosphere/docs/reference/download.GFDL.html
index c07b923..6e598b3 100644
--- a/modules/data.atmosphere/docs/reference/download.GFDL.html
+++ b/modules/data.atmosphere/docs/reference/download.GFDL.html
@@ -2,208 +2,307 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
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-<script src="../pkgdown.js"></script>
-
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-
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-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and
+      convert to CF — download.GFDL • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CF — download.GFDL"
+    />
+
+    <meta
+      property="og:description"
+      content="Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CF"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
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-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
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-  </a>
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-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CF</h1>
-    
-    <div class="hidden name"><code>download.GFDL.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CF</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>download.GFDL</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Download GFDL CMIP5 outputs for a single grid point using OPeNDAP
+              and convert to CF
+            </h1>
+
+            <div class="hidden name"><code>download.GFDL.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Download GFDL CMIP5 outputs for a single grid point using OPeNDAP
+              and convert to CF
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>download.GFDL</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"CM3"</span>,
   <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='st'>"rcp45"</span>, <span class='kw'>ensemble_member</span> <span class='kw'>=</span> <span class='st'>"r1i1p1"</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>Directory for storing output</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start date for met (will be converted via [base::as.POSIXlt])</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End date for met (will be converted via [base::as.POSIXlt])</p></td>
-    </tr>
-    <tr>
-      <th>lat.in</th>
-      <td><p>Latitude coordinate for met</p></td>
-    </tr>
-    <tr>
-      <th>lon.in</th>
-      <td><p>Longitude coordinate for met</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>Logical: Download a fresh version even if a local file with
-the same name already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>Logical, passed on to <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncvar_def'>ncvar_def</a></code> and
-<code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/nc_create'>nc_create</a></code> to control printing of debug info</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>Which GFDL model to run (options are CM3, ESM2M, ESM2G)</p></td>
-    </tr>
-    <tr>
-      <th>scenario</th>
-      <td><p>Which scenario to run (options are rcp26, rcp45, rcp60, rcp85)</p></td>
-    </tr>
-    <tr>
-      <th>ensemble_member</th>
-      <td><p>Which ensemble_member to initialize the run (options are r1i1p1, r3i1p1, r5i1p1)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-James Simkins, Alexey Shiklomanov, Ankur Desai
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>Directory for storing output</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  Start date for met (will be converted via [base::as.POSIXlt])
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  End date for met (will be converted via [base::as.POSIXlt])
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lat.in</th>
+              <td><p>Latitude coordinate for met</p></td>
+            </tr>
+            <tr>
+              <th>lon.in</th>
+              <td><p>Longitude coordinate for met</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>
+                  Logical: Download a fresh version even if a local file with
+                  the same name already exists?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  Logical, passed on to
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncvar_def"
+                      >ncvar_def</a
+                    ></code
+                  >
+                  and
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/nc_create"
+                      >nc_create</a
+                    ></code
+                  >
+                  to control printing of debug info
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td>
+                <p>Which GFDL model to run (options are CM3, ESM2M, ESM2G)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>scenario</th>
+              <td>
+                <p>
+                  Which scenario to run (options are rcp26, rcp45, rcp60, rcp85)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ensemble_member</th>
+              <td>
+                <p>
+                  Which ensemble_member to initialize the run (options are
+                  r1i1p1, r3i1p1, r5i1p1)
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          James Simkins, Alexey Shiklomanov, Ankur Desai
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.GLDAS.html b/modules/data.atmosphere/docs/reference/download.GLDAS.html
index b127e75..3235f40 100644
--- a/modules/data.atmosphere/docs/reference/download.GLDAS.html
+++ b/modules/data.atmosphere/docs/reference/download.GLDAS.html
@@ -2,169 +2,219 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Download GLDAS data — download.GLDAS • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-
-<meta property="og:title" content="Download GLDAS data — download.GLDAS" />
-
-<meta property="og:description" content="Download and convert single grid point GLDAS to CF single grid point from hydro1.sci.gsfc.nasa.gov using OPENDAP interface" />
-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Download GLDAS data — download.GLDAS • PEcAn.data.atmosphere</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Download GLDAS data — download.GLDAS" />
+
+    <meta
+      property="og:description"
+      content="Download and convert single grid point GLDAS to CF single grid point from hydro1.sci.gsfc.nasa.gov using OPENDAP interface"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
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-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
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-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
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+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              >
+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
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+
+            <div id="navbar" class="navbar-collapse collapse">
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download GLDAS data</h1>
-    
-    <div class="hidden name"><code>download.GLDAS.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download GLDAS data</h1>
 
-    <div class="ref-description">
-    
-    <p>Download and convert single grid point GLDAS to CF single grid point from hydro1.sci.gsfc.nasa.gov using OPENDAP interface</p>
-    
-    </div>
+            <div class="hidden name"><code>download.GLDAS.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.GLDAS</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>lon.in</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Christy Rollinson
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Download and convert single grid point GLDAS to CF single grid
+              point from hydro1.sci.gsfc.nasa.gov using OPENDAP interface
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>download.GLDAS</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>lon.in</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Christy Rollinson
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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+    </div>
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 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.Geostreams.html b/modules/data.atmosphere/docs/reference/download.Geostreams.html
index 6a4096c..7029541 100644
--- a/modules/data.atmosphere/docs/reference/download.Geostreams.html
+++ b/modules/data.atmosphere/docs/reference/download.Geostreams.html
@@ -2,173 +2,245 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+      Download Geostreams data from Clowder API — download.Geostreams •
+      PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
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+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Download Geostreams data from Clowder API — download.Geostreams"
+    />
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+      property="og:description"
+      content="Download Geostreams data from Clowder API"
+    />
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+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download Geostreams data from Clowder API</h1>
-    
-    <div class="hidden name"><code>download.Geostreams.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download Geostreams data from Clowder API</h1>
 
-    <div class="ref-description">
-    
-    <p>Download Geostreams data from Clowder API</p>
-    
-    </div>
+            <div class="hidden name"><code>download.Geostreams.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Download Geostreams data from Clowder API</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.Geostreams</span>(<span class='no'>outfolder</span>, <span class='no'>sitename</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>download.Geostreams</span>(<span class='no'>outfolder</span>, <span class='no'>sitename</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>url</span> <span class='kw'>=</span> <span class='st'>"https://terraref.ncsa.illinois.edu/clowder/api/geostreams"</span>,
   <span class='kw'>key</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>user</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>pass</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>directory in which to save json result. Will be created if necessary</p></td>
-    </tr>
-    <tr>
-      <th>sitename</th>
-      <td><p>character. Must match a Geostreams sensor_name</p></td>
-    </tr>
-    <tr>
-      <th>start_date, end_date</th>
-      <td><p>datetime</p></td>
-    </tr>
-    <tr>
-      <th>url</th>
-      <td><p>base url for Clowder host</p></td>
-    </tr>
-    <tr>
-      <th>key, user, pass</th>
-      <td><p>authentication info for Clowder host.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>other arguments passed as query parameters</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Depending on the setup of your Clowder host, authentication may be by
-  username/password, by API key, or skipped entirely. <code>download.Geostreams</code>
-  looks first in its call arguments for an API key, then a username and password,
-  then if these are NULL it looks in the user's home directory for a file named
-  `~/.pecan.clowder.xml`, and finally if no keys or passwords are found there it
-  attempts to connect unauthenticated.</p>
-<p>If using `~/.pecan.clowder.xml`, it must be a valid PEcAn-formatted XML settings
- file and must contain a <code>&lt;clowder&gt;</code> key that specifies hostname, user, and
- password for your Clowder server:</p>
-<pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td>
+                <p>
+                  directory in which to save json result. Will be created if
+                  necessary
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sitename</th>
+              <td><p>character. Must match a Geostreams sensor_name</p></td>
+            </tr>
+            <tr>
+              <th>start_date, end_date</th>
+              <td><p>datetime</p></td>
+            </tr>
+            <tr>
+              <th>url</th>
+              <td><p>base url for Clowder host</p></td>
+            </tr>
+            <tr>
+              <th>key, user, pass</th>
+              <td><p>authentication info for Clowder host.</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>other arguments passed as query parameters</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Depending on the setup of your Clowder host, authentication may be
+            by username/password, by API key, or skipped entirely.
+            <code>download.Geostreams</code> looks first in its call arguments
+            for an API key, then a username and password, then if these are NULL
+            it looks in the user's home directory for a file named
+            `~/.pecan.clowder.xml`, and finally if no keys or passwords are
+            found there it attempts to connect unauthenticated.
+          </p>
+          <p>
+            If using `~/.pecan.clowder.xml`, it must be a valid PEcAn-formatted
+            XML settings file and must contain a
+            <code>&lt;clowder&gt;</code> key that specifies hostname, user, and
+            password for your Clowder server:
+          </p>
+          <pre>
   &lt;?xml version="1.0"?&gt;
   &lt;pecan&gt;
     &lt;clowder&gt;
@@ -177,48 +249,46 @@ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details
       &lt;password&gt;superSecretPassw0rd&lt;/password&gt;
     &lt;/clowder&gt;
   &lt;/pecan&gt;
-</pre>
-    
+</pre
+          >
 
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
  <span class='fu'>download.Geostreams</span>(<span class='kw'>outfolder</span> <span class='kw'>=</span> <span class='st'>"~/output/dbfiles/Clowder_EF"</span>,
                      <span class='kw'>sitename</span> <span class='kw'>=</span> <span class='st'>"UIUC Energy Farm - CEN"</span>,
                      <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='st'>"2016-01-01"</span>, <span class='kw'>end_date</span><span class='kw'>=</span><span class='st'>"2016-12-31"</span>,
                      <span class='kw'>key</span><span class='kw'>=</span><span class='st'>"verysecret"</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Harsh Agrawal, Chris Black
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Harsh Agrawal, Chris Black
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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+
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-
diff --git a/modules/data.atmosphere/docs/reference/download.MACA.html b/modules/data.atmosphere/docs/reference/download.MACA.html
index abb0543..87e679e 100644
--- a/modules/data.atmosphere/docs/reference/download.MACA.html
+++ b/modules/data.atmosphere/docs/reference/download.MACA.html
@@ -2,187 +2,252 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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-
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-
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="download.MACA — download.MACA" />
+
+    <meta
+      property="og:description"
+      content="Download MACA CMIP5 outputs for a single grid point using OPeNDAP and convert to CF"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
-    </li>
-    <li>
-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="../articles/compare_narr_cruncep_met.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="../articles/tdm_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.MACA</h1>
-    
-    <div class="hidden name"><code>download.MACA.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.MACA</h1>
 
-    <div class="ref-description">
-    
-    <p>Download MACA CMIP5 outputs for a single grid point using OPeNDAP and convert to CF</p>
-    
-    </div>
+            <div class="hidden name"><code>download.MACA.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Download MACA CMIP5 outputs for a single grid point using OPeNDAP
+              and convert to CF
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.MACA</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>download.MACA</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
   <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"IPSL-CM5A-LR"</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='st'>"rcp85"</span>,
   <span class='kw'>ensemble_member</span> <span class='kw'>=</span> <span class='st'>"r1i1p1"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>start_date</th>
-      <td><p>, of the format "YEAR-01-01 00:00:00"</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>, of the format "YEAR-12-31 23:59:59"</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>, select which MACA model to run (options are BNU-ESM, CNRM-CM5, CSIRO-Mk3-6-0, bcc-csm1-1, bcc-csm1-1-m, CanESM2, GFDL-ESM2M, GFDL-ESM2G, HadGEM2-CC365, HadGEM2-ES365, inmcm4, MIROC5, MIROC-ESM, MIROC-ESM-CHEM, MRI-CGCM3, CCSM4, IPSL-CM5A-LR, IPSL-CM5A-MR, IPSL-CM5B-LR, NorESM1-M)</p></td>
-    </tr>
-    <tr>
-      <th>scenario</th>
-      <td><p>, select which scenario to run (options are rcp45, rcp85)</p></td>
-    </tr>
-    <tr>
-      <th>ensemble_member</th>
-      <td><p>, r1i1p1 is the only ensemble member available for this dataset, CCSM4 uses r6i1p1 instead</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-James Simkins
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>start_date</th>
+              <td><p>, of the format "YEAR-01-01 00:00:00"</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>, of the format "YEAR-12-31 23:59:59"</p></td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td>
+                <p>
+                  , select which MACA model to run (options are BNU-ESM,
+                  CNRM-CM5, CSIRO-Mk3-6-0, bcc-csm1-1, bcc-csm1-1-m, CanESM2,
+                  GFDL-ESM2M, GFDL-ESM2G, HadGEM2-CC365, HadGEM2-ES365, inmcm4,
+                  MIROC5, MIROC-ESM, MIROC-ESM-CHEM, MRI-CGCM3, CCSM4,
+                  IPSL-CM5A-LR, IPSL-CM5A-MR, IPSL-CM5B-LR, NorESM1-M)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>scenario</th>
+              <td>
+                <p>, select which scenario to run (options are rcp45, rcp85)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>ensemble_member</th>
+              <td>
+                <p>
+                  , r1i1p1 is the only ensemble member available for this
+                  dataset, CCSM4 uses r6i1p1 instead
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          James Simkins
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.MsTMIP_NARR.html b/modules/data.atmosphere/docs/reference/download.MsTMIP_NARR.html
index 2fd362d..307d6f0 100644
--- a/modules/data.atmosphere/docs/reference/download.MsTMIP_NARR.html
+++ b/modules/data.atmosphere/docs/reference/download.MsTMIP_NARR.html
@@ -2,181 +2,236 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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+      download.MsTMIP_NARR — download.MsTMIP_NARR • PEcAn.data.atmosphere
+    </title>
+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="download.MsTMIP_NARR — download.MsTMIP_NARR"
+    />
+
+    <meta
+      property="og:description"
+      content="Download and conver to CF NARR single grid point from MSTIMIP server using OPENDAP interface"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
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+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.MsTMIP_NARR</h1>
-    
-    <div class="hidden name"><code>download.MsTMIP_NARR.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.MsTMIP_NARR</h1>
 
-    <div class="ref-description">
-    
-    <p>Download and conver to CF NARR single grid point from MSTIMIP server using OPENDAP interface</p>
-    
-    </div>
+            <div class="hidden name"><code>download.MsTMIP_NARR.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.MsTMIP_NARR</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>,
-  <span class='no'>lon.in</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>start_date</th>
-      <td><p>YYYY-MM-DD</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>YYYY-MM-DD</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>decimal degrees [-90, 90]</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>decimal degrees [-180, 180]</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-James Simkins
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Download and conver to CF NARR single grid point from MSTIMIP
+              server using OPENDAP interface
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>download.MsTMIP_NARR</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>,
+  <span class='no'>lon.in</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>start_date</th>
+              <td><p>YYYY-MM-DD</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>YYYY-MM-DD</p></td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>decimal degrees [-90, 90]</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>decimal degrees [-180, 180]</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          James Simkins
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.NARR.html b/modules/data.atmosphere/docs/reference/download.NARR.html
index 98b5645..dc3d71c 100644
--- a/modules/data.atmosphere/docs/reference/download.NARR.html
+++ b/modules/data.atmosphere/docs/reference/download.NARR.html
@@ -2,186 +2,238 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Download NARR files — download.NARR • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Download NARR files — download.NARR" />
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+    <meta property="og:description" content="Download NARR files" />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
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-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download NARR files</h1>
-    
-    <div class="hidden name"><code>download.NARR.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download NARR files</h1>
 
-    <div class="ref-description">
-    
-    <p>Download NARR files</p>
-    
-    </div>
+            <div class="hidden name"><code>download.NARR.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.NARR</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+          <div class="ref-description">
+            <p>Download NARR files</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>download.NARR</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>method</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>overwrite</th>
-      <td><p>Overwrite existing files?  Default=FALSE</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>Turn on verbose output? Default=FALSE</p></td>
-    </tr>
-    <tr>
-      <th>method</th>
-      <td><p>Method of file retrieval. Can set this using the options(download.ftp.method=[method]) in your Rprofile.
-example options(download.ftp.method="ncftpget")</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>overwrite</th>
+              <td><p>Overwrite existing files? Default=FALSE</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>Turn on verbose output? Default=FALSE</p></td>
+            </tr>
+            <tr>
+              <th>method</th>
+              <td>
+                <p>
+                  Method of file retrieval. Can set this using the
+                  options(download.ftp.method=[method]) in your Rprofile.
+                  example options(download.ftp.method="ncftpget")
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>download.NARR</span>(<span class='st'>"~/"</span>,<span class='st'>'2000/01/01'</span>,<span class='st'>'2000/01/02'</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery, Shawn Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Betsy Cowdery, Shawn Serbin
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.NARR_site.html b/modules/data.atmosphere/docs/reference/download.NARR_site.html
index b6de0a2..5b28152 100644
--- a/modules/data.atmosphere/docs/reference/download.NARR_site.html
+++ b/modules/data.atmosphere/docs/reference/download.NARR_site.html
@@ -2,178 +2,242 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Download NARR time series for a single site — download.NARR_site • PEcAn.data.atmosphere</title>
-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Download NARR time series for a single site — download.NARR_site •
+      PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Download NARR time series for a single site — download.NARR_site"
+    />
+
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+      property="og:description"
+      content="Download NARR time series for a single site"
+    />
+    <meta name="twitter:card" content="summary" />
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+                type="button"
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
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+              <ul class="nav navbar-nav">
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+                    aria-expanded="false"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download NARR time series for a single site</h1>
-    
-    <div class="hidden name"><code>download.NARR_site.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download NARR time series for a single site</h1>
 
-    <div class="ref-description">
-    
-    <p>Download NARR time series for a single site</p>
-    
-    </div>
+            <div class="hidden name"><code>download.NARR_site.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.NARR_site</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
+          <div class="ref-description">
+            <p>Download NARR time series for a single site</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>download.NARR_site</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>parallel</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>ncores</span> <span class='kw'>=</span> <span class='kw'>if</span> (<span class='no'>parallel</span>) <span class='kw pkg'>parallel</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/parallel/topics/detectCores'>detectCores</a></span>() <span class='kw'>else</span>
   <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>Target directory for storing output</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start date for met data</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End date for met data</p></td>
-    </tr>
-    <tr>
-      <th>lat.in</th>
-      <td><p>Site latitude coordinate</p></td>
-    </tr>
-    <tr>
-      <th>lon.in</th>
-      <td><p>Site longitude coordinate</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>Overwrite existing files?  Default=FALSE</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>Turn on verbose output? Default=FALSE</p></td>
-    </tr>
-    <tr>
-      <th>parallel</th>
-      <td><p>Download in parallel? Default = TRUE</p></td>
-    </tr>
-    <tr>
-      <th>ncores</th>
-      <td><p>Number of cores for parallel download. Default is 
-`parallel::detectCores()`</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"># NOT RUN {
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>Target directory for storing output</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start date for met data</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End date for met data</p></td>
+            </tr>
+            <tr>
+              <th>lat.in</th>
+              <td><p>Site latitude coordinate</p></td>
+            </tr>
+            <tr>
+              <th>lon.in</th>
+              <td><p>Site longitude coordinate</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>Overwrite existing files? Default=FALSE</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>Turn on verbose output? Default=FALSE</p></td>
+            </tr>
+            <tr>
+              <th>parallel</th>
+              <td><p>Download in parallel? Default = TRUE</p></td>
+            </tr>
+            <tr>
+              <th>ncores</th>
+              <td>
+                <p>
+                  Number of cores for parallel download. Default is
+                  `parallel::detectCores()`
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"># NOT RUN {
 # }
 <span class='co'># NOT RUN {</span>
 <span class='fu'>download.NARR_site</span>(<span class='fu'>tempdir</span>(), <span class='st'>"2001-01-01"</span>, <span class='st'>"2001-01-12"</span>, <span class='fl'>43.372</span>, -<span class='fl'>89.907</span>)
@@ -181,36 +245,32 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Alexey Shiklomanov
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-
diff --git a/modules/data.atmosphere/docs/reference/download.NEONmet.html b/modules/data.atmosphere/docs/reference/download.NEONmet.html
index dd8b408..4c79355 100644
--- a/modules/data.atmosphere/docs/reference/download.NEONmet.html
+++ b/modules/data.atmosphere/docs/reference/download.NEONmet.html
@@ -2,198 +2,274 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
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+      PEcAn.data.atmosphere
+    </title>
+
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+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      content="Download NEON Site Met CSV files — download.NEONmet"
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download NEON Site Met CSV files</h1>
-    
-    <div class="hidden name"><code>download.NEONmet.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download NEON Site Met CSV files</h1>
 
-    <div class="ref-description">
-    
-    <p>download.NEONmet</p>
-    
-    </div>
+            <div class="hidden name"><code>download.NEONmet.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>download.NEONmet</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.NEONmet</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>download.NEONmet</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sitename</th>
-      <td><p>the NEON ID of the site to be downloaded, used as file name prefix. 
-The 4-letter SITE code  in <a href='http://www.neonscience.org/science-design/field-sites/list'>list of NEON sites</a></p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year and month of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded. Format is YYYY-MM-DD (will only use the year and month part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>makes the function output more text</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Uses NEON v0 API to download met data from NEON towers and convert to CF NetCDF</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sitename</th>
+              <td>
+                <p>
+                  the NEON ID of the site to be downloaded, used as file name
+                  prefix. The 4-letter SITE code in
+                  <a
+                    href="http://www.neonscience.org/science-design/field-sites/list"
+                    >list of NEON sites</a
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year and month of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded. Format is
+                  YYYY-MM-DD (will only use the year and month part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>makes the function output more text</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Uses NEON v0 API to download met data from NEON towers and convert
+            to CF NetCDF
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>result</span> <span class='kw'>&lt;-</span> <span class='fu'>download.NEONmet</span>(<span class='st'>'HARV'</span>,<span class='st'>'~/'</span>,<span class='st'>'2017-01-01'</span>,<span class='st'>'2017-01-31'</span>,<span class='kw'>overwrite</span><span class='kw'>=</span><span class='fl'>TRUE</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.NLDAS.html b/modules/data.atmosphere/docs/reference/download.NLDAS.html
index 3fff950..101c52e 100644
--- a/modules/data.atmosphere/docs/reference/download.NLDAS.html
+++ b/modules/data.atmosphere/docs/reference/download.NLDAS.html
@@ -2,159 +2,208 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-
-<meta property="og:title" content="Download NLDAS met data — download.NLDAS" />
-
-<meta property="og:description" content="Download and convert single grid point NLDAS to CF single grid point from hydro1.sci.gsfc.nasa.gov using OPENDAP interface" />
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Download NLDAS met data — download.NLDAS • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Download NLDAS met data — download.NLDAS"
+    />
+
+    <meta
+      property="og:description"
+      content="Download and convert single grid point NLDAS to CF single grid point from hydro1.sci.gsfc.nasa.gov using OPENDAP interface"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
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+                  class="label label-default"
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download NLDAS met data</h1>
-    
-    <div class="hidden name"><code>download.NLDAS.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download NLDAS met data</h1>
 
-    <div class="ref-description">
-    
-    <p>Download and convert single grid point NLDAS to CF single grid point from hydro1.sci.gsfc.nasa.gov using OPENDAP interface</p>
-    
-    </div>
+            <div class="hidden name"><code>download.NLDAS.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.NLDAS</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-        
+          <div class="ref-description">
+            <p>
+              Download and convert single grid point NLDAS to CF single grid
+              point from hydro1.sci.gsfc.nasa.gov using OPENDAP interface
+            </p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>download.NLDAS</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson (with help from Ankur Desai)
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson (with help from Ankur Desai)
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/data.atmosphere/docs/reference/download.NOAA_GEFS.html b/modules/data.atmosphere/docs/reference/download.NOAA_GEFS.html
index 4393f56..c6fa400 100644
--- a/modules/data.atmosphere/docs/reference/download.NOAA_GEFS.html
+++ b/modules/data.atmosphere/docs/reference/download.NOAA_GEFS.html
@@ -2,256 +2,364 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
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-<!-- Bootstrap -->
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download NOAA GEFS Weather Data</h1>
-    
-    <div class="hidden name"><code>download.NOAA_GEFS.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download NOAA GEFS Weather Data</h1>
 
-    <div class="ref-description">
-    
-    <p>Download NOAA GEFS Weather Data</p>
-    
-    </div>
+            <div class="hidden name"><code>download.NOAA_GEFS.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Download NOAA GEFS Weather Data</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.NOAA_GEFS</span>(<span class='no'>outfolder</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>, <span class='no'>sitename</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>download.NOAA_GEFS</span>(<span class='no'>outfolder</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>, <span class='no'>sitename</span>,
   <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='fu'>Sys.time</span>(), <span class='kw'>end_date</span> <span class='kw'>=</span> (<span class='fu'>as.POSIXct</span>(<span class='no'>start_date</span>, <span class='kw'>tz</span> <span class='kw'>=</span>
   <span class='st'>"UTC"</span>) + <span class='kw pkg'>lubridate</span><span class='kw ns'>::</span><span class='fu'><a href='http://lubridate.tidyverse.org/reference/period.html'>days</a></span>(<span class='fl'>16</span>)), <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>Directory where results should be written</p></td>
-    </tr>
-    <tr>
-      <th>sitename</th>
-      <td><p>The unique ID given to each site. This is used as part of the file name.</p></td>
-    </tr>
-    <tr>
-      <th>start_date, </th>
-      <td><p>end_date Range of dates/times to be downloaded (default assumed time of day is 0:00, midnight)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical. Download a fresh version even if a local file with the same name already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical.  Print additional debug information.  Passed on to functions in the netcdf4 package to provide debugging info.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Other arguments, currently ignored</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>site latitude in decimal degrees</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>site longitude in decimal degrees</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A list of data frames is returned containing information about the data file that can be used to locate it later.  Each
-data frame contains information about one file.</p>
-    
-    <h2 class="hasAnchor" id="information-on-units"><a class="anchor" href="#information-on-units"></a>Information on Units</h2>
-
-    
-    <p>Information on NOAA weather units can be found below. Note that the temperature is measured in degrees C, but is converted at the station and downlaoded
-in Kelvin.</p>
-    
-    <h2 class="hasAnchor" id="noaa-gefs-general-information"><a class="anchor" href="#noaa-gefs-general-information"></a>NOAA_GEFS General Information</h2>
-
-    
-    <p>This function downloads NOAA GEFS weather data.  GEFS is an ensemble of 21 different weather forecast models.  A 16 day forecast is avaliable
-every 6 hours.  Each forecast includes information on a total of 8 variables.  These are transformed from the NOAA standard to the internal PEcAn
-standard.</p>
-    
-    <h2 class="hasAnchor" id="data-avaliability"><a class="anchor" href="#data-avaliability"></a>Data Avaliability</h2>
-
-    
-    <p>NOAA GEFS weather data is avaliable on a rolling 12 day basis; dates provided in "start_date" must be within this range. The end date can be any point after
-that, but if the end date is beyond 16 days, only 16 days worth of forecast are recorded.  Times are rounded down to the previous 6 hour forecast.  NOAA
-GEFS weather data isn't always posted immediately, and to compensate, this function adjusts requests made in the last two hours
-back two hours (approximately the amount of time it takes to post the data) to make sure the most current forecast is used.</p>
-    
-    <h2 class="hasAnchor" id="data-save-format"><a class="anchor" href="#data-save-format"></a>Data Save Format</h2>
-
-    
-    <p>Data is saved in the netcdf format to the specified directory.  File names reflect the precision of the data to the given range of days.
-NOAA.GEFS.willow creek.3.2018-06-08T06:00.2018-06-24T06:00.nc specifies the forecast, using ensemble nubmer 3 at willow creek on
-June 6th, 2018 at 6:00 a.m. to June 24th, 2018 at 6:00 a.m.</p>
-    
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
-    <p>https://www.ncdc.noaa.gov/crn/measurements.html</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>Directory where results should be written</p></td>
+            </tr>
+            <tr>
+              <th>sitename</th>
+              <td>
+                <p>
+                  The unique ID given to each site. This is used as part of the
+                  file name.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>start_date,</th>
+              <td>
+                <p>
+                  end_date Range of dates/times to be downloaded (default
+                  assumed time of day is 0:00, midnight)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>
+                  logical. Download a fresh version even if a local file with
+                  the same name already exists?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical. Print additional debug information. Passed on to
+                  functions in the netcdf4 package to provide debugging info.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>Other arguments, currently ignored</p></td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>site latitude in decimal degrees</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>site longitude in decimal degrees</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            A list of data frames is returned containing information about the
+            data file that can be used to locate it later. Each data frame
+            contains information about one file.
+          </p>
+
+          <h2 class="hasAnchor" id="information-on-units">
+            <a class="anchor" href="#information-on-units"></a>Information on
+            Units
+          </h2>
+
+          <p>
+            Information on NOAA weather units can be found below. Note that the
+            temperature is measured in degrees C, but is converted at the
+            station and downlaoded in Kelvin.
+          </p>
+
+          <h2 class="hasAnchor" id="noaa-gefs-general-information">
+            <a class="anchor" href="#noaa-gefs-general-information"></a
+            >NOAA_GEFS General Information
+          </h2>
+
+          <p>
+            This function downloads NOAA GEFS weather data. GEFS is an ensemble
+            of 21 different weather forecast models. A 16 day forecast is
+            avaliable every 6 hours. Each forecast includes information on a
+            total of 8 variables. These are transformed from the NOAA standard
+            to the internal PEcAn standard.
+          </p>
+
+          <h2 class="hasAnchor" id="data-avaliability">
+            <a class="anchor" href="#data-avaliability"></a>Data Avaliability
+          </h2>
+
+          <p>
+            NOAA GEFS weather data is avaliable on a rolling 12 day basis; dates
+            provided in "start_date" must be within this range. The end date can
+            be any point after that, but if the end date is beyond 16 days, only
+            16 days worth of forecast are recorded. Times are rounded down to
+            the previous 6 hour forecast. NOAA GEFS weather data isn't always
+            posted immediately, and to compensate, this function adjusts
+            requests made in the last two hours back two hours (approximately
+            the amount of time it takes to post the data) to make sure the most
+            current forecast is used.
+          </p>
+
+          <h2 class="hasAnchor" id="data-save-format">
+            <a class="anchor" href="#data-save-format"></a>Data Save Format
+          </h2>
+
+          <p>
+            Data is saved in the netcdf format to the specified directory. File
+            names reflect the precision of the data to the given range of days.
+            NOAA.GEFS.willow creek.3.2018-06-08T06:00.2018-06-24T06:00.nc
+            specifies the forecast, using ensemble nubmer 3 at willow creek on
+            June 6th, 2018 at 6:00 a.m. to June 24th, 2018 at 6:00 a.m.
+          </p>
+
+          <h2 class="hasAnchor" id="references">
+            <a class="anchor" href="#references"></a>References
+          </h2>
+
+          <p>https://www.ncdc.noaa.gov/crn/measurements.html</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
  <span class='fu'>download.NOAA_GEFS</span>(<span class='kw'>outfolder</span><span class='kw'>=</span><span class='st'>"~/Working/results"</span>, <span class='kw'>lat.in</span><span class='kw'>=</span> <span class='fl'>45.805925</span>, <span class='kw'>lon.in</span> <span class='kw'>=</span> -<span class='fl'>90.07961</span>, <span class='kw'>sitename</span><span class='kw'>=</span><span class='st'>"US-WCr"</span>)
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <li><a href="#information-on-units">Information on Units</a></li>
+            <li><a href="#value">Value</a></li>
 
-      <li><a href="#noaa-gefs-general-information">NOAA_GEFS General Information</a></li>
+            <li><a href="#information-on-units">Information on Units</a></li>
 
-      <li><a href="#data-avaliability">Data Avaliability</a></li>
+            <li>
+              <a href="#noaa-gefs-general-information"
+                >NOAA_GEFS General Information</a
+              >
+            </li>
 
-      <li><a href="#data-save-format">Data Save Format</a></li>
+            <li><a href="#data-avaliability">Data Avaliability</a></li>
 
-      <li><a href="#references">References</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
+            <li><a href="#data-save-format">Data Save Format</a></li>
 
-    <h2>Author</h2>
-    
-Luke Dramko
+            <li><a href="#references">References</a></li>
 
-  </div>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <h2>Author</h2>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          Luke Dramko
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
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 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.PalEON.html b/modules/data.atmosphere/docs/reference/download.PalEON.html
index 806535e..1e86883 100644
--- a/modules/data.atmosphere/docs/reference/download.PalEON.html
+++ b/modules/data.atmosphere/docs/reference/download.PalEON.html
@@ -2,169 +2,213 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
+                      >
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+                        >UNKNOWN TITLE</a
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.PalEON</h1>
-    
-    <div class="hidden name"><code>download.PalEON.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.PalEON</h1>
 
-    <div class="ref-description">
-    
-    <p>Download PalEON files</p>
-    
-    </div>
+            <div class="hidden name"><code>download.PalEON.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.PalEON</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>end_date</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Download PalEON files</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>download.PalEON</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>end_date</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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diff --git a/modules/data.atmosphere/docs/reference/download.PalEON_ENS.html b/modules/data.atmosphere/docs/reference/download.PalEON_ENS.html
index 68b8080..44d9722 100644
--- a/modules/data.atmosphere/docs/reference/download.PalEON_ENS.html
+++ b/modules/data.atmosphere/docs/reference/download.PalEON_ENS.html
@@ -2,169 +2,222 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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+      Download PalEON met ensemble files — download.PalEON_ENS •
+      PEcAn.data.atmosphere
+    </title>
+
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+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Download PalEON met ensemble files</h1>
-    
-    <div class="hidden name"><code>download.PalEON_ENS.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Download PalEON met ensemble files</h1>
 
-    <div class="ref-description">
-    
-    <p>Download PalEON met ensemble files</p>
-    
-    </div>
+            <div class="hidden name"><code>download.PalEON_ENS.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>download.PalEON_ENS</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>end_date</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery, Mike Dietze
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Download PalEON met ensemble files</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>download.PalEON_ENS</span>(<span class='no'>sitename</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>end_date</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery, Mike Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/download.US_WCr.html b/modules/data.atmosphere/docs/reference/download.US_WCr.html
index 2f42aaf..61a59d2 100644
--- a/modules/data.atmosphere/docs/reference/download.US_WCr.html
+++ b/modules/data.atmosphere/docs/reference/download.US_WCr.html
@@ -2,187 +2,243 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
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+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+    <![endif]-->
   </head>
 
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.US-WCr</h1>
-    
-    <div class="hidden name"><code>download.US_WCr.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>download.US-WCr</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>download.US_WCr</span>(<span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>timestep</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start date/time data should be downloaded for</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End date/time data should be downloaded for</p></td>
-    </tr>
-    <tr>
-      <th>timestep</th>
-      <td><p>How often to take data points from the file.  Must be a multiple of 0.5</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="general-description"><a class="anchor" href="#general-description"></a>General Description</h2>
-
-    
-    <p>Obtains data from Ankur Desai's Willow Creek flux tower, and selects certain variables (NEE and LE) to return
-Data is retruned at the given timestep in the given range.</p>
-<p>This data includes information on a number of flux variables.</p>
-<p>The timestep parameter is measured in hours, but is then converted to half hours because the data's timestep
-is every half hour.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#general-description">General Description</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.US-WCr</h1>
+
+            <div class="hidden name"><code>download.US_WCr.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>download.US-WCr</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>download.US_WCr</span>(<span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>timestep</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start date/time data should be downloaded for</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End date/time data should be downloaded for</p></td>
+            </tr>
+            <tr>
+              <th>timestep</th>
+              <td>
+                <p>
+                  How often to take data points from the file. Must be a
+                  multiple of 0.5
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="general-description">
+            <a class="anchor" href="#general-description"></a>General
+            Description
+          </h2>
+
+          <p>
+            Obtains data from Ankur Desai's Willow Creek flux tower, and selects
+            certain variables (NEE and LE) to return Data is retruned at the
+            given timestep in the given range.
+          </p>
+          <p>This data includes information on a number of flux variables.</p>
+          <p>
+            The timestep parameter is measured in hours, but is then converted
+            to half hours because the data's timestep is every half hour.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#general-description">General Description</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Luke Dramko
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Luke Dramko
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/equation_of_time.html b/modules/data.atmosphere/docs/reference/equation_of_time.html
index 3470e84..26d0e58 100644
--- a/modules/data.atmosphere/docs/reference/equation_of_time.html
+++ b/modules/data.atmosphere/docs/reference/equation_of_time.html
@@ -2,174 +2,232 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Equation of time: Eccentricity and obliquity</h1>
-    
-    <div class="hidden name"><code>equation_of_time.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>For description of calculations, see https://en.wikipedia.org/wiki/Equation_of_time#Calculating_the_equation_of_time</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>equation_of_time</span>(<span class='no'>doy</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>doy</th>
-      <td><p>Day of year</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`numeric(1)` length of the solar day, in hours.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Equation of time: Eccentricity and obliquity</h1>
+
+            <div class="hidden name"><code>equation_of_time.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              For description of calculations, see
+              https://en.wikipedia.org/wiki/Equation_of_time#Calculating_the_equation_of_time
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>equation_of_time</span>(<span class='no'>doy</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>doy</th>
+              <td><p>Day of year</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>`numeric(1)` length of the solar day, in hours.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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index a2e0ed8..22ae41a 100644
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+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Exner function</h1>
-    
-    <div class="hidden name"><code>exner.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>estimated exner function</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>exner</span>(<span class='no'>pres</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pres</th>
-      <td><p>air pressure (Bar)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Exner function</h1>
+
+            <div class="hidden name"><code>exner.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>estimated exner function</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>exner</span>(<span class='no'>pres</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pres</th>
+              <td><p>air pressure (Bar)</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index 291682d..b955286 100644
--- a/modules/data.atmosphere/docs/reference/extract.local.CMIP5.html
+++ b/modules/data.atmosphere/docs/reference/extract.local.CMIP5.html
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+    <!-- clipboard.js -->
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+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <meta
+      property="og:description"
+      content="This function extracts CMIP5 data from grids that have been downloaded and stored locally.
              Files are saved as a netCDF file in CF conventions at *DAILY* resolution.  Note: At this point
              in time, variables that are only available at a native monthly resolution will be repeated to
              give a pseudo-daily record (and can get dealt with in the downscaling workflow).  These files 
-             are ready to be used in the general PEcAn workflow or fed into the downscaling workflow." />
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+    />
+    <meta name="twitter:card" content="summary" />
 
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+                type="button"
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+                  >PEcAn.data.atmosphere</a
+                >
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+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
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+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>extract.local.CMIP5</h1>
-    
-    <div class="hidden name"><code>extract.local.CMIP5.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function extracts CMIP5 data from grids that have been downloaded and stored locally.
-             Files are saved as a netCDF file in CF conventions at *DAILY* resolution.  Note: At this point
-             in time, variables that are only available at a native monthly resolution will be repeated to
-             give a pseudo-daily record (and can get dealt with in the downscaling workflow).  These files 
-             are ready to be used in the general PEcAn workflow or fed into the downscaling workflow.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>extract.local.CMIP5</span>(<span class='no'>outfolder</span>, <span class='no'>in.path</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>extract.local.CMIP5</h1>
+
+            <div class="hidden name"><code>extract.local.CMIP5.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function extracts CMIP5 data from grids that have been
+              downloaded and stored locally. Files are saved as a netCDF file in
+              CF conventions at *DAILY* resolution. Note: At this point in time,
+              variables that are only available at a native monthly resolution
+              will be repeated to give a pseudo-daily record (and can get dealt
+              with in the downscaling workflow). These files are ready to be
+              used in the general PEcAn workflow or fed into the downscaling
+              workflow.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>extract.local.CMIP5</span>(<span class='no'>outfolder</span>, <span class='no'>in.path</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>,
   <span class='no'>lat.in</span>, <span class='no'>lon.in</span>, <span class='no'>model</span>, <span class='no'>scenario</span>, <span class='kw'>ensemble_member</span> <span class='kw'>=</span> <span class='st'>"r1i1p1"</span>,
   <span class='kw'>date.origin</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>no.leap</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>- directory where output files will be stored</p></td>
-    </tr>
-    <tr>
-      <th>in.path</th>
-      <td><p>- path to the raw full grids</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>- first day for which you want to extract met (yyyy-mm-dd)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>- last day for which you want to extract met (yyyy-mm-dd)</p></td>
-    </tr>
-    <tr>
-      <th>site_id</th>
-      <td><p>name to associate with extracted files</p></td>
-    </tr>
-    <tr>
-      <th>lat.in</th>
-      <td><p>site latitude in decimal degrees</p></td>
-    </tr>
-    <tr>
-      <th>lon.in</th>
-      <td><p>site longitude in decimal degrees</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>which GCM to extract data from</p></td>
-    </tr>
-    <tr>
-      <th>scenario</th>
-      <td><p>which experiment to pull (p1000, historical, ...)</p></td>
-    </tr>
-    <tr>
-      <th>ensemble_member</th>
-      <td><p>which CMIP5 experiment ensemble member</p></td>
-    </tr>
-    <tr>
-      <th>date.origin</th>
-      <td><p>(optional) specify the date of origin for timestamps in the files being read.
-If NULL defaults to 1850 for historical simulations (except MPI-ESM-P) and 
-850 for p1000 simulations (plus MPI-ESM-P historical).  Format: YYYY-MM-DD</p></td>
-    </tr>
-    <tr>
-      <th>no.leap</th>
-      <td><p>(optional, logical) if you know your GCM of interest is missing leap year, you can specify it here.
-otherwise the code will automatically determine if leap year is missing and if it should be 
-added in.</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical. Download a fresh version even if a local file with the same name already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical. to control printing of debug info</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Other arguments, currently ignored</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Extract NLDAS from local download
-Extract NLDAS meteorology for a poimt from a local download of the full grid</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>- directory where output files will be stored</p></td>
+            </tr>
+            <tr>
+              <th>in.path</th>
+              <td><p>- path to the raw full grids</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  - first day for which you want to extract met (yyyy-mm-dd)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>- last day for which you want to extract met (yyyy-mm-dd)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>site_id</th>
+              <td><p>name to associate with extracted files</p></td>
+            </tr>
+            <tr>
+              <th>lat.in</th>
+              <td><p>site latitude in decimal degrees</p></td>
+            </tr>
+            <tr>
+              <th>lon.in</th>
+              <td><p>site longitude in decimal degrees</p></td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td><p>which GCM to extract data from</p></td>
+            </tr>
+            <tr>
+              <th>scenario</th>
+              <td><p>which experiment to pull (p1000, historical, ...)</p></td>
+            </tr>
+            <tr>
+              <th>ensemble_member</th>
+              <td><p>which CMIP5 experiment ensemble member</p></td>
+            </tr>
+            <tr>
+              <th>date.origin</th>
+              <td>
+                <p>
+                  (optional) specify the date of origin for timestamps in the
+                  files being read. If NULL defaults to 1850 for historical
+                  simulations (except MPI-ESM-P) and 850 for p1000 simulations
+                  (plus MPI-ESM-P historical). Format: YYYY-MM-DD
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>no.leap</th>
+              <td>
+                <p>
+                  (optional, logical) if you know your GCM of interest is
+                  missing leap year, you can specify it here. otherwise the code
+                  will automatically determine if leap year is missing and if it
+                  should be added in.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>
+                  logical. Download a fresh version even if a local file with
+                  the same name already exists?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>logical. to control printing of debug info</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>Other arguments, currently ignored</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Extract NLDAS from local download Extract NLDAS meteorology for a
+            poimt from a local download of the full grid
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson,
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson,
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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 </html>
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index 7dc496f..73c3b9c 100644
--- a/modules/data.atmosphere/docs/reference/extract.local.NLDAS.html
+++ b/modules/data.atmosphere/docs/reference/extract.local.NLDAS.html
@@ -2,221 +2,308 @@
 <!DOCTYPE html>
 <html>
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-
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+
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+
+    <!-- pkgdown -->
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+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="extract.local.NLDAS — extract.local.NLDAS"
+    />
+
+    <meta
+      property="og:description"
+      content="This function extracts NLDAS data from grids that have been downloaded and stored locally.
              Once upon a time, you could query these files directly from the internet, but now they're 
              behind a tricky authentication wall. Files are saved as a netCDF file in CF conventions. 
              These files are ready to be used in the general PEcAn workflow or fed into the downscalign 
-             workflow." />
-<meta name="twitter:card" content="summary" />
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+             workflow."
+    />
+    <meta name="twitter:card" content="summary" />
 
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              </button>
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
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+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>extract.local.NLDAS</h1>
-    
-    <div class="hidden name"><code>extract.local.NLDAS.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function extracts NLDAS data from grids that have been downloaded and stored locally.
-             Once upon a time, you could query these files directly from the internet, but now they're 
-             behind a tricky authentication wall. Files are saved as a netCDF file in CF conventions. 
-             These files are ready to be used in the general PEcAn workflow or fed into the downscalign 
-             workflow.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>extract.local.NLDAS</span>(<span class='no'>outfolder</span>, <span class='no'>in.path</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>extract.local.NLDAS</h1>
+
+            <div class="hidden name"><code>extract.local.NLDAS.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function extracts NLDAS data from grids that have been
+              downloaded and stored locally. Once upon a time, you could query
+              these files directly from the internet, but now they're behind a
+              tricky authentication wall. Files are saved as a netCDF file in CF
+              conventions. These files are ready to be used in the general PEcAn
+              workflow or fed into the downscalign workflow.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>extract.local.NLDAS</span>(<span class='no'>outfolder</span>, <span class='no'>in.path</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>site_id</span>,
   <span class='no'>lat.in</span>, <span class='no'>lon.in</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>- directory where output files will be stored</p></td>
-    </tr>
-    <tr>
-      <th>in.path</th>
-      <td><p>- path to the raw full grids</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>- first day for which you want to extract met (yyyy-mm-dd)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>- last day for which you want to extract met (yyyy-mm-dd)</p></td>
-    </tr>
-    <tr>
-      <th>site_id</th>
-      <td><p>name to associate with extracted files</p></td>
-    </tr>
-    <tr>
-      <th>lat.in</th>
-      <td><p>site latitude in decimal degrees</p></td>
-    </tr>
-    <tr>
-      <th>lon.in</th>
-      <td><p>site longitude in decimal degrees</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical. Download a fresh version even if a local file with the same name already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical. Passed on to <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncvar_def'>ncvar_def</a></code> and <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/nc_create'>nc_create</a></code>
-to control printing of debug info</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Other arguments, currently ignored</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Extract NLDAS from local download
-Extract NLDAS meteorology for a poimt from a local download of the full grid</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>- directory where output files will be stored</p></td>
+            </tr>
+            <tr>
+              <th>in.path</th>
+              <td><p>- path to the raw full grids</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  - first day for which you want to extract met (yyyy-mm-dd)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>- last day for which you want to extract met (yyyy-mm-dd)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>site_id</th>
+              <td><p>name to associate with extracted files</p></td>
+            </tr>
+            <tr>
+              <th>lat.in</th>
+              <td><p>site latitude in decimal degrees</p></td>
+            </tr>
+            <tr>
+              <th>lon.in</th>
+              <td><p>site longitude in decimal degrees</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>
+                  logical. Download a fresh version even if a local file with
+                  the same name already exists?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical. Passed on to
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncvar_def"
+                      >ncvar_def</a
+                    ></code
+                  >
+                  and
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/nc_create"
+                      >nc_create</a
+                    ></code
+                  >
+                  to control printing of debug info
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>Other arguments, currently ignored</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Extract NLDAS from local download Extract NLDAS meteorology for a
+            poimt from a local download of the full grid
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson,
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson,
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/extract.nc.html b/modules/data.atmosphere/docs/reference/extract.nc.html
index bf1c90f..eda0bd9 100644
--- a/modules/data.atmosphere/docs/reference/extract.nc.html
+++ b/modules/data.atmosphere/docs/reference/extract.nc.html
@@ -2,201 +2,261 @@
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-<!-- Bootstrap -->
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-
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>extract.nc</h1>
-    
-    <div class="hidden name"><code>extract.nc.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>extract.nc</h1>
 
-    <div class="ref-description">
-    
-    <p>Given latitude and longitude coordinates, extract site data from NARR file</p>
-    
-    </div>
+            <div class="hidden name"><code>extract.nc.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>extract.nc</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>slat</span>, <span class='no'>slon</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be permuted (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be permuted (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>slat</th>
-      <td><p>the latitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>slon</th>
-      <td><p>the longitude of the site</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should ouput of function be extra verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Given latitude and longitude coordinates, extract site data from
+              NARR file
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>extract.nc</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>slat</span>, <span class='no'>slon</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be permuted (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be permuted (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>slat</th>
+              <td><p>the latitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>slon</th>
+              <td><p>the longitude of the site</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should ouput of function be extra verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
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diff --git a/modules/data.atmosphere/docs/reference/gen.subdaily.models.html b/modules/data.atmosphere/docs/reference/gen.subdaily.models.html
index c5ec6a0..a1a0715 100644
--- a/modules/data.atmosphere/docs/reference/gen.subdaily.models.html
+++ b/modules/data.atmosphere/docs/reference/gen.subdaily.models.html
@@ -2,260 +2,381 @@
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-
-<meta property="og:description" content="This is the 2nd function in the tdm workflow that takes the dat.train_file that is created from the
-             nc2dat.train function and generates &quot;lag.days&quot; and &quot;next.days&quot;. These variables pass along information
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      gen.subdaily.models — gen.subdaily.models • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
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+    ></script>
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+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="gen.subdaily.models — gen.subdaily.models"
+    />
+
+    <meta
+      property="og:description"
+      content='This is the 2nd function in the tdm workflow that takes the dat.train_file that is created from the
+             nc2dat.train function and generates "lag.days" and "next.days". These variables pass along information
              of the previous time step and provides a preview of the next time step. After these variables are created,
              the models are generated by calling the tdm_temporal_downscale_functions.R scripts and these models
              and betas are saved separately. Please note that these models and betas require a significant
              amount of space. The storage required varies by the size of the training dataset, but prepare for
              &amp;gt;100 GB. These will be called later in tdm_predict_subdaily_met to perform the linear regression
-             analysis." />
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+             analysis.'
+    />
+    <meta name="twitter:card" content="summary" />
 
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+                type="button"
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+                  >PEcAn.data.atmosphere</a
+                >
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+                  class="label label-default"
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
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+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>gen.subdaily.models</h1>
-    
-    <div class="hidden name"><code>gen.subdaily.models.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This is the 2nd function in the tdm workflow that takes the dat.train_file that is created from the
-             nc2dat.train function and generates "lag.days" and "next.days". These variables pass along information
-             of the previous time step and provides a preview of the next time step. After these variables are created,
-             the models are generated by calling the tdm_temporal_downscale_functions.R scripts and these models
-             and betas are saved separately. Please note that these models and betas require a significant
-             amount of space. The storage required varies by the size of the training dataset, but prepare for
-             &gt;100 GB. These will be called later in tdm_predict_subdaily_met to perform the linear regression
-             analysis.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>gen.subdaily.models</span>(<span class='no'>outfolder</span>, <span class='no'>path.train</span>, <span class='no'>yrs.train</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>gen.subdaily.models</h1>
+
+            <div class="hidden name"><code>gen.subdaily.models.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This is the 2nd function in the tdm workflow that takes the
+              dat.train_file that is created from the nc2dat.train function and
+              generates "lag.days" and "next.days". These variables pass along
+              information of the previous time step and provides a preview of
+              the next time step. After these variables are created, the models
+              are generated by calling the tdm_temporal_downscale_functions.R
+              scripts and these models and betas are saved separately. Please
+              note that these models and betas require a significant amount of
+              space. The storage required varies by the size of the training
+              dataset, but prepare for &gt;100 GB. These will be called later in
+              tdm_predict_subdaily_met to perform the linear regression
+              analysis.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>gen.subdaily.models</span>(<span class='no'>outfolder</span>, <span class='no'>path.train</span>, <span class='no'>yrs.train</span>,
   <span class='kw'>direction.filter</span> <span class='kw'>=</span> <span class='st'>"forward"</span>, <span class='no'>in.prefix</span>, <span class='no'>n.beta</span>, <span class='no'>day.window</span>,
   <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fu'>Sys.time</span>(), <span class='kw'>resids</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>parallel</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>n.cores</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>print.progress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>- directory where models will be stored *** storage required varies by size of training dataset, but prepare for &gt;10 GB</p></td>
-    </tr>
-    <tr>
-      <th>path.train</th>
-      <td><p>- path to CF/PEcAn style training data where each year is in a separate file.</p></td>
-    </tr>
-    <tr>
-      <th>yrs.train</th>
-      <td><p>- which years of the training data should be used for to generate the model for 
-the subdaily cycle.  If NULL, will default to all years</p></td>
-    </tr>
-    <tr>
-      <th>direction.filter</th>
-      <td><p>- Whether the model will be filtered backward or forward in time. options = c("backward", "forward")
-(PalEON will go backward, anybody interested in the future will go forward)</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>n.beta</th>
-      <td><p>- number of betas to save from linear regression model</p></td>
-    </tr>
-    <tr>
-      <th>day.window</th>
-      <td><p>- integer specifying number of days around the day being modeled you want to use data from for that 
-specific hours coefficients. Must be integer because we want statistics from the same time of day
-for each day surrounding the model day</p></td>
-    </tr>
-    <tr>
-      <th>seed</th>
-      <td><p>- seed for randomization to allow for reproducible results</p></td>
-    </tr>
-    <tr>
-      <th>resids</th>
-      <td><p>- logical stating whether to pass on residual data or not (this increases both memory &amp; storage requirements)</p></td>
-    </tr>
-    <tr>
-      <th>parallel</th>
-      <td><p>- logical stating whether to run temporal_downscale_functions.R in parallel</p></td>
-    </tr>
-    <tr>
-      <th>n.cores</th>
-      <td><p>- deals with parallelization</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: replace output file if it already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical, currently ignored</p></td>
-    </tr>
-    <tr>
-      <th>print.progress</th>
-      <td><p>- print progress bar? (gets passed through)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
 
-    <p>Generate Subdaily Models
-Create statistical models to predict subdaily meteorology</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other tdm - Temporally Downscale Meteorology: <code><a href='lm_ensemble_sims.html'>lm_ensemble_sims</a></code>,
-  <code><a href='model.train.html'>model.train</a></code>, <code><a href='nc.merge.html'>nc.merge</a></code>,
-  <code><a href='predict_subdaily_met.html'>predict_subdaily_met</a></code>,
-  <code><a href='save.betas.html'>save.betas</a></code>, <code><a href='save.model.html'>save.model</a></code>,
-  <code><a href='subdaily_pred.html'>subdaily_pred</a></code>,
-  <code><a href='temporal.downscale.functions.html'>temporal.downscale.functions</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td>
+                <p>
+                  - directory where models will be stored *** storage required
+                  varies by size of training dataset, but prepare for &gt;10 GB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>path.train</th>
+              <td>
+                <p>
+                  - path to CF/PEcAn style training data where each year is in a
+                  separate file.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>yrs.train</th>
+              <td>
+                <p>
+                  - which years of the training data should be used for to
+                  generate the model for the subdaily cycle. If NULL, will
+                  default to all years
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>direction.filter</th>
+              <td>
+                <p>
+                  - Whether the model will be filtered backward or forward in
+                  time. options = c("backward", "forward") (PalEON will go
+                  backward, anybody interested in the future will go forward)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>n.beta</th>
+              <td>
+                <p>- number of betas to save from linear regression model</p>
+              </td>
+            </tr>
+            <tr>
+              <th>day.window</th>
+              <td>
+                <p>
+                  - integer specifying number of days around the day being
+                  modeled you want to use data from for that specific hours
+                  coefficients. Must be integer because we want statistics from
+                  the same time of day for each day surrounding the model day
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>seed</th>
+              <td>
+                <p>
+                  - seed for randomization to allow for reproducible results
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>resids</th>
+              <td>
+                <p>
+                  - logical stating whether to pass on residual data or not
+                  (this increases both memory &amp; storage requirements)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>parallel</th>
+              <td>
+                <p>
+                  - logical stating whether to run
+                  temporal_downscale_functions.R in parallel
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.cores</th>
+              <td><p>- deals with parallelization</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical: replace output file if it already exists?</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>logical, currently ignored</p></td>
+            </tr>
+            <tr>
+              <th>print.progress</th>
+              <td><p>- print progress bar? (gets passed through)</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Generate Subdaily Models Create statistical models to predict
+            subdaily meteorology
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other tdm - Temporally Downscale Meteorology:
+              <code><a href="lm_ensemble_sims.html">lm_ensemble_sims</a></code
+              >, <code><a href="model.train.html">model.train</a></code
+              >, <code><a href="nc.merge.html">nc.merge</a></code
+              >,
+              <code
+                ><a href="predict_subdaily_met.html"
+                  >predict_subdaily_met</a
+                ></code
+              >, <code><a href="save.betas.html">save.betas</a></code
+              >, <code><a href="save.model.html">save.model</a></code
+              >, <code><a href="subdaily_pred.html">subdaily_pred</a></code
+              >,
+              <code
+                ><a href="temporal.downscale.functions.html"
+                  >temporal.downscale.functions</a
+                ></code
+              >
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson, James Simkins
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson, James Simkins
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
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-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
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diff --git a/modules/data.atmosphere/docs/reference/generate_narr_url.html b/modules/data.atmosphere/docs/reference/generate_narr_url.html
index 0cbe648..841a4e4 100644
--- a/modules/data.atmosphere/docs/reference/generate_narr_url.html
+++ b/modules/data.atmosphere/docs/reference/generate_narr_url.html
@@ -2,175 +2,234 @@
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
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+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
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+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
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+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate NARR url from a vector of dates</h1>
-    
-    <div class="hidden name"><code>generate_narr_url.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Figures out file names for the given dates, based on NARR's convoluted and 
-inconsistent naming scheme.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>generate_narr_url</span>(<span class='no'>dates</span>, <span class='no'>flx</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dates</th>
-      <td><p>Vector of dates for which to generate URL</p></td>
-    </tr>
-    <tr>
-      <th>flx</th>
-      <td><p>(Logical) If `TRUE`, format for `flx` variables. Otherwise, 
-format for `sfc` variables. See [narr_flx_vars].</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generate NARR url from a vector of dates</h1>
+
+            <div class="hidden name"><code>generate_narr_url.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Figures out file names for the given dates, based on NARR's
+              convoluted and inconsistent naming scheme.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>generate_narr_url</span>(<span class='no'>dates</span>, <span class='no'>flx</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dates</th>
+              <td><p>Vector of dates for which to generate URL</p></td>
+            </tr>
+            <tr>
+              <th>flx</th>
+              <td>
+                <p>
+                  (Logical) If `TRUE`, format for `flx` variables. Otherwise,
+                  format for `sfc` variables. See [narr_flx_vars].
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
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diff --git a/modules/data.atmosphere/docs/reference/get.es.html b/modules/data.atmosphere/docs/reference/get.es.html
index bbea8ab..1c1237c 100644
--- a/modules/data.atmosphere/docs/reference/get.es.html
+++ b/modules/data.atmosphere/docs/reference/get.es.html
@@ -2,181 +2,233 @@
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+      crossorigin="anonymous"
+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
+                class="navbar-toggle collapsed"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get es</h1>
-    
-    <div class="hidden name"><code>get.es.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate saturation vapor pressure</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.es</span>(<span class='no'>temp</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>temp</th>
-      <td><p>temperature in degrees C</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>saturation vapor pressure in mb</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get es</h1>
+
+            <div class="hidden name"><code>get.es.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate saturation vapor pressure</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.es</span>(<span class='no'>temp</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>temp</th>
+              <td><p>temperature in degrees C</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>saturation vapor pressure in mb</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>temp</span> <span class='kw'>&lt;-</span> -<span class='fl'>30</span>:<span class='fl'>30</span>
 <span class='fu'>plot</span>(<span class='no'>temp</span>, <span class='fu'>get.es</span>(<span class='no'>temp</span>))
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          David LeBauer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/data.atmosphere/docs/reference/get.lv.html b/modules/data.atmosphere/docs/reference/get.lv.html
index d5f9ccc..cd00cdf 100644
--- a/modules/data.atmosphere/docs/reference/get.lv.html
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@@ -2,174 +2,223 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Latent heat of vaporization</h1>
-    
-    <div class="hidden name"><code>get.lv.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>calculate latent heat of vaporization for water</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.lv</span>(<span class='kw'>airtemp</span> <span class='kw'>=</span> <span class='fl'>268.6465</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>airtemp</th>
-      <td><p>air temperature (Kelvin)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>lV   latent heat of vaporization (J kg-1)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Latent heat of vaporization</h1>
+
+            <div class="hidden name"><code>get.lv.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>calculate latent heat of vaporization for water</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.lv</span>(<span class='kw'>airtemp</span> <span class='kw'>=</span> <span class='fl'>268.6465</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>airtemp</th>
+              <td><p>air temperature (Kelvin)</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>lV latent heat of vaporization (J kg-1)</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
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index f72e56b..9a32d45 100644
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get time series vector from netCDF file</h1>
-    
-    <div class="hidden name"><code>get.ncvector.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get time series vector from netCDF file</h1>
 
-    <div class="ref-description">
-    
-    <p>Get time series vector from netCDF file</p>
-    
-    </div>
+            <div class="hidden name"><code>get.ncvector.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get time series vector from netCDF file</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>get.ncvector</span>(<span class='no'>var</span>, <span class='kw'>lati</span> <span class='kw'>=</span> <span class='no'>lati</span>, <span class='kw'>loni</span> <span class='kw'>=</span> <span class='no'>loni</span>, <span class='kw'>run.dates</span> <span class='kw'>=</span> <span class='no'>run.dates</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>get.ncvector</span>(<span class='no'>var</span>, <span class='kw'>lati</span> <span class='kw'>=</span> <span class='no'>lati</span>, <span class='kw'>loni</span> <span class='kw'>=</span> <span class='no'>loni</span>, <span class='kw'>run.dates</span> <span class='kw'>=</span> <span class='no'>run.dates</span>,
   <span class='no'>met.nc</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>met.nc</th>
-      <td><p>netcdf file with CF variable names</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>numeric vector</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>internal convenience function for
-streamlining extraction of data from netCDF files
-with CF-compliant variable names</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>met.nc</th>
+              <td><p>netcdf file with CF variable names</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>numeric vector</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            internal convenience function for streamlining extraction of data
+            from netCDF files with CF-compliant variable names
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David Shaner LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David Shaner LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/get.rh.html b/modules/data.atmosphere/docs/reference/get.rh.html
index 9522e5f..85e774e 100644
--- a/modules/data.atmosphere/docs/reference/get.rh.html
+++ b/modules/data.atmosphere/docs/reference/get.rh.html
@@ -2,186 +2,239 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="get RH — get.rh" />
+
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+      property="og:description"
+      content="Calculate RH from temperature and dewpoint"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
   </head>
 
   <body>
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../index.html">
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-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
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-      
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-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get RH</h1>
-    
-    <div class="hidden name"><code>get.rh.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate RH from temperature and dewpoint</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.rh</span>(<span class='no'>T</span>, <span class='no'>Td</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>T</th>
-      <td><p>temperature</p></td>
-    </tr>
-    <tr>
-      <th>Td</th>
-      <td><p>dewpoint</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>numeric vector</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Based on equation 12 ( in Lawrence 2005, The Relationship between
-Relative Humidity and the Dewpoint Temperature in Moist Air
-A Simple Conversion and Applications.)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get RH</h1>
+
+            <div class="hidden name"><code>get.rh.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate RH from temperature and dewpoint</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.rh</span>(<span class='no'>T</span>, <span class='no'>Td</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>T</th>
+              <td><p>temperature</p></td>
+            </tr>
+            <tr>
+              <th>Td</th>
+              <td><p>dewpoint</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>numeric vector</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Based on equation 12 ( in Lawrence 2005, The Relationship between
+            Relative Humidity and the Dewpoint Temperature in Moist Air A Simple
+            Conversion and Applications.)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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+    </div>
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-
diff --git a/modules/data.atmosphere/docs/reference/get.vpd.html b/modules/data.atmosphere/docs/reference/get.vpd.html
index cf57e7c..b6e3e95 100644
--- a/modules/data.atmosphere/docs/reference/get.vpd.html
+++ b/modules/data.atmosphere/docs/reference/get.vpd.html
@@ -2,191 +2,245 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>VPD</h1>
-    
-    <div class="hidden name"><code>get.vpd.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate VPD</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.vpd</span>(<span class='no'>rh</span>, <span class='no'>temp</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>rh</th>
-      <td><p>relative humidity, in percent</p></td>
-    </tr>
-    <tr>
-      <th>temp</th>
-      <td><p>temperature, degrees celsius</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>vpd: vapor pressure deficit, in mb</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Calculate vapor pressure deficit from relative humidity and temperature.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>VPD</h1>
+
+            <div class="hidden name"><code>get.vpd.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate VPD</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.vpd</span>(<span class='no'>rh</span>, <span class='no'>temp</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>rh</th>
+              <td><p>relative humidity, in percent</p></td>
+            </tr>
+            <tr>
+              <th>temp</th>
+              <td><p>temperature, degrees celsius</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>vpd: vapor pressure deficit, in mb</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Calculate vapor pressure deficit from relative humidity and
+            temperature.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>temp</span> <span class='kw'>&lt;-</span> -<span class='fl'>30</span>:<span class='fl'>30</span>
 <span class='fu'>plot</span>(<span class='no'>temp</span>, <span class='fu'>get.vpd</span>(<span class='fl'>0</span>, <span class='no'>temp</span>))
 <span class='co'># }</span></pre>
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-      
-      <li><a href="#value">Value</a></li>
-
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-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
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+            <li><a href="#arguments">Arguments</a></li>
 
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Retrieve NARR data using thredds</h1>
-    
-    <div class="hidden name"><code>get_NARR_thredds.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Retrieve NARR data using thredds</h1>
 
-    <div class="ref-description">
-    
-    <p>Retrieve NARR data using thredds</p>
-    
-    </div>
+            <div class="hidden name"><code>get_NARR_thredds.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Retrieve NARR data using thredds</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>get_NARR_thredds</span>(<span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>get_NARR_thredds</span>(<span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>, <span class='kw'>progress</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>drop_outside</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>parallel</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>ncores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>start_date</th>
-      <td><p>Start date for meteorology</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>End date for meteorology</p></td>
-    </tr>
-    <tr>
-      <th>lat.in</th>
-      <td><p>Latitude coordinate</p></td>
-    </tr>
-    <tr>
-      <th>lon.in</th>
-      <td><p>Longitude coordinate</p></td>
-    </tr>
-    <tr>
-      <th>progress</th>
-      <td><p>Whether or not to show a progress bar (default = `TRUE`).
-Requires the `progress` package to be installed.</p></td>
-    </tr>
-    <tr>
-      <th>drop_outside</th>
-      <td><p>Whether or not to drop dates outside of `start_date` to 
-`end_date` range (default = `TRUE`).</p></td>
-    </tr>
-    <tr>
-      <th>parallel</th>
-      <td><p>Download in parallel? Default = TRUE</p></td>
-    </tr>
-    <tr>
-      <th>ncores</th>
-      <td><p>Number of cores for parallel download. Default is 
-`parallel::detectCores()`</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`tibble` containing time series of NARR data for the given site</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>start_date</th>
+              <td><p>Start date for meteorology</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>End date for meteorology</p></td>
+            </tr>
+            <tr>
+              <th>lat.in</th>
+              <td><p>Latitude coordinate</p></td>
+            </tr>
+            <tr>
+              <th>lon.in</th>
+              <td><p>Longitude coordinate</p></td>
+            </tr>
+            <tr>
+              <th>progress</th>
+              <td>
+                <p>
+                  Whether or not to show a progress bar (default = `TRUE`).
+                  Requires the `progress` package to be installed.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>drop_outside</th>
+              <td>
+                <p>
+                  Whether or not to drop dates outside of `start_date` to
+                  `end_date` range (default = `TRUE`).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>parallel</th>
+              <td><p>Download in parallel? Default = TRUE</p></td>
+            </tr>
+            <tr>
+              <th>ncores</th>
+              <td>
+                <p>
+                  Number of cores for parallel download. Default is
+                  `parallel::detectCores()`
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>`tibble` containing time series of NARR data for the given site</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>dat</span> <span class='kw'>&lt;-</span> <span class='fu'>get_NARR_thredds</span>(<span class='st'>"2008-01-01"</span>, <span class='st'>"2008-01-15"</span>, <span class='fl'>43.3724</span>, -<span class='fl'>89.9071</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Alexey Shiklomanov
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
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index 7c3e861..45cecf8 100644
--- a/modules/data.atmosphere/docs/reference/get_cf_variables_table.html
+++ b/modules/data.atmosphere/docs/reference/get_cf_variables_table.html
@@ -2,179 +2,249 @@
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+      Retrieve the current CF variables table from
+      <code>cfconventions.org</code> and convert it into a
+      <code>data.frame</code> — get_cf_variables_table • PEcAn.data.atmosphere
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+and convert it into a <code>data.frame</code> — get_cf_variables_table"
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+and convert it into a data.frame"
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Retrieve the current CF variables table from <code>cfconventions.org</code>
-and convert it into a <code>data.frame</code></h1>
-    
-    <div class="hidden name"><code>get_cf_variables_table.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Retrieve the current CF variables table from <code>cfconventions.org</code>
-and convert it into a <code>data.frame</code></p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_cf_variables_table</span>(<span class='kw'>cf_url</span> <span class='kw'>=</span> <span class='fu'><a href='build_cf_variables_table_url.html'>build_cf_variables_table_url</a></span>(<span class='fl'>57</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>cf_url</th>
-      <td><p>URL of CF variables table XML. See also <a href='build_cf_variables_table_url.html'>build_cf_variables_table_url</a>.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>CF variables table, as a <code>tibble</code></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Retrieve the current CF variables table from
+              <code>cfconventions.org</code> and convert it into a
+              <code>data.frame</code>
+            </h1>
+
+            <div class="hidden name">
+              <code>get_cf_variables_table.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Retrieve the current CF variables table from
+              <code>cfconventions.org</code> and convert it into a
+              <code>data.frame</code>
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_cf_variables_table</span>(<span class='kw'>cf_url</span> <span class='kw'>=</span> <span class='fu'><a href='build_cf_variables_table_url.html'>build_cf_variables_table_url</a></span>(<span class='fl'>57</span>))</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>cf_url</th>
+              <td>
+                <p>
+                  URL of CF variables table XML. See also
+                  <a href="build_cf_variables_table_url.html"
+                    >build_cf_variables_table_url</a
+                  >.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>CF variables table, as a <code>tibble</code></p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/get_clowderauth.html b/modules/data.atmosphere/docs/reference/get_clowderauth.html
index ab93228..72887f0 100644
--- a/modules/data.atmosphere/docs/reference/get_clowderauth.html
+++ b/modules/data.atmosphere/docs/reference/get_clowderauth.html
@@ -2,172 +2,241 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authentication lookup helper — get_clowderauth • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Authentication lookup helper — get_clowderauth" />
-
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-<meta name="twitter:card" content="summary" />
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-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Authentication lookup helper — get_clowderauth • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Authentication lookup helper — get_clowderauth"
+    />
+
+    <meta property="og:description" content="Authentication lookup helper" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Authentication lookup helper</h1>
-    
-    <div class="hidden name"><code>get_clowderauth.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Authentication lookup helper</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_clowderauth</span>(<span class='no'>key</span>, <span class='no'>user</span>, <span class='no'>pass</span>, <span class='no'>url</span>, <span class='kw'>authfile</span> <span class='kw'>=</span> <span class='st'>"~/.pecan.clowder.xml"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>key, user, pass</th>
-      <td><p>passed unchanged from <code><a href='download.Geostreams.html'>download.Geostreams</a></code> call, possibly null</p></td>
-    </tr>
-    <tr>
-      <th>url</th>
-      <td><p>matched against <code>&lt;hostname&gt;</code> in authfile, ignored if authfile contains no hostname.</p></td>
-    </tr>
-    <tr>
-      <th>authfile</th>
-      <td><p>path to a PEcAn-formatted XML settings file; must contain a <code>&lt;clowder&gt;</code> key</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Authentication lookup helper</h1>
+
+            <div class="hidden name"><code>get_clowderauth.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Authentication lookup helper</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_clowderauth</span>(<span class='no'>key</span>, <span class='no'>user</span>, <span class='no'>pass</span>, <span class='no'>url</span>, <span class='kw'>authfile</span> <span class='kw'>=</span> <span class='st'>"~/.pecan.clowder.xml"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>key, user, pass</th>
+              <td>
+                <p>
+                  passed unchanged from
+                  <code
+                    ><a href="download.Geostreams.html"
+                      >download.Geostreams</a
+                    ></code
+                  >
+                  call, possibly null
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>url</th>
+              <td>
+                <p>
+                  matched against <code>&lt;hostname&gt;</code> in authfile,
+                  ignored if authfile contains no hostname.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>authfile</th>
+              <td>
+                <p>
+                  path to a PEcAn-formatted XML settings file; must contain a
+                  <code>&lt;clowder&gt;</code> key
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-   </div>
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+    </div>
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 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/get_narr_url.html b/modules/data.atmosphere/docs/reference/get_narr_url.html
index cb6f27f..586ea64 100644
--- a/modules/data.atmosphere/docs/reference/get_narr_url.html
+++ b/modules/data.atmosphere/docs/reference/get_narr_url.html
@@ -2,181 +2,237 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Retrieve NARR data from a given URL — get_narr_url • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Retrieve NARR data from a given URL — get_narr_url • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
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+      crossorigin="anonymous"
+    ></script>
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+                        station</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Retrieve NARR data from a given URL</h1>
-    
-    <div class="hidden name"><code>get_narr_url.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Retrieve NARR data from a given URL</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_narr_url</span>(<span class='no'>url</span>, <span class='no'>xy</span>, <span class='no'>flx</span>, <span class='kw'>pb</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>url</th>
-      <td><p>Full URL to NARR thredds file</p></td>
-    </tr>
-    <tr>
-      <th>xy</th>
-      <td><p>Vector length 2 containing NARR coordinates</p></td>
-    </tr>
-    <tr>
-      <th>flx</th>
-      <td><p>(Logical) If `TRUE`, format for `flx` variables. Otherwise, 
-format for `sfc` variables. See [narr_flx_vars].</p></td>
-    </tr>
-    <tr>
-      <th>pb</th>
-      <td><p>Progress bar R6 object (default = `NULL`)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Retrieve NARR data from a given URL</h1>
+
+            <div class="hidden name"><code>get_narr_url.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Retrieve NARR data from a given URL</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_narr_url</span>(<span class='no'>url</span>, <span class='no'>xy</span>, <span class='no'>flx</span>, <span class='kw'>pb</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>url</th>
+              <td><p>Full URL to NARR thredds file</p></td>
+            </tr>
+            <tr>
+              <th>xy</th>
+              <td><p>Vector length 2 containing NARR coordinates</p></td>
+            </tr>
+            <tr>
+              <th>flx</th>
+              <td>
+                <p>
+                  (Logical) If `TRUE`, format for `flx` variables. Otherwise,
+                  format for `sfc` variables. See [narr_flx_vars].
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pb</th>
+              <td><p>Progress bar R6 object (default = `NULL`)</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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+      <div class="row">
+        <div class="contents col-md-9">
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+          </div>
 
-    <colgroup>
-      
-      <col class="alias" />
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+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
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-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="AirDens.html">AirDens()</a></code> </p>
-        </td>
-        <td><p>Air Density</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="align.met.html">align.met()</a></code> </p>
-        </td>
-        <td><p>align.met</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="browndog.met.html">browndog.met()</a></code> </p>
-        </td>
-        <td><p>get met data from browndog</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="build_cf_variables_table_url.html">build_cf_variables_table_url()</a></code> </p>
-        </td>
-        <td><p>Construct a URL to a specific version of the CF variables table XML</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="cfmet.downscale.daily.html">cfmet.downscale.daily()</a></code> </p>
-        </td>
-        <td><p>daily to subdaily downscaling</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="cfmet.downscale.subdaily.html">cfmet.downscale.subdaily()</a></code> </p>
-        </td>
-        <td><p>subdaily downscaling</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="cfmet.downscale.time.html">cfmet.downscale.time()</a></code> </p>
-        </td>
-        <td><p>Downscale CF met data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_met_input_file.html">check_met_input_file()</a></code> </p>
-        </td>
-        <td><p>Check a meteorology data file for compliance with the PEcAn standard</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check_unit.html">check_unit()</a></code> </p>
-        </td>
-        <td><p>Check that the unit of a variable in a NetCDF file is equivalent to
-the expected unit.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="closest_xy.html">closest_xy()</a></code> </p>
-        </td>
-        <td><p>closest_xy</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="col2ncvar.html">col2ncvar()</a></code> </p>
-        </td>
-        <td><p>Create `ncvar` object from variable name</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="cos_solar_zenith_angle.html">cos_solar_zenith_angle()</a></code> </p>
-        </td>
-        <td><p>Cosine of solar zenith angle</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="daygroup.html">daygroup()</a></code> </p>
-        </td>
-        <td><p>Assign daygroup tag for a given date</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="db.site.lat.lon.html">db.site.lat.lon()</a></code> </p>
-        </td>
-        <td><p>db.site.lat.lon</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="debias.met.regression.html">debias.met.regression()</a></code> </p>
-        </td>
-        <td><p>debias.met.regression</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="debias_met.html">debias.met()</a></code> </p>
-        </td>
-        <td><p>debias_met</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.Ameriflux.html">download.Ameriflux()</a></code> </p>
-        </td>
-        <td><p>download.Ameriflux</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.AmerifluxLBL.html">download.AmerifluxLBL()</a></code> </p>
-        </td>
-        <td><p>Download Ameriflux LBL CSV files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.CRUNCEP.html">download.CRUNCEP()</a></code> </p>
-        </td>
-        <td><p>Download CRUNCEP data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.FACE.html">download.FACE()</a></code> </p>
-        </td>
-        <td><p>download.FACE</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.Fluxnet2015.html">download.Fluxnet2015()</a></code> </p>
-        </td>
-        <td><p>download.Fluxnet2015</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.FluxnetLaThuile.html">download.FluxnetLaThuile()</a></code> </p>
-        </td>
-        <td><p>download.FluxnetLaThuile</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.GFDL.html">download.GFDL()</a></code> </p>
-        </td>
-        <td><p>Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CF</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.GLDAS.html">download.GLDAS()</a></code> </p>
-        </td>
-        <td><p>Download GLDAS data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.Geostreams.html">download.Geostreams()</a></code> </p>
-        </td>
-        <td><p>Download Geostreams data from Clowder API</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.MACA.html">download.MACA()</a></code> </p>
-        </td>
-        <td><p>download.MACA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.MsTMIP_NARR.html">download.MsTMIP_NARR()</a></code> </p>
-        </td>
-        <td><p>download.MsTMIP_NARR</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.NARR.html">download.NARR()</a></code> </p>
-        </td>
-        <td><p>Download NARR files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.NARR_site.html">download.NARR_site()</a></code> </p>
-        </td>
-        <td><p>Download NARR time series for a single site</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.NEONmet.html">download.NEONmet()</a></code> </p>
-        </td>
-        <td><p>Download NEON Site Met CSV files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.NLDAS.html">download.NLDAS()</a></code> </p>
-        </td>
-        <td><p>Download NLDAS met data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.NOAA_GEFS.html">download.NOAA_GEFS()</a></code> </p>
-        </td>
-        <td><p>Download NOAA GEFS Weather Data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.PalEON.html">download.PalEON()</a></code> </p>
-        </td>
-        <td><p>download.PalEON</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.PalEON_ENS.html">download.PalEON_ENS()</a></code> </p>
-        </td>
-        <td><p>Download PalEON met ensemble files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download.US_WCr.html">download.US_WCr()</a></code> </p>
-        </td>
-        <td><p>download.US-WCr</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="equation_of_time.html">equation_of_time()</a></code> </p>
-        </td>
-        <td><p>Equation of time: Eccentricity and obliquity</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="exner.html">exner()</a></code> </p>
-        </td>
-        <td><p>Exner function</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="extract.local.CMIP5.html">extract.local.CMIP5()</a></code> </p>
-        </td>
-        <td><p>extract.local.CMIP5</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="extract.local.NLDAS.html">extract.local.NLDAS()</a></code> </p>
-        </td>
-        <td><p>extract.local.NLDAS</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="extract.nc.html">extract.nc()</a></code> </p>
-        </td>
-        <td><p>extract.nc</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="gen.subdaily.models.html">gen.subdaily.models()</a></code> </p>
-        </td>
-        <td><p>gen.subdaily.models</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="generate_narr_url.html">generate_narr_url()</a></code> </p>
-        </td>
-        <td><p>Generate NARR url from a vector of dates</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.es.html">get.es()</a></code> </p>
-        </td>
-        <td><p>get es</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.lv.html">get.lv()</a></code> </p>
-        </td>
-        <td><p>Latent heat of vaporization</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.ncvector.html">get.ncvector()</a></code> </p>
-        </td>
-        <td><p>Get time series vector from netCDF file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.rh.html">get.rh()</a></code> </p>
-        </td>
-        <td><p>get RH</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.vpd.html">get.vpd()</a></code> </p>
-        </td>
-        <td><p>VPD</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_NARR_thredds.html">get_NARR_thredds()</a></code> </p>
-        </td>
-        <td><p>Retrieve NARR data using thredds</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_cf_variables_table.html">get_cf_variables_table()</a></code> </p>
-        </td>
-        <td><p>Retrieve the current CF variables table from <code>cfconventions.org</code>
-and convert it into a <code>data.frame</code></p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_clowderauth.html">get_clowderauth()</a></code> </p>
-        </td>
-        <td><p>Authentication lookup helper</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_narr_url.html">get_narr_url()</a></code> </p>
-        </td>
-        <td><p>Retrieve NARR data from a given URL</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="latlon2lcc.html">latlon2lcc()</a></code> </p>
-        </td>
-        <td><p>Convert latitude and longitude to x-y coordinates (in km) in Lambert 
-conformal conic projection (used by NARR)</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="latlon2narr.html">latlon2narr()</a></code> </p>
-        </td>
-        <td><p>Convert latitude and longitude coordinates to NARR indices</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="lightME.html">lightME()</a></code> </p>
-        </td>
-        <td><p>Simulates the light macro environment</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="lm_ensemble_sims.html">lm_ensemble_sims()</a></code> </p>
-        </td>
-        <td><p>lm_ensemble_sims</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load.cfmet.html">load.cfmet()</a></code> </p>
-        </td>
-        <td><p>load CF met</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="merge_met_variable.html">merge_met_variable()</a></code> </p>
-        </td>
-        <td><p>Merge a new met variable from an external file (e.g. CO2) into existing met files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met.process.html">met.process()</a></code> </p>
-        </td>
-        <td><p>met.process</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met.process.stage.html">met.process.stage()</a></code> </p>
-        </td>
-        <td><p>met.process.stage</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2CF.ALMA.html">met2CF.ALMA()</a></code> </p>
-        </td>
-        <td><p>met2CF.ALMA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2CF.Ameriflux.html">met2CF.Ameriflux()</a></code> </p>
-        </td>
-        <td><p>met2CF.Ameriflux</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2CF.AmerifluxLBL.html">met2CF.AmerifluxLBL()</a></code> </p>
-        </td>
-        <td><p>met2CF.AmerifluxLBL</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2CF.FACE.html">met2CF.FACE()</a></code> </p>
-        </td>
-        <td><p>convert FACE files to CF files</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2CF.Geostreams.html">met2CF.Geostreams()</a></code> </p>
-        </td>
-        <td><p>Convert geostreams JSON to CF met file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2CF.NARR.html">met2CF.NARR()</a></code> </p>
-        </td>
-        <td><p>met2CF.NARR</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2CF.PalEON.html">met2CF.PalEON()</a></code> </p>
-        </td>
-        <td><p>met2CF.PalEON</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2CF.PalEONregional.html">met2CF.PalEONregional()</a></code> <code><a href="met2CF.PalEONregional.html">met2CF.PalEONregional()</a></code> </p>
-        </td>
-        <td><p>met2CF.PalEONregional</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met2CF.csv.html">met2CF.csv()</a></code> </p>
-        </td>
-        <td><p>met2CF.csv</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="met_temporal_downscale.Gaussian_ensemble.html">met_temporal_downscale.Gaussian_ensemble()</a></code> </p>
-        </td>
-        <td><p>met_temporal_downscale.Gaussian_ensemble</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metgapfill.NOAA_GEFS.html">metgapfill.NOAA_GEFS()</a></code> </p>
-        </td>
-        <td><p>Gapfill NOAA_GEFS weather data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="metgapfill.html">metgapfill()</a></code> </p>
-        </td>
-        <td><p>Take an Ameriflux NetCDF file
-Fill missing met values using MDS approach using MPI-BGC REddyProc library
-Currently
-Future version: Choose which variables to gap fill
-Future version will first downscale and fill with NARR, then REddyProc</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="model.train.html">model.train()</a></code> </p>
-        </td>
-        <td><p>model.train</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="narr_flx_vars.html">narr_flx_vars</a></code> <code><a href="narr_flx_vars.html">narr_sfc_vars</a></code> <code><a href="narr_flx_vars.html">narr_all_vars</a></code> </p>
-        </td>
-        <td><p>NARR flux and sfc variables</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="nc.merge.html">nc.merge()</a></code> </p>
-        </td>
-        <td><p>nc.merge</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="par2ppfd.html">par2ppfd()</a></code> </p>
-        </td>
-        <td><p>par2ppfd</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pecan_standard_met_table.html">pecan_standard_met_table</a></code> </p>
-        </td>
-        <td><p>Conversion table for PEcAn standard meteorology</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="permute.nc.html">permute.nc()</a></code> </p>
-        </td>
-        <td><p>permute.nc</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="post_process.html">post_process()</a></code> </p>
-        </td>
-        <td><p>Post process raw NARR downloaded data frame</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="predict_subdaily_met.html">predict_subdaily_met()</a></code> </p>
-        </td>
-        <td><p>predict_subdaily_met</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="prepare_narr_year.html">prepare_narr_year()</a></code> </p>
-        </td>
-        <td><p>Write NetCDF file for a single year of data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="qair2rh.html">qair2rh()</a></code> </p>
-        </td>
-        <td><p>qair2rh</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.register.html">read.register()</a></code> </p>
-        </td>
-        <td><p>read.register</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_narr_var.html">read_narr_var()</a></code> </p>
-        </td>
-        <td><p>Read a specific variable from a NARR NetCDF file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="rh2qair.html">rh2qair()</a></code> </p>
-        </td>
-        <td><p>RH to SH</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="robustly.html">robustly()</a></code> </p>
-        </td>
-        <td><p>Adverb to try calling a function `n` times before giving up</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="save.betas.html">save.betas()</a></code> </p>
-        </td>
-        <td><p>save.betas</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="save.model.html">save.model()</a></code> </p>
-        </td>
-        <td><p>save.model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="site.lst.html">site.lst()</a></code> </p>
-        </td>
-        <td><p>site.lst</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="site_from_tag.html">site_from_tag()</a></code> </p>
-        </td>
-        <td><p>site_from_tag</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="solarMJ2ppfd.html">solarMJ2ppfd()</a></code> </p>
-        </td>
-        <td><p>MJ to PPFD</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="spin.met.html">spin.met()</a></code> </p>
-        </td>
-        <td><p>Spin-up meteorology</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="split_wind.html">split_wind()</a></code> </p>
-        </td>
-        <td><p>Split wind_speed into eastward_wind and northward_wind</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="step_means.html">step_means()</a></code> </p>
-        </td>
-        <td><p>take mean at fixed intervals along a vector</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="subdaily_pred.html">subdaily_pred()</a></code> </p>
-        </td>
-        <td><p>subdaily_pred</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sw2par.html">sw2par()</a></code> </p>
-        </td>
-        <td><p>SW to PAR</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sw2ppfd.html">sw2ppfd()</a></code> </p>
-        </td>
-        <td><p>SW to PPFD</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="temporal.downscale.functions.html">temporal.downscale.functions()</a></code> </p>
-        </td>
-        <td><p>temporal_downscale_functions</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="upscale_met.html">upscale_met()</a></code> </p>
-        </td>
-        <td><p>upscale_met</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="wide2long.html">wide2long()</a></code> </p>
-        </td>
-        <td><p>Wide to Long</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="AirDens.html">AirDens()</a></code>
+                  </p>
+                </td>
+                <td><p>Air Density</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="align.met.html">align.met()</a></code>
+                  </p>
+                </td>
+                <td><p>align.met</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="browndog.met.html">browndog.met()</a></code>
+                  </p>
+                </td>
+                <td><p>get met data from browndog</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="build_cf_variables_table_url.html"
+                        >build_cf_variables_table_url()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Construct a URL to a specific version of the CF variables
+                    table XML
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="cfmet.downscale.daily.html"
+                        >cfmet.downscale.daily()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>daily to subdaily downscaling</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="cfmet.downscale.subdaily.html"
+                        >cfmet.downscale.subdaily()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>subdaily downscaling</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="cfmet.downscale.time.html"
+                        >cfmet.downscale.time()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Downscale CF met data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check_met_input_file.html"
+                        >check_met_input_file()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Check a meteorology data file for compliance with the PEcAn
+                    standard
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="check_unit.html">check_unit()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Check that the unit of a variable in a NetCDF file is
+                    equivalent to the expected unit.
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="closest_xy.html">closest_xy()</a></code>
+                  </p>
+                </td>
+                <td><p>closest_xy</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="col2ncvar.html">col2ncvar()</a></code>
+                  </p>
+                </td>
+                <td><p>Create `ncvar` object from variable name</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="cos_solar_zenith_angle.html"
+                        >cos_solar_zenith_angle()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Cosine of solar zenith angle</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="daygroup.html">daygroup()</a></code>
+                  </p>
+                </td>
+                <td><p>Assign daygroup tag for a given date</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="db.site.lat.lon.html"
+                        >db.site.lat.lon()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>db.site.lat.lon</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="debias.met.regression.html"
+                        >debias.met.regression()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>debias.met.regression</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="debias_met.html">debias.met()</a></code>
+                  </p>
+                </td>
+                <td><p>debias_met</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.Ameriflux.html"
+                        >download.Ameriflux()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.Ameriflux</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.AmerifluxLBL.html"
+                        >download.AmerifluxLBL()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download Ameriflux LBL CSV files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.CRUNCEP.html"
+                        >download.CRUNCEP()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download CRUNCEP data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.FACE.html">download.FACE()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.FACE</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.Fluxnet2015.html"
+                        >download.Fluxnet2015()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.Fluxnet2015</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.FluxnetLaThuile.html"
+                        >download.FluxnetLaThuile()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.FluxnetLaThuile</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.GFDL.html">download.GFDL()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Download GFDL CMIP5 outputs for a single grid point using
+                    OPeNDAP and convert to CF
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.GLDAS.html">download.GLDAS()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download GLDAS data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.Geostreams.html"
+                        >download.Geostreams()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download Geostreams data from Clowder API</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.MACA.html">download.MACA()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.MACA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.MsTMIP_NARR.html"
+                        >download.MsTMIP_NARR()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.MsTMIP_NARR</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.NARR.html">download.NARR()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download NARR files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.NARR_site.html"
+                        >download.NARR_site()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download NARR time series for a single site</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.NEONmet.html"
+                        >download.NEONmet()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download NEON Site Met CSV files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.NLDAS.html">download.NLDAS()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download NLDAS met data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.NOAA_GEFS.html"
+                        >download.NOAA_GEFS()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download NOAA GEFS Weather Data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.PalEON.html"
+                        >download.PalEON()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.PalEON</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.PalEON_ENS.html"
+                        >download.PalEON_ENS()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Download PalEON met ensemble files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.US_WCr.html"
+                        >download.US_WCr()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.US-WCr</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="equation_of_time.html"
+                        >equation_of_time()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Equation of time: Eccentricity and obliquity</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="exner.html">exner()</a></code>
+                  </p>
+                </td>
+                <td><p>Exner function</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="extract.local.CMIP5.html"
+                        >extract.local.CMIP5()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>extract.local.CMIP5</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="extract.local.NLDAS.html"
+                        >extract.local.NLDAS()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>extract.local.NLDAS</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="extract.nc.html">extract.nc()</a></code>
+                  </p>
+                </td>
+                <td><p>extract.nc</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="gen.subdaily.models.html"
+                        >gen.subdaily.models()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>gen.subdaily.models</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="generate_narr_url.html"
+                        >generate_narr_url()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Generate NARR url from a vector of dates</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.es.html">get.es()</a></code>
+                  </p>
+                </td>
+                <td><p>get es</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.lv.html">get.lv()</a></code>
+                  </p>
+                </td>
+                <td><p>Latent heat of vaporization</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.ncvector.html">get.ncvector()</a></code>
+                  </p>
+                </td>
+                <td><p>Get time series vector from netCDF file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.rh.html">get.rh()</a></code>
+                  </p>
+                </td>
+                <td><p>get RH</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.vpd.html">get.vpd()</a></code>
+                  </p>
+                </td>
+                <td><p>VPD</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_NARR_thredds.html"
+                        >get_NARR_thredds()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Retrieve NARR data using thredds</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_cf_variables_table.html"
+                        >get_cf_variables_table()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Retrieve the current CF variables table from
+                    <code>cfconventions.org</code> and convert it into a
+                    <code>data.frame</code>
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_clowderauth.html"
+                        >get_clowderauth()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Authentication lookup helper</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get_narr_url.html">get_narr_url()</a></code>
+                  </p>
+                </td>
+                <td><p>Retrieve NARR data from a given URL</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="latlon2lcc.html">latlon2lcc()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Convert latitude and longitude to x-y coordinates (in km) in
+                    Lambert conformal conic projection (used by NARR)
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="latlon2narr.html">latlon2narr()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Convert latitude and longitude coordinates to NARR indices
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="lightME.html">lightME()</a></code>
+                  </p>
+                </td>
+                <td><p>Simulates the light macro environment</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="lm_ensemble_sims.html"
+                        >lm_ensemble_sims()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>lm_ensemble_sims</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="load.cfmet.html">load.cfmet()</a></code>
+                  </p>
+                </td>
+                <td><p>load CF met</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="merge_met_variable.html"
+                        >merge_met_variable()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Merge a new met variable from an external file (e.g. CO2)
+                    into existing met files
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="met.process.html">met.process()</a></code>
+                  </p>
+                </td>
+                <td><p>met.process</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met.process.stage.html"
+                        >met.process.stage()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met.process.stage</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="met2CF.ALMA.html">met2CF.ALMA()</a></code>
+                  </p>
+                </td>
+                <td><p>met2CF.ALMA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2CF.Ameriflux.html"
+                        >met2CF.Ameriflux()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2CF.Ameriflux</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2CF.AmerifluxLBL.html"
+                        >met2CF.AmerifluxLBL()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2CF.AmerifluxLBL</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="met2CF.FACE.html">met2CF.FACE()</a></code>
+                  </p>
+                </td>
+                <td><p>convert FACE files to CF files</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2CF.Geostreams.html"
+                        >met2CF.Geostreams()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Convert geostreams JSON to CF met file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="met2CF.NARR.html">met2CF.NARR()</a></code>
+                  </p>
+                </td>
+                <td><p>met2CF.NARR</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2CF.PalEON.html">met2CF.PalEON()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2CF.PalEON</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met2CF.PalEONregional.html"
+                        >met2CF.PalEONregional()</a
+                      ></code
+                    >
+                    <code
+                      ><a href="met2CF.PalEONregional.html"
+                        >met2CF.PalEONregional()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met2CF.PalEONregional</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="met2CF.csv.html">met2CF.csv()</a></code>
+                  </p>
+                </td>
+                <td><p>met2CF.csv</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="met_temporal_downscale.Gaussian_ensemble.html"
+                        >met_temporal_downscale.Gaussian_ensemble()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>met_temporal_downscale.Gaussian_ensemble</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="metgapfill.NOAA_GEFS.html"
+                        >metgapfill.NOAA_GEFS()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Gapfill NOAA_GEFS weather data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="metgapfill.html">metgapfill()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Take an Ameriflux NetCDF file Fill missing met values using
+                    MDS approach using MPI-BGC REddyProc library Currently
+                    Future version: Choose which variables to gap fill Future
+                    version will first downscale and fill with NARR, then
+                    REddyProc
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="model.train.html">model.train()</a></code>
+                  </p>
+                </td>
+                <td><p>model.train</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="narr_flx_vars.html">narr_flx_vars</a></code>
+                    <code><a href="narr_flx_vars.html">narr_sfc_vars</a></code>
+                    <code><a href="narr_flx_vars.html">narr_all_vars</a></code>
+                  </p>
+                </td>
+                <td><p>NARR flux and sfc variables</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="nc.merge.html">nc.merge()</a></code>
+                  </p>
+                </td>
+                <td><p>nc.merge</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="par2ppfd.html">par2ppfd()</a></code>
+                  </p>
+                </td>
+                <td><p>par2ppfd</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pecan_standard_met_table.html"
+                        >pecan_standard_met_table</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Conversion table for PEcAn standard meteorology</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="permute.nc.html">permute.nc()</a></code>
+                  </p>
+                </td>
+                <td><p>permute.nc</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="post_process.html">post_process()</a></code>
+                  </p>
+                </td>
+                <td><p>Post process raw NARR downloaded data frame</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="predict_subdaily_met.html"
+                        >predict_subdaily_met()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>predict_subdaily_met</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="prepare_narr_year.html"
+                        >prepare_narr_year()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write NetCDF file for a single year of data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="qair2rh.html">qair2rh()</a></code>
+                  </p>
+                </td>
+                <td><p>qair2rh</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.register.html">read.register()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>read.register</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read_narr_var.html">read_narr_var()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read a specific variable from a NARR NetCDF file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="rh2qair.html">rh2qair()</a></code>
+                  </p>
+                </td>
+                <td><p>RH to SH</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="robustly.html">robustly()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Adverb to try calling a function `n` times before giving up
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="save.betas.html">save.betas()</a></code>
+                  </p>
+                </td>
+                <td><p>save.betas</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="save.model.html">save.model()</a></code>
+                  </p>
+                </td>
+                <td><p>save.model</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="site.lst.html">site.lst()</a></code>
+                  </p>
+                </td>
+                <td><p>site.lst</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="site_from_tag.html">site_from_tag()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>site_from_tag</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="solarMJ2ppfd.html">solarMJ2ppfd()</a></code>
+                  </p>
+                </td>
+                <td><p>MJ to PPFD</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="spin.met.html">spin.met()</a></code>
+                  </p>
+                </td>
+                <td><p>Spin-up meteorology</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="split_wind.html">split_wind()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Split wind_speed into eastward_wind and northward_wind</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="step_means.html">step_means()</a></code>
+                  </p>
+                </td>
+                <td><p>take mean at fixed intervals along a vector</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="subdaily_pred.html">subdaily_pred()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>subdaily_pred</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sw2par.html">sw2par()</a></code>
+                  </p>
+                </td>
+                <td><p>SW to PAR</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sw2ppfd.html">sw2ppfd()</a></code>
+                  </p>
+                </td>
+                <td><p>SW to PPFD</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="temporal.downscale.functions.html"
+                        >temporal.downscale.functions()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>temporal_downscale_functions</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="upscale_met.html">upscale_met()</a></code>
+                  </p>
+                </td>
+                <td><p>upscale_met</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="wide2long.html">wide2long()</a></code>
+                  </p>
+                </td>
+                <td><p>Wide to Long</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
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-  </div>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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index 0fda84b..b85e7fb 100644
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+++ b/modules/data.atmosphere/docs/reference/latlon2lcc.html
@@ -2,184 +2,245 @@
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+      Convert latitude and longitude to x-y coordinates (in km) in Lambert
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+      PEcAn.data.atmosphere
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+conformal conic projection (used by NARR)"
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+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert latitude and longitude to x-y coordinates (in km) in Lambert 
-conformal conic projection (used by NARR)</h1>
-    
-    <div class="hidden name"><code>latlon2lcc.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert latitude and longitude to x-y coordinates (in km) in Lambert 
-conformal conic projection (used by NARR)</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>latlon2lcc</span>(<span class='no'>lat.in</span>, <span class='no'>lon.in</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>lat.in</th>
-      <td><p>Latitude coordinate</p></td>
-    </tr>
-    <tr>
-      <th>lon.in</th>
-      <td><p>Longitude coordinate</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>`sp::SpatialPoints` object containing transformed x and y 
-coordinates, in km, which should match NARR coordinates</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Convert latitude and longitude to x-y coordinates (in km) in
+              Lambert conformal conic projection (used by NARR)
+            </h1>
+
+            <div class="hidden name"><code>latlon2lcc.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Convert latitude and longitude to x-y coordinates (in km) in
+              Lambert conformal conic projection (used by NARR)
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>latlon2lcc</span>(<span class='no'>lat.in</span>, <span class='no'>lon.in</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>lat.in</th>
+              <td><p>Latitude coordinate</p></td>
+            </tr>
+            <tr>
+              <th>lon.in</th>
+              <td><p>Longitude coordinate</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            `sp::SpatialPoints` object containing transformed x and y
+            coordinates, in km, which should match NARR coordinates
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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diff --git a/modules/data.atmosphere/docs/reference/latlon2narr.html b/modules/data.atmosphere/docs/reference/latlon2narr.html
index 10a0f4c..cf02ec5 100644
--- a/modules/data.atmosphere/docs/reference/latlon2narr.html
+++ b/modules/data.atmosphere/docs/reference/latlon2narr.html
@@ -2,183 +2,240 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert latitude and longitude coordinates to NARR indices</h1>
-    
-    <div class="hidden name"><code>latlon2narr.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert latitude and longitude coordinates to NARR indices</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>latlon2narr</span>(<span class='no'>nc</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>nc</th>
-      <td><p>`ncdf4` connection object</p></td>
-    </tr>
-    <tr>
-      <th>lat.in</th>
-      <td><p>Latitude coordinate</p></td>
-    </tr>
-    <tr>
-      <th>lon.in</th>
-      <td><p>Longitude coordinate</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Vector length 2 containing NARR `x` and `y` indices, which can be 
-used in `ncdf4::ncvar_get` `start` argument.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert latitude and longitude coordinates to NARR indices</h1>
+
+            <div class="hidden name"><code>latlon2narr.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert latitude and longitude coordinates to NARR indices</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>latlon2narr</span>(<span class='no'>nc</span>, <span class='no'>lat.in</span>, <span class='no'>lon.in</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>nc</th>
+              <td><p>`ncdf4` connection object</p></td>
+            </tr>
+            <tr>
+              <th>lat.in</th>
+              <td><p>Latitude coordinate</p></td>
+            </tr>
+            <tr>
+              <th>lon.in</th>
+              <td><p>Longitude coordinate</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Vector length 2 containing NARR `x` and `y` indices, which can be
+            used in `ncdf4::ncvar_get` `start` argument.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Simulates the light macro environment</h1>
-    
-    <div class="hidden name"><code>lightME.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Simulates the light macro environment</h1>
 
-    <div class="ref-description">
-    
-    <p>Simulates light macro environment based on latitude, day of the year.
-Other coefficients can be adjusted.</p>
-    
-    </div>
+            <div class="hidden name"><code>lightME.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>lightME</span>(<span class='kw'>lat</span> <span class='kw'>=</span> <span class='fl'>40</span>, <span class='kw'>DOY</span> <span class='kw'>=</span> <span class='fl'>190</span>, <span class='kw'>t.d</span> <span class='kw'>=</span> <span class='fl'>12</span>, <span class='kw'>t.sn</span> <span class='kw'>=</span> <span class='fl'>12</span>, <span class='kw'>atm.P</span> <span class='kw'>=</span> <span class='fl'>1e+05</span>,
+          <div class="ref-description">
+            <p>
+              Simulates light macro environment based on latitude, day of the
+              year. Other coefficients can be adjusted.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>lightME</span>(<span class='kw'>lat</span> <span class='kw'>=</span> <span class='fl'>40</span>, <span class='kw'>DOY</span> <span class='kw'>=</span> <span class='fl'>190</span>, <span class='kw'>t.d</span> <span class='kw'>=</span> <span class='fl'>12</span>, <span class='kw'>t.sn</span> <span class='kw'>=</span> <span class='fl'>12</span>, <span class='kw'>atm.P</span> <span class='kw'>=</span> <span class='fl'>1e+05</span>,
   <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.85</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>lat</th>
-      <td><p>the latitude, default is 40 (Urbana, IL, U.S.).</p></td>
-    </tr>
-    <tr>
-      <th>DOY</th>
-      <td><p>the day of the year (1--365), default 190.</p></td>
-    </tr>
-    <tr>
-      <th>t.d</th>
-      <td><p>time of the day in hours (0--23), default 12.</p></td>
-    </tr>
-    <tr>
-      <th>t.sn</th>
-      <td><p>time of solar noon, default 12.</p></td>
-    </tr>
-    <tr>
-      <th>atm.P</th>
-      <td><p>atmospheric pressure, default 1e5 (kPa).</p></td>
-    </tr>
-    <tr>
-      <th>alpha</th>
-      <td><p>atmospheric transmittance, default 0.85.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a <code>list</code> structure with components:</p><ul>
-<li><p>'I.dir'Direct radiation (\(\mu\) mol \(m^{-2}s^{-1}\)</p></li>
-<li><p>'I.diff'Indirect (diffuse) radiation (\(\mu\) mol\(m^{-2}s^{-1}\)</p></li>
-<li><p>'cos.th'cosine of \(\theta\), solar zenith angle.</p></li>
-<li><p>'propIdir'proportion of direct radiation.</p></li>
-<li><p>'propIdiff'proportion of indirect (diffuse) radiation.</p></li>
-</ul>
-
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>lat</th>
+              <td><p>the latitude, default is 40 (Urbana, IL, U.S.).</p></td>
+            </tr>
+            <tr>
+              <th>DOY</th>
+              <td><p>the day of the year (1--365), default 190.</p></td>
+            </tr>
+            <tr>
+              <th>t.d</th>
+              <td><p>time of the day in hours (0--23), default 12.</p></td>
+            </tr>
+            <tr>
+              <th>t.sn</th>
+              <td><p>time of solar noon, default 12.</p></td>
+            </tr>
+            <tr>
+              <th>atm.P</th>
+              <td><p>atmospheric pressure, default 1e5 (kPa).</p></td>
+            </tr>
+            <tr>
+              <th>alpha</th>
+              <td><p>atmospheric transmittance, default 0.85.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>a <code>list</code> structure with components:</p>
+          <ul>
+            <li>
+              <p>'I.dir'Direct radiation (\(\mu\) mol \(m^{-2}s^{-1}\)</p>
+            </li>
+            <li>
+              <p>
+                'I.diff'Indirect (diffuse) radiation (\(\mu\)
+                mol\(m^{-2}s^{-1}\)
+              </p>
+            </li>
+            <li><p>'cos.th'cosine of \(\theta\), solar zenith angle.</p></li>
+            <li><p>'propIdir'proportion of direct radiation.</p></li>
+            <li>
+              <p>'propIdiff'proportion of indirect (diffuse) radiation.</p>
+            </li>
           </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-  </div>
-</div>
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
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+      property="og:description"
+      content="This function does the heavy lifting in the final
              function of the tdm workflow titled predict_subdaily_met(). It uses a linear
              regression approach by generating the hourly values from the coarse data of
              the file the user selects to downscale based on the hourly models and betas
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+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                        >UNKNOWN TITLE</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>lm_ensemble_sims</h1>
-    
-    <div class="hidden name"><code>lm_ensemble_sims.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function does the heavy lifting in the final
-             function of the tdm workflow titled predict_subdaily_met(). It uses a linear
-             regression approach by generating the hourly values from the coarse data of
-             the file the user selects to downscale based on the hourly models and betas
-             generated by gen.subdaily.models().</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>lm_ensemble_sims</span>(<span class='no'>dat.mod</span>, <span class='no'>n.ens</span>, <span class='no'>path.model</span>, <span class='no'>direction.filter</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>lm_ensemble_sims</h1>
+
+            <div class="hidden name"><code>lm_ensemble_sims.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function does the heavy lifting in the final function of the
+              tdm workflow titled predict_subdaily_met(). It uses a linear
+              regression approach by generating the hourly values from the
+              coarse data of the file the user selects to downscale based on the
+              hourly models and betas generated by gen.subdaily.models().
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>lm_ensemble_sims</span>(<span class='no'>dat.mod</span>, <span class='no'>n.ens</span>, <span class='no'>path.model</span>, <span class='no'>direction.filter</span>,
   <span class='kw'>lags.list</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>lags.init</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>dat.train</span>, <span class='no'>precip.distribution</span>,
   <span class='kw'>force.sanity</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>sanity.tries</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fu'>Sys.time</span>(),
   <span class='kw'>print.progress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat.mod</th>
-      <td><p>- dataframe to be predicted at the time step of the training data</p></td>
-    </tr>
-    <tr>
-      <th>n.ens</th>
-      <td><p>- number of hourly ensemble members to generate</p></td>
-    </tr>
-    <tr>
-      <th>path.model</th>
-      <td><p>- path to where the training model &amp; betas is stored</p></td>
-    </tr>
-    <tr>
-      <th>direction.filter</th>
-      <td><p>- Whether the model will be filtered backward or forward in time. options = c("backward", "forward")
-(PalEON will go backward, anybody interested in the future will go forward)</p></td>
-    </tr>
-    <tr>
-      <th>lags.init</th>
-      <td><p>- a data frame of initialization parameters to match the data in dat.mod</p></td>
-    </tr>
-    <tr>
-      <th>dat.train</th>
-      <td><p>- the training data used to fit the model; needed for night/day in 
-surface_downwelling_shortwave_flux_in_air</p></td>
-    </tr>
-    <tr>
-      <th>precip.distribution</th>
-      <td><p>- a list with 2 sub-lists containing the number of observations with precip in the training data per day &amp; 
-the hour of max rain in the training data.  This will be used to help solve the "constant drizzle" problem</p></td>
-    </tr>
-    <tr>
-      <th>force.sanity</th>
-      <td><p>- (logical) do we force the data to meet sanity checks?</p></td>
-    </tr>
-    <tr>
-      <th>sanity.tries</th>
-      <td><p>- how many time should we try to predict a reasonable value before giving up?  We don't want to end up in an infinite loop</p></td>
-    </tr>
-    <tr>
-      <th>seed</th>
-      <td><p>- (optional) set the seed manually to allow reproducible results</p></td>
-    </tr>
-    <tr>
-      <th>print.progress</th>
-      <td><p>- if TRUE will print progress bar</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Linear Regression Ensemble Simulation
-Met downscaling function that predicts ensembles of downscaled meteorology</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other tdm - Temporally Downscale Meteorology: <code><a href='gen.subdaily.models.html'>gen.subdaily.models</a></code>,
-  <code><a href='model.train.html'>model.train</a></code>, <code><a href='nc.merge.html'>nc.merge</a></code>,
-  <code><a href='predict_subdaily_met.html'>predict_subdaily_met</a></code>,
-  <code><a href='save.betas.html'>save.betas</a></code>, <code><a href='save.model.html'>save.model</a></code>,
-  <code><a href='subdaily_pred.html'>subdaily_pred</a></code>,
-  <code><a href='temporal.downscale.functions.html'>temporal.downscale.functions</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat.mod</th>
+              <td>
+                <p>
+                  - dataframe to be predicted at the time step of the training
+                  data
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.ens</th>
+              <td><p>- number of hourly ensemble members to generate</p></td>
+            </tr>
+            <tr>
+              <th>path.model</th>
+              <td>
+                <p>- path to where the training model &amp; betas is stored</p>
+              </td>
+            </tr>
+            <tr>
+              <th>direction.filter</th>
+              <td>
+                <p>
+                  - Whether the model will be filtered backward or forward in
+                  time. options = c("backward", "forward") (PalEON will go
+                  backward, anybody interested in the future will go forward)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lags.init</th>
+              <td>
+                <p>
+                  - a data frame of initialization parameters to match the data
+                  in dat.mod
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>dat.train</th>
+              <td>
+                <p>
+                  - the training data used to fit the model; needed for
+                  night/day in surface_downwelling_shortwave_flux_in_air
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>precip.distribution</th>
+              <td>
+                <p>
+                  - a list with 2 sub-lists containing the number of
+                  observations with precip in the training data per day &amp;
+                  the hour of max rain in the training data. This will be used
+                  to help solve the "constant drizzle" problem
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>force.sanity</th>
+              <td>
+                <p>- (logical) do we force the data to meet sanity checks?</p>
+              </td>
+            </tr>
+            <tr>
+              <th>sanity.tries</th>
+              <td>
+                <p>
+                  - how many time should we try to predict a reasonable value
+                  before giving up? We don't want to end up in an infinite loop
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>seed</th>
+              <td>
+                <p>
+                  - (optional) set the seed manually to allow reproducible
+                  results
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>print.progress</th>
+              <td><p>- if TRUE will print progress bar</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Linear Regression Ensemble Simulation Met downscaling function that
+            predicts ensembles of downscaled meteorology
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other tdm - Temporally Downscale Meteorology:
+              <code
+                ><a href="gen.subdaily.models.html"
+                  >gen.subdaily.models</a
+                ></code
+              >, <code><a href="model.train.html">model.train</a></code
+              >, <code><a href="nc.merge.html">nc.merge</a></code
+              >,
+              <code
+                ><a href="predict_subdaily_met.html"
+                  >predict_subdaily_met</a
+                ></code
+              >, <code><a href="save.betas.html">save.betas</a></code
+              >, <code><a href="save.model.html">save.model</a></code
+              >, <code><a href="subdaily_pred.html">subdaily_pred</a></code
+              >,
+              <code
+                ><a href="temporal.downscale.functions.html"
+                  >temporal.downscale.functions</a
+                ></code
+              >
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson, James Simkins
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson, James Simkins
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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diff --git a/modules/data.atmosphere/docs/reference/load.cfmet.html b/modules/data.atmosphere/docs/reference/load.cfmet.html
index 9f24f54..0930549 100644
--- a/modules/data.atmosphere/docs/reference/load.cfmet.html
+++ b/modules/data.atmosphere/docs/reference/load.cfmet.html
@@ -2,196 +2,255 @@
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+
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+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="load CF met — load.cfmet" />
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+      content="Load met data from PEcAn formatted met driver"
+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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-    Articles
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-    <span class="caret"></span>
-  </a>
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-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
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+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
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+                    role="button"
+                    aria-expanded="false"
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>load CF met</h1>
-    
-    <div class="hidden name"><code>load.cfmet.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Load met data from PEcAn formatted met driver</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>load.cfmet</span>(<span class='no'>met.nc</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>start.date</span>, <span class='no'>end.date</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>met.nc</th>
-      <td><p>object of class ncdf4 representing an open CF compliant, PEcAn standard netcdf file with met data</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>numeric value of latutude</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>numeric value of longitude</p></td>
-    </tr>
-    <tr>
-      <th>start.date</th>
-      <td><p>format is 'YYYY-MM-DD'</p></td>
-    </tr>
-    <tr>
-      <th>end.date</th>
-      <td><p>format is 'YYYY-MM-DD'</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data.table of met data</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>subsets a PEcAn formatted met driver file and converts to a data.table / data.frame object</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load CF met</h1>
+
+            <div class="hidden name"><code>load.cfmet.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Load met data from PEcAn formatted met driver</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load.cfmet</span>(<span class='no'>met.nc</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>start.date</span>, <span class='no'>end.date</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>met.nc</th>
+              <td>
+                <p>
+                  object of class ncdf4 representing an open CF compliant, PEcAn
+                  standard netcdf file with met data
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>numeric value of latutude</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>numeric value of longitude</p></td>
+            </tr>
+            <tr>
+              <th>start.date</th>
+              <td><p>format is 'YYYY-MM-DD'</p></td>
+            </tr>
+            <tr>
+              <th>end.date</th>
+              <td><p>format is 'YYYY-MM-DD'</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>data.table of met data</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            subsets a PEcAn formatted met driver file and converts to a
+            data.table / data.frame object
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
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index 6225c41..92021b5 100644
--- a/modules/data.atmosphere/docs/reference/merge_met_variable.html
+++ b/modules/data.atmosphere/docs/reference/merge_met_variable.html
@@ -2,179 +2,260 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Merge a new met variable from an external file (e.g. CO2) into existing met files</h1>
-    
-    <div class="hidden name"><code>merge_met_variable.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Merge a new met variable from an external file (e.g. CO2) into existing met files</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>merge_met_variable</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>merge.file</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Merge a new met variable from an external file (e.g. CO2) into
+              existing met files
+            </h1>
+
+            <div class="hidden name"><code>merge_met_variable.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Merge a new met variable from an external file (e.g. CO2) into
+              existing met files
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>merge_met_variable</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>merge.file</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>path to original data</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of original data</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>merge.file</th>
-      <td><p>path of file to be merged in</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: replace output file if it already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical: should <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package'>ncdf4</a></code> functions
-print debugging information as they run?</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Currently modifies the files IN PLACE rather than creating a new copy of the files an a new DB record. 
-Currently unit and name checking only implemented for CO2. 
-Currently does not yet support merge data that has lat/lon
-New variable only has time dimension and thus MIGHT break downstream code....</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>path to original data</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of original data</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>merge.file</th>
+              <td><p>path of file to be merged in</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical: replace output file if it already exists?</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical: should
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package"
+                      >ncdf4</a
+                    ></code
+                  >
+                  functions print debugging information as they run?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Currently modifies the files IN PLACE rather than creating a new
+            copy of the files an a new DB record. Currently unit and name
+            checking only implemented for CO2. Currently does not yet support
+            merge data that has lat/lon New variable only has time dimension and
+            thus MIGHT break downstream code....
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>in.path</span>    <span class='kw'>&lt;-</span> <span class='st'>"~/paleon/PalEONregional_CF_site_1-24047/"</span>
 <span class='no'>in.prefix</span>  <span class='kw'>&lt;-</span> <span class='st'>""</span>
 <span class='no'>outfolder</span>  <span class='kw'>&lt;-</span> <span class='st'>"~/paleon/metTest/"</span>
@@ -187,34 +268,30 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='fu'>merge_met_variable</span>(<span class='no'>in.path</span>,<span class='no'>in.prefix</span>,<span class='no'>start_date</span>,<span class='no'>end_date</span>,<span class='no'>merge.file</span>,<span class='no'>overwrite</span>,<span class='no'>verbose</span>)
 <span class='kw pkg'>PEcAn.DALEC</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.DALEC/topics/met2model.DALEC'>met2model.DALEC</a></span>(<span class='no'>in.path</span>,<span class='no'>in.prefix</span>,<span class='no'>outfolder</span>,<span class='no'>start_date</span>,<span class='no'>end_date</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+            <li><a href="#examples">Examples</a></li>
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index 517e316..614cc78 100644
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+++ b/modules/data.atmosphere/docs/reference/met.process.html
@@ -2,212 +2,282 @@
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+                        station</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met.process</h1>
-    
-    <div class="hidden name"><code>met.process.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met.process</h1>
 
-    <div class="ref-description">
-    
-    <p>met.process</p>
-    
-    </div>
+            <div class="hidden name"><code>met.process.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>met.process</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>met.process</span>(<span class='no'>site</span>, <span class='no'>input_met</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>model</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>met.process</span>(<span class='no'>site</span>, <span class='no'>input_met</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>model</span>,
   <span class='kw'>host</span> <span class='kw'>=</span> <span class='st'>"localhost"</span>, <span class='no'>dbparms</span>, <span class='no'>dir</span>, <span class='kw'>browndog</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>spin</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>site</th>
-      <td><p>Site info from settings file</p></td>
-    </tr>
-    <tr>
-      <th>input_met</th>
-      <td><p>Which data source to process.</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>model_type name</p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>Host info from settings file</p></td>
-    </tr>
-    <tr>
-      <th>dbparms</th>
-      <td><p>database settings from settings file</p></td>
-    </tr>
-    <tr>
-      <th>dir</th>
-      <td><p>directory to write outputs to</p></td>
-    </tr>
-    <tr>
-      <th>spin</th>
-      <td><p>spin-up settings passed to model-specific met2model. List containing nyear (number of years of spin-up), nsample (first n years to cycle), and resample (TRUE/FALSE)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>Whether to force met.process to proceed.</p>
-<p>`overwrite` may be a list with individual components corresponding to 
-       `download`, `met2cf`, `standardize`, and `met2model`. If it is instead a simple boolean,
-       the default behavior for `overwrite=FALSE` is to overwrite nothing, as you might expect.
-       Note however that the default behavior for `overwrite=TRUE` is to overwrite everything
-       *except* raw met downloads. I.e., it corresponds to:</p>
-<p>list(download = FALSE, met2cf = TRUE, standardize = TRUE,  met2model = TRUE)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Elizabeth Cowdery, Michael Dietze, Ankur Desai, James Simkins, Ryan Kelly
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>site</th>
+              <td><p>Site info from settings file</p></td>
+            </tr>
+            <tr>
+              <th>input_met</th>
+              <td><p>Which data source to process.</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td><p>model_type name</p></td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td><p>Host info from settings file</p></td>
+            </tr>
+            <tr>
+              <th>dbparms</th>
+              <td><p>database settings from settings file</p></td>
+            </tr>
+            <tr>
+              <th>dir</th>
+              <td><p>directory to write outputs to</p></td>
+            </tr>
+            <tr>
+              <th>spin</th>
+              <td>
+                <p>
+                  spin-up settings passed to model-specific met2model. List
+                  containing nyear (number of years of spin-up), nsample (first
+                  n years to cycle), and resample (TRUE/FALSE)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>Whether to force met.process to proceed.</p>
+                <p>
+                  `overwrite` may be a list with individual components
+                  corresponding to `download`, `met2cf`, `standardize`, and
+                  `met2model`. If it is instead a simple boolean, the default
+                  behavior for `overwrite=FALSE` is to overwrite nothing, as you
+                  might expect. Note however that the default behavior for
+                  `overwrite=TRUE` is to overwrite everything *except* raw met
+                  downloads. I.e., it corresponds to:
+                </p>
+                <p>
+                  list(download = FALSE, met2cf = TRUE, standardize = TRUE,
+                  met2model = TRUE)
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Elizabeth Cowdery, Michael Dietze, Ankur Desai, James Simkins, Ryan
+          Kelly
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met.process.stage</h1>
-    
-    <div class="hidden name"><code>met.process.stage.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>met.process.stage</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>met.process.stage</span>(<span class='no'>input.id</span>, <span class='no'>raw.id</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>raw.id</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Elizabeth Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met.process.stage</h1>
+
+            <div class="hidden name"><code>met.process.stage.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>met.process.stage</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>met.process.stage</span>(<span class='no'>input.id</span>, <span class='no'>raw.id</span>, <span class='no'>con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>raw.id</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Elizabeth Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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-  
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+    </div>
   </body>
 </html>
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diff --git a/modules/data.atmosphere/docs/reference/met2CF.ALMA.html b/modules/data.atmosphere/docs/reference/met2CF.ALMA.html
index 2d9f3c6..d7c8018 100644
--- a/modules/data.atmosphere/docs/reference/met2CF.ALMA.html
+++ b/modules/data.atmosphere/docs/reference/met2CF.ALMA.html
@@ -2,189 +2,249 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="met2CF.ALMA — met2CF.ALMA" />
-
-<meta property="og:description" content="Get meteorology variables from ALMA netCDF files and convert to netCDF CF format" />
-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>met2CF.ALMA — met2CF.ALMA • PEcAn.data.atmosphere</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:description"
+      content="Get meteorology variables from ALMA netCDF files and convert to netCDF CF format"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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-    </li>
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+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2CF.ALMA</h1>
-    
-    <div class="hidden name"><code>met2CF.ALMA.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2CF.ALMA</h1>
 
-    <div class="ref-description">
-    
-    <p>Get meteorology variables from ALMA netCDF files and convert to netCDF CF format</p>
-    
-    </div>
+            <div class="hidden name"><code>met2CF.ALMA.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2CF.ALMA</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Get meteorology variables from ALMA netCDF files and convert to
+              netCDF CF format
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2CF.ALMA</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/met2CF.Ameriflux.html b/modules/data.atmosphere/docs/reference/met2CF.Ameriflux.html
index 8c089a2..439bed6 100644
--- a/modules/data.atmosphere/docs/reference/met2CF.Ameriflux.html
+++ b/modules/data.atmosphere/docs/reference/met2CF.Ameriflux.html
@@ -2,193 +2,253 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>met2CF.Ameriflux — met2CF.Ameriflux • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
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+    ></script>
+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    />
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+                  >PEcAn.data.atmosphere</a
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+                  title="Released package"
+                  >1.6.0</span
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
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+                  </ul>
+                </li>
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+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2CF.Ameriflux</h1>
-    
-    <div class="hidden name"><code>met2CF.Ameriflux.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2CF.Ameriflux</h1>
 
-    <div class="ref-description">
-    
-    <p>Get meteorology variables from Ameriflux L2 netCDF files and convert to netCDF CF format</p>
-    
-    </div>
+            <div class="hidden name"><code>met2CF.Ameriflux.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2CF.Ameriflux</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should ouput of function be extra verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Josh Mantooth, Mike Dietze, Elizabeth Cowdery, Ankur Desai
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Get meteorology variables from Ameriflux L2 netCDF files and
+              convert to netCDF CF format
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2CF.Ameriflux</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should ouput of function be extra verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Josh Mantooth, Mike Dietze, Elizabeth Cowdery, Ankur Desai
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
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 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/met2CF.AmerifluxLBL.html b/modules/data.atmosphere/docs/reference/met2CF.AmerifluxLBL.html
index 162dc3d..5419acb 100644
--- a/modules/data.atmosphere/docs/reference/met2CF.AmerifluxLBL.html
+++ b/modules/data.atmosphere/docs/reference/met2CF.AmerifluxLBL.html
@@ -2,214 +2,283 @@
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      met2CF.AmerifluxLBL — met2CF.AmerifluxLBL • PEcAn.data.atmosphere
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+      content="met2CF.AmerifluxLBL — met2CF.AmerifluxLBL"
+    />
+
+    <meta
+      property="og:description"
+      content="Get meteorology variables from Ameriflux LBL and convert to netCDF CF format"
+    />
+    <meta name="twitter:card" content="summary" />
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-    Articles
-     
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-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2CF.AmerifluxLBL</h1>
-    
-    <div class="hidden name"><code>met2CF.AmerifluxLBL.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2CF.AmerifluxLBL</h1>
 
-    <div class="ref-description">
-    
-    <p>Get meteorology variables from Ameriflux LBL and convert to netCDF CF format</p>
-    
-    </div>
+            <div class="hidden name"><code>met2CF.AmerifluxLBL.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2CF.AmerifluxLBL</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='no'>format</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>format</th>
-      <td><p>is data frame or list with elements as described below
-The AmerifluxLBL format is Bety record 5000000002
-which could be returned from PEcAn.DB::query.format.vars(format.id=5000000002)
-format is output from db/R/query.format.vars, and should have:
-  REQUIRED:
-  format$lat = latitude of site
-  format$lon = longitude of site
-  format$header = number of lines of header
-  format$vars is a data.frame with lists of information for each variable to read, at least airT is required
-    format$vars$input_name = Name in CSV file
-    format$vars$input_units = Units in CSV file
-    format$vars$bety_name = Name in BETY
-  OPTIONAL:
-  format$na.strings = list of missing values to convert to NA, such as -9999
-  format$skip = lines to skip excluding header
-  format$vars$column_number = Column number in CSV file (optional, will use header name first)
-Columns with NA for bety variable name are dropped. 
-Units for datetime field are the lubridate function that will be used to parse the date (e.g. <code>ymd_hms</code> or <code>mdy_hm</code>).</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should ouput of function be extra verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Ankur Desai
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Get meteorology variables from Ameriflux LBL and convert to netCDF
+              CF format
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2CF.AmerifluxLBL</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='no'>format</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>format</th>
+              <td>
+                <p>
+                  is data frame or list with elements as described below The
+                  AmerifluxLBL format is Bety record 5000000002 which could be
+                  returned from
+                  PEcAn.DB::query.format.vars(format.id=5000000002) format is
+                  output from db/R/query.format.vars, and should have: REQUIRED:
+                  format$lat = latitude of site format$lon = longitude of site
+                  format$header = number of lines of header format$vars is a
+                  data.frame with lists of information for each variable to
+                  read, at least airT is required format$vars$input_name = Name
+                  in CSV file format$vars$input_units = Units in CSV file
+                  format$vars$bety_name = Name in BETY OPTIONAL:
+                  format$na.strings = list of missing values to convert to NA,
+                  such as -9999 format$skip = lines to skip excluding header
+                  format$vars$column_number = Column number in CSV file
+                  (optional, will use header name first) Columns with NA for
+                  bety variable name are dropped. Units for datetime field are
+                  the lubridate function that will be used to parse the date
+                  (e.g. <code>ymd_hms</code> or <code>mdy_hm</code>).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should ouput of function be extra verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Ankur Desai
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/met2CF.FACE.html b/modules/data.atmosphere/docs/reference/met2CF.FACE.html
index 21fa58a..898d93e 100644
--- a/modules/data.atmosphere/docs/reference/met2CF.FACE.html
+++ b/modules/data.atmosphere/docs/reference/met2CF.FACE.html
@@ -2,159 +2,202 @@
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 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      convert FACE files to CF files — met2CF.FACE • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
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+    <script src="../pkgdown.js"></script>
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+    <![endif]-->
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+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>convert FACE files to CF files</h1>
-    
-    <div class="hidden name"><code>met2CF.FACE.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>convert FACE files to CF files</h1>
 
-    <div class="ref-description">
-    
-    <p>convert FACE files to CF files</p>
-    
-    </div>
+            <div class="hidden name"><code>met2CF.FACE.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2CF.FACE</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>input.id</span>,
-  <span class='no'>site</span>, <span class='no'>format</span>, <span class='no'>...</span>)</pre>
-        
+          <div class="ref-description">
+            <p>convert FACE files to CF files</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>met2CF.FACE</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>input.id</span>,
+  <span class='no'>site</span>, <span class='no'>format</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Elizabeth Cowdery
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Elizabeth Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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diff --git a/modules/data.atmosphere/docs/reference/met2CF.Geostreams.html b/modules/data.atmosphere/docs/reference/met2CF.Geostreams.html
index 3ba4b69..f86e715 100644
--- a/modules/data.atmosphere/docs/reference/met2CF.Geostreams.html
+++ b/modules/data.atmosphere/docs/reference/met2CF.Geostreams.html
@@ -2,194 +2,273 @@
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+      Convert geostreams JSON to CF met file — met2CF.Geostreams •
+      PEcAn.data.atmosphere
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
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+                  title="Released package"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert geostreams JSON to CF met file</h1>
-    
-    <div class="hidden name"><code>met2CF.Geostreams.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert geostreams JSON to CF met file</h1>
 
-    <div class="ref-description">
-    
-    <p>Convert geostreams JSON to CF met file</p>
-    
-    </div>
+            <div class="hidden name"><code>met2CF.Geostreams.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2CF.Geostreams</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>directory containing Geostreams JSON file(s) to be converted</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>initial portion of input filenames (everything before the dates)</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>directory where nc output files should be written. Will be created if necessary</p></td>
-    </tr>
-    <tr>
-      <th>start_date, end_date</th>
-      <td><p>beginning and end of run, YYYY-MM-DD.</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: Regenerate existing files of the same name?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical, passed on to <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/nc_create'>nc_create</a></code> 
-to control how chatty it should be during netCDF creation</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>other arguments, currently ignored</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Harsh Agrawal, Chris Black
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Convert geostreams JSON to CF met file</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2CF.Geostreams</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td>
+                <p>
+                  directory containing Geostreams JSON file(s) to be converted
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td>
+                <p>
+                  initial portion of input filenames (everything before the
+                  dates)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td>
+                <p>
+                  directory where nc output files should be written. Will be
+                  created if necessary
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>start_date, end_date</th>
+              <td><p>beginning and end of run, YYYY-MM-DD.</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>logical: Regenerate existing files of the same name?</p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical, passed on to
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/nc_create"
+                      >nc_create</a
+                    ></code
+                  >
+                  to control how chatty it should be during netCDF creation
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>other arguments, currently ignored</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Harsh Agrawal, Chris Black
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/met2CF.NARR.html b/modules/data.atmosphere/docs/reference/met2CF.NARR.html
index d81b950..05ba246 100644
--- a/modules/data.atmosphere/docs/reference/met2CF.NARR.html
+++ b/modules/data.atmosphere/docs/reference/met2CF.NARR.html
@@ -2,181 +2,235 @@
 <!DOCTYPE html>
 <html>
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
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+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="met2CF.NARR — met2CF.NARR" />
+
+    <meta property="og:description" content="Convert NARR files to CF files" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+              <span class="navbar-brand">
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+                  >PEcAn.data.atmosphere</a
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+                  class="label label-default"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2CF.NARR</h1>
-    
-    <div class="hidden name"><code>met2CF.NARR.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2CF.NARR</h1>
 
-    <div class="ref-description">
-    
-    <p>Convert NARR files to CF files</p>
-    
-    </div>
+            <div class="hidden name"><code>met2CF.NARR.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2CF.NARR</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should ouput of function be extra verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Elizabeth Cowdery, Rob Kooper
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Convert NARR files to CF files</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2CF.NARR</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should ouput of function be extra verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Elizabeth Cowdery, Rob Kooper
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/met2CF.PalEON.html b/modules/data.atmosphere/docs/reference/met2CF.PalEON.html
index efc1771..492ef4b 100644
--- a/modules/data.atmosphere/docs/reference/met2CF.PalEON.html
+++ b/modules/data.atmosphere/docs/reference/met2CF.PalEON.html
@@ -2,189 +2,249 @@
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-
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-<meta property="og:title" content="met2CF.PalEON — met2CF.PalEON" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
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+
+    <meta property="og:title" content="met2CF.PalEON — met2CF.PalEON" />
+
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+      property="og:description"
+      content="Get meteorology variables from PalEON netCDF files and convert to netCDF CF format"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
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+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+                <li class="dropdown">
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+                    data-toggle="dropdown"
+                    role="button"
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+                  >
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2CF.PalEON</h1>
-    
-    <div class="hidden name"><code>met2CF.PalEON.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2CF.PalEON</h1>
 
-    <div class="ref-description">
-    
-    <p>Get meteorology variables from PalEON netCDF files and convert to netCDF CF format</p>
-    
-    </div>
+            <div class="hidden name"><code>met2CF.PalEON.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2CF.PalEON</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>lat</span>,
-  <span class='no'>lon</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Get meteorology variables from PalEON netCDF files and convert to
+              netCDF CF format
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>met2CF.PalEON</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>lat</span>,
+  <span class='no'>lon</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/met2CF.PalEONregional.html b/modules/data.atmosphere/docs/reference/met2CF.PalEONregional.html
index a9de2fb..d6abab1 100644
--- a/modules/data.atmosphere/docs/reference/met2CF.PalEONregional.html
+++ b/modules/data.atmosphere/docs/reference/met2CF.PalEONregional.html
@@ -2,220 +2,296 @@
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-Get meteorology variables from PalEON netCDF files and convert to netCDF CF format" />
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      met2CF.PalEONregional — met2CF.PalEONregional • PEcAn.data.atmosphere
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="met2CF.PalEONregional — met2CF.PalEONregional"
+    />
+
+    <meta
+      property="og:description"
+      content="Get meteorology variables from PalEON netCDF files and convert to netCDF CF format
+Get meteorology variables from PalEON netCDF files and convert to netCDF CF format"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
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-  <a href="../index.html">
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-  <a href="../reference/index.html">Reference</a>
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
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+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+            </div>
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+              <ul class="nav navbar-nav">
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+                  <a href="../reference/index.html">Reference</a>
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+                    class="dropdown-toggle"
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+                    role="button"
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+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2CF.PalEONregional</h1>
-    
-    <div class="hidden name"><code>met2CF.PalEONregional.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get meteorology variables from PalEON netCDF files and convert to netCDF CF format</p>
-<p>Get meteorology variables from PalEON netCDF files and convert to netCDF CF format</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>met2CF.PalEONregional</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2CF.PalEONregional</h1>
+
+            <div class="hidden name"><code>met2CF.PalEONregional.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Get meteorology variables from PalEON netCDF files and convert to
+              netCDF CF format
+            </p>
+            <p>
+              Get meteorology variables from PalEON netCDF files and convert to
+              netCDF CF format
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>met2CF.PalEONregional</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
 
 <span class='fu'>met2CF.PalEONregional</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-Mike Dietze
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze Mike Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/met2CF.csv.html b/modules/data.atmosphere/docs/reference/met2CF.csv.html
index d7b0b5d..4480ddb 100644
--- a/modules/data.atmosphere/docs/reference/met2CF.csv.html
+++ b/modules/data.atmosphere/docs/reference/met2CF.csv.html
@@ -2,163 +2,220 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<![endif]-->
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+    <meta charset="utf-8" />
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>met2CF.csv — met2CF.csv • PEcAn.data.atmosphere</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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+                  >PEcAn.data.atmosphere</a
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met2CF.csv</h1>
-    
-    <div class="hidden name"><code>met2CF.csv.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met2CF.csv</h1>
 
-    <div class="ref-description">
-    
-    <p>met2CF.csv</p>
-    
-    </div>
+            <div class="hidden name"><code>met2CF.csv.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>met2CF.csv</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>format</span>,
+          <div class="ref-description">
+            <p>met2CF.csv</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>met2CF.csv</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>format</span>,
   <span class='kw'>lat</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>lon</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>nc_verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>format</th>
-      <td><p>data frame or list with elements as described below
-format is output from db/R/query.format.vars, and should have:
-  REQUIRED:
-  format$lat = latitude of site (unless passed by lat)
-  format$lon = longitude of site (unless passed by lon)
-  format$header = number of lines of header
-  format$vars is a data.frame with lists of information for each variable to read, at least airT is required
-    format$vars$input_name = Name in CSV file
-    format$vars$input_units = Units in CSV file
-    format$vars$bety_name = Name in BETY - see https://pecan.gitbooks.io/pecan-documentation/content/developers_guide/Adding-an-Input-Converter.html for allowable ones
-  OPTIONAL:
-  format$na.strings = list of missing values to convert to NA, such as -9999
-  format$skip = lines to skip excluding header
-  format$vars$column_number = Column number in CSV file (optional, will use header name first)
-Columns with NA for bety variable name are dropped. 
-Units for datetime field are the lubridate function that will be used to parse the date (e.g. <code>ymd_hms</code> or <code>mdy_hm</code>).</p></td>
-    </tr>
-    <tr>
-      <th>nc_verbose</th>
-      <td><p>logical: run ncvar_add in verbose mode?</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>format</th>
+              <td>
+                <p>
+                  data frame or list with elements as described below format is
+                  output from db/R/query.format.vars, and should have: REQUIRED:
+                  format$lat = latitude of site (unless passed by lat)
+                  format$lon = longitude of site (unless passed by lon)
+                  format$header = number of lines of header format$vars is a
+                  data.frame with lists of information for each variable to
+                  read, at least airT is required format$vars$input_name = Name
+                  in CSV file format$vars$input_units = Units in CSV file
+                  format$vars$bety_name = Name in BETY - see
+                  https://pecan.gitbooks.io/pecan-documentation/content/developers_guide/Adding-an-Input-Converter.html
+                  for allowable ones OPTIONAL: format$na.strings = list of
+                  missing values to convert to NA, such as -9999 format$skip =
+                  lines to skip excluding header format$vars$column_number =
+                  Column number in CSV file (optional, will use header name
+                  first) Columns with NA for bety variable name are dropped.
+                  Units for datetime field are the lubridate function that will
+                  be used to parse the date (e.g. <code>ymd_hms</code> or
+                  <code>mdy_hm</code>).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>nc_verbose</th>
+              <td><p>logical: run ncvar_add in verbose mode?</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>bety</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>user</span><span class='kw'>=</span><span class='st'>'bety'</span>, <span class='kw'>password</span><span class='kw'>=</span><span class='st'>'bety'</span>, <span class='kw'>host</span><span class='kw'>=</span><span class='st'>'localhost'</span>,
   <span class='kw'>dbname</span><span class='kw'>=</span><span class='st'>'bety'</span>, <span class='kw'>driver</span><span class='kw'>=</span><span class='st'>'PostgreSQL'</span>,<span class='kw'>write</span><span class='kw'>=</span><span class='fl'>TRUE</span>)
 <span class='no'>con</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>PEcAn.DB</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.DB/topics/db.open'>db.open</a></span>(<span class='no'>bety</span>)
@@ -179,36 +236,32 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
   <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>format</span>,
   <span class='kw'>overwrite</span><span class='kw'>=</span><span class='fl'>TRUE</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze, David LeBauer, Ankur Desai
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Mike Dietze, David LeBauer, Ankur Desai
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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-
diff --git a/modules/data.atmosphere/docs/reference/met_temporal_downscale.Gaussian_ensemble.html b/modules/data.atmosphere/docs/reference/met_temporal_downscale.Gaussian_ensemble.html
index c6cf07f..6db4047 100644
--- a/modules/data.atmosphere/docs/reference/met_temporal_downscale.Gaussian_ensemble.html
+++ b/modules/data.atmosphere/docs/reference/met_temporal_downscale.Gaussian_ensemble.html
@@ -2,210 +2,301 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="met_temporal_downscale.Gaussian_ensemble — met_temporal_downscale.Gaussian_ensemble" />
-
-<meta property="og:description" content="met_temporal_downscale.Gaussian_ensemble takes source data and a training dataset from the same site and temporally 
-   downscales the source dataset to the resolution of the training dataset based on statistics of the training dataset." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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+      content="met_temporal_downscale.Gaussian_ensemble takes source data and a training dataset from the same site and temporally 
+   downscales the source dataset to the resolution of the training dataset based on statistics of the training dataset."
+    />
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+                  >1.6.0</span
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
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+                        >UNKNOWN TITLE</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>met_temporal_downscale.Gaussian_ensemble</h1>
-    
-    <div class="hidden name"><code>met_temporal_downscale.Gaussian_ensemble.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>met_temporal_downscale.Gaussian_ensemble takes source data and a training dataset from the same site and temporally 
-   downscales the source dataset to the resolution of the training dataset based on statistics of the training dataset.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>met_temporal_downscale.Gaussian_ensemble</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>met_temporal_downscale.Gaussian_ensemble</h1>
+
+            <div class="hidden name">
+              <code>met_temporal_downscale.Gaussian_ensemble.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              met_temporal_downscale.Gaussian_ensemble takes source data and a
+              training dataset from the same site and temporally downscales the
+              source dataset to the resolution of the training dataset based on
+              statistics of the training dataset.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>met_temporal_downscale.Gaussian_ensemble</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>,
   <span class='no'>input_met</span>, <span class='no'>train_met</span>, <span class='no'>site_id</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>swdn_method</span> <span class='kw'>=</span> <span class='st'>"sine"</span>, <span class='kw'>n_ens</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>w_len</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>utc_diff</span> <span class='kw'>=</span> -<span class='fl'>6</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>input_met</th>
-      <td><p>- the source dataset that will temporally downscaled by the train_met dataset</p></td>
-    </tr>
-    <tr>
-      <th>train_met</th>
-      <td><p>- the observed dataset that will be used to train the modeled dataset in NC format. i.e. Flux Tower dataset 
-(see download.Fluxnet2015 or download.Ameriflux)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: replace output file if it already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical: should <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package'>ncdf4</a></code> functions
-print debugging information as they run?</p></td>
-    </tr>
-    <tr>
-      <th>swdn_method</th>
-      <td><p>- Downwelling shortwave flux in air downscaling method (options are "sine", "spline", and "Waichler")</p></td>
-    </tr>
-    <tr>
-      <th>n_ens</th>
-      <td><p>- numeric value with the number of ensembles to run</p></td>
-    </tr>
-    <tr>
-      <th>w_len</th>
-      <td><p>- numeric value that is the window length in days</p></td>
-    </tr>
-    <tr>
-      <th>utc_diff</th>
-      <td><p>- numeric value in HOURS that is local standard time difference from UTC time. CST is -6</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-James Simkins
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>input_met</th>
+              <td>
+                <p>
+                  - the source dataset that will temporally downscaled by the
+                  train_met dataset
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>train_met</th>
+              <td>
+                <p>
+                  - the observed dataset that will be used to train the modeled
+                  dataset in NC format. i.e. Flux Tower dataset (see
+                  download.Fluxnet2015 or download.Ameriflux)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical: replace output file if it already exists?</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical: should
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package"
+                      >ncdf4</a
+                    ></code
+                  >
+                  functions print debugging information as they run?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>swdn_method</th>
+              <td>
+                <p>
+                  - Downwelling shortwave flux in air downscaling method
+                  (options are "sine", "spline", and "Waichler")
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n_ens</th>
+              <td>
+                <p>- numeric value with the number of ensembles to run</p>
+              </td>
+            </tr>
+            <tr>
+              <th>w_len</th>
+              <td><p>- numeric value that is the window length in days</p></td>
+            </tr>
+            <tr>
+              <th>utc_diff</th>
+              <td>
+                <p>
+                  - numeric value in HOURS that is local standard time
+                  difference from UTC time. CST is -6
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          James Simkins
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
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 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/metgapfill.NOAA_GEFS.html b/modules/data.atmosphere/docs/reference/metgapfill.NOAA_GEFS.html
index c7d2a42..6603f36 100644
--- a/modules/data.atmosphere/docs/reference/metgapfill.NOAA_GEFS.html
+++ b/modules/data.atmosphere/docs/reference/metgapfill.NOAA_GEFS.html
@@ -2,202 +2,263 @@
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+      PEcAn.data.atmosphere
+    </title>
+
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+    ></script>
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
-    </li>
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+          <div class="container">
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+                type="button"
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
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+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Gapfill NOAA_GEFS weather data</h1>
-    
-    <div class="hidden name"><code>metgapfill.NOAA_GEFS.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Gapfill NOAA_GEFS weather data</h1>
 
-    <div class="ref-description">
-    
-    <p>Gapfill NOAA_GEFS weather data</p>
-    
-    </div>
+            <div class="hidden name"><code>metgapfill.NOAA_GEFS.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Gapfill NOAA_GEFS weather data</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>metgapfill.NOAA_GEFS</span>(<span class='no'>in.prefix</span>, <span class='no'>in.path</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>metgapfill.NOAA_GEFS</span>(<span class='no'>in.prefix</span>, <span class='no'>in.path</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>the met file name</p></td>
-    </tr>
-    <tr>
-      <th>in.path</th>
-      <td><p>The location of the file</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>The place to write the output file to</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>The start date of the contents of the file</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>The end date of the contents of the file</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>Whether or not to overwrite the output file if it exists or not</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>Passed to nc writing functions for additional output</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="purpose"><a class="anchor" href="#purpose"></a>Purpose</h2>
-
-    
-    <p>This function uses simple methods to gapfill NOAA GEFS met data
-Temperature and Precipitation are gapfilled with spline; other data sources are gapfilled with
-using linear models fitted to other fitted data.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#purpose">Purpose</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>the met file name</p></td>
+            </tr>
+            <tr>
+              <th>in.path</th>
+              <td><p>The location of the file</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>The place to write the output file to</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>The start date of the contents of the file</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>The end date of the contents of the file</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td>
+                <p>
+                  Whether or not to overwrite the output file if it exists or
+                  not
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>Passed to nc writing functions for additional output</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="purpose">
+            <a class="anchor" href="#purpose"></a>Purpose
+          </h2>
+
+          <p>
+            This function uses simple methods to gapfill NOAA GEFS met data
+            Temperature and Precipitation are gapfilled with spline; other data
+            sources are gapfilled with using linear models fitted to other
+            fitted data.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#purpose">Purpose</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Luke Dramko
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Luke Dramko
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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 </html>
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diff --git a/modules/data.atmosphere/docs/reference/metgapfill.html b/modules/data.atmosphere/docs/reference/metgapfill.html
index 932c216..9f6e89b 100644
--- a/modules/data.atmosphere/docs/reference/metgapfill.html
+++ b/modules/data.atmosphere/docs/reference/metgapfill.html
@@ -2,217 +2,286 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Take an Ameriflux NetCDF file
-Fill missing met values using MDS approach using MPI-BGC REddyProc library
-Currently
-Future version: Choose which variables to gap fill
-Future version will first downscale and fill with NARR, then REddyProc — metgapfill • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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-
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Take an Ameriflux NetCDF file Fill missing met values using MDS approach
+      using MPI-BGC REddyProc library Currently Future version: Choose which
+      variables to gap fill Future version will first downscale and fill with
+      NARR, then REddyProc — metgapfill • PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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 Fill missing met values using MDS approach using MPI-BGC REddyProc library
 Currently
 Future version: Choose which variables to gap fill
-Future version will first downscale and fill with NARR, then REddyProc — metgapfill" />
+Future version will first downscale and fill with NARR, then REddyProc — metgapfill"
+    />
 
-<meta property="og:description" content="Take an Ameriflux NetCDF file
+    <meta
+      property="og:description"
+      content="Take an Ameriflux NetCDF file
 Fill missing met values using MDS approach using MPI-BGC REddyProc library
 Currently
 Future version: Choose which variables to gap fill
-Future version will first downscale and fill with NARR, then REddyProc" />
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+Future version will first downscale and fill with NARR, then REddyProc"
+    />
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+    <![endif]-->
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+                  >PEcAn.data.atmosphere</a
+                >
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Take an Ameriflux NetCDF file
-Fill missing met values using MDS approach using MPI-BGC REddyProc library
-Currently
-Future version: Choose which variables to gap fill
-Future version will first downscale and fill with NARR, then REddyProc</h1>
-    
-    <div class="hidden name"><code>metgapfill.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Take an Ameriflux NetCDF file
-Fill missing met values using MDS approach using MPI-BGC REddyProc library
-Currently
-Future version: Choose which variables to gap fill
-Future version will first downscale and fill with NARR, then REddyProc</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>metgapfill</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>lst</span> <span class='kw'>=</span> <span class='fl'>0</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Take an Ameriflux NetCDF file Fill missing met values using MDS
+              approach using MPI-BGC REddyProc library Currently Future version:
+              Choose which variables to gap fill Future version will first
+              downscale and fill with NARR, then REddyProc
+            </h1>
+
+            <div class="hidden name"><code>metgapfill.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Take an Ameriflux NetCDF file Fill missing met values using MDS
+              approach using MPI-BGC REddyProc library Currently Future version:
+              Choose which variables to gap fill Future version will first
+              downscale and fill with NARR, then REddyProc
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>metgapfill</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>lst</span> <span class='kw'>=</span> <span class='fl'>0</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stord</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be downloaded (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>lst</th>
-      <td><p>is timezone offset from UTC, if timezone is available in time:units atribute in file, it will use that, default is to assume UTC</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should the function be very verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Ankur Desai
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stord</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be downloaded (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lst</th>
+              <td>
+                <p>
+                  is timezone offset from UTC, if timezone is available in
+                  time:units atribute in file, it will use that, default is to
+                  assume UTC
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should the function be very verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Ankur Desai
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/model.train.html b/modules/data.atmosphere/docs/reference/model.train.html
index d0898f1..1a470ab 100644
--- a/modules/data.atmosphere/docs/reference/model.train.html
+++ b/modules/data.atmosphere/docs/reference/model.train.html
@@ -2,206 +2,291 @@
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 <html>
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
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+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="model.train — model.train" />
+
+    <meta
+      property="og:description"
+      content="Function to create linear regression models for specific met
              variables. This is used in conjunction with temporal.downscale.functions()
              to generate linear regression statistics and save their output to be called
-             later in lm_ensemble_sims()." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<![endif]-->
+             later in lm_ensemble_sims()."
+    />
+    <meta name="twitter:card" content="summary" />
 
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
-    </li>
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-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
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-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+                <span class="icon-bar"></span>
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
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+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>model.train</h1>
-    
-    <div class="hidden name"><code>model.train.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to create linear regression models for specific met
-             variables. This is used in conjunction with temporal.downscale.functions()
-             to generate linear regression statistics and save their output to be called
-             later in lm_ensemble_sims().</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>model.train</span>(<span class='no'>dat.subset</span>, <span class='no'>v</span>, <span class='no'>n.beta</span>, <span class='kw'>resids</span> <span class='kw'>=</span> <span class='no'>resids</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>model.train</h1>
+
+            <div class="hidden name"><code>model.train.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to create linear regression models for specific met
+              variables. This is used in conjunction with
+              temporal.downscale.functions() to generate linear regression
+              statistics and save their output to be called later in
+              lm_ensemble_sims().
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>model.train</span>(<span class='no'>dat.subset</span>, <span class='no'>v</span>, <span class='no'>n.beta</span>, <span class='kw'>resids</span> <span class='kw'>=</span> <span class='no'>resids</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat.subset</th>
-      <td><p>data.frame containing lags, next, and downscale period data</p></td>
-    </tr>
-    <tr>
-      <th>n.beta</th>
-      <td><p>number of betas to pull from</p></td>
-    </tr>
-    <tr>
-      <th>resids</th>
-      <td><p>TRUE or FALSE, whether to use residuals or not</p></td>
-    </tr>
-    <tr>
-      <th>threshold</th>
-      <td><p>NULL except for surface_downwelling_shortwave_radiation, helps with our
-distinction between day and night (no shortwave without sunlight)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>TDM Model Train
-Linear regression calculations for specific met variables</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other tdm - Temporally Downscale Meteorology: <code><a href='gen.subdaily.models.html'>gen.subdaily.models</a></code>,
-  <code><a href='lm_ensemble_sims.html'>lm_ensemble_sims</a></code>, <code><a href='nc.merge.html'>nc.merge</a></code>,
-  <code><a href='predict_subdaily_met.html'>predict_subdaily_met</a></code>,
-  <code><a href='save.betas.html'>save.betas</a></code>, <code><a href='save.model.html'>save.model</a></code>,
-  <code><a href='subdaily_pred.html'>subdaily_pred</a></code>,
-  <code><a href='temporal.downscale.functions.html'>temporal.downscale.functions</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat.subset</th>
+              <td>
+                <p>
+                  data.frame containing lags, next, and downscale period data
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.beta</th>
+              <td><p>number of betas to pull from</p></td>
+            </tr>
+            <tr>
+              <th>resids</th>
+              <td><p>TRUE or FALSE, whether to use residuals or not</p></td>
+            </tr>
+            <tr>
+              <th>threshold</th>
+              <td>
+                <p>
+                  NULL except for surface_downwelling_shortwave_radiation, helps
+                  with our distinction between day and night (no shortwave
+                  without sunlight)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            TDM Model Train Linear regression calculations for specific met
+            variables
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other tdm - Temporally Downscale Meteorology:
+              <code
+                ><a href="gen.subdaily.models.html"
+                  >gen.subdaily.models</a
+                ></code
+              >,
+              <code><a href="lm_ensemble_sims.html">lm_ensemble_sims</a></code
+              >, <code><a href="nc.merge.html">nc.merge</a></code
+              >,
+              <code
+                ><a href="predict_subdaily_met.html"
+                  >predict_subdaily_met</a
+                ></code
+              >, <code><a href="save.betas.html">save.betas</a></code
+              >, <code><a href="save.model.html">save.model</a></code
+              >, <code><a href="subdaily_pred.html">subdaily_pred</a></code
+              >,
+              <code
+                ><a href="temporal.downscale.functions.html"
+                  >temporal.downscale.functions</a
+                ></code
+              >
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson, James Simkins
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson, James Simkins
+        </div>
+      </div>
 
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index 1b85799..2a2a254 100644
--- a/modules/data.atmosphere/docs/reference/narr_flx_vars.html
+++ b/modules/data.atmosphere/docs/reference/narr_flx_vars.html
@@ -2,164 +2,211 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>NARR flux and sfc variables</h1>
-    
-    <div class="hidden name"><code>narr_flx_vars.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>NARR flux and sfc variables</h1>
 
-    <div class="ref-description">
-    
-    <p>NARR flux and sfc variables</p>
-    
-    </div>
+            <div class="hidden name"><code>narr_flx_vars.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='no'>narr_flx_vars</span>
+          <div class="ref-description">
+            <p>NARR flux and sfc variables</p>
+          </div>
+
+          <pre class="usage"><span class='no'>narr_flx_vars</span>
 
 <span class='no'>narr_sfc_vars</span>
 
 <span class='no'>narr_all_vars</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 5 rows and 3 columns.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
+
+          <p>
+            An object of class <code>tbl_df</code> (inherits from
+            <code>tbl</code>, <code>data.frame</code>) with 5 rows and 3
+            columns.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
+          </ul>
+        </div>
+      </div>
 
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index 7173231..f7381ec 100644
--- a/modules/data.atmosphere/docs/reference/nc.merge.html
+++ b/modules/data.atmosphere/docs/reference/nc.merge.html
@@ -2,223 +2,320 @@
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              parses multiple netCDF files into one central training data file called 'dat.train_file'. This netCDF
              file will be used to generate the subdaily models in the next step of the workflow, generate.subdaily.models(). 
-             It is also called in tdm_predict_subdaily_met which is the final step of the tdm workflow." />
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
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+                    class="dropdown-toggle"
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>nc.merge</h1>
-    
-    <div class="hidden name"><code>nc.merge.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This is the 1st function for the tdm (Temporally Downscale Meteorology) workflow. The nc2dat.train function
-             parses multiple netCDF files into one central training data file called 'dat.train_file'. This netCDF
-             file will be used to generate the subdaily models in the next step of the workflow, generate.subdaily.models(). 
-             It is also called in tdm_predict_subdaily_met which is the final step of the tdm workflow.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>nc.merge</span>(<span class='no'>outfolder</span>, <span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>nc.merge</h1>
+
+            <div class="hidden name"><code>nc.merge.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This is the 1st function for the tdm (Temporally Downscale
+              Meteorology) workflow. The nc2dat.train function parses multiple
+              netCDF files into one central training data file called
+              'dat.train_file'. This netCDF file will be used to generate the
+              subdaily models in the next step of the workflow,
+              generate.subdaily.models(). It is also called in
+              tdm_predict_subdaily_met which is the final step of the tdm
+              workflow.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>nc.merge</span>(<span class='no'>outfolder</span>, <span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='kw'>upscale</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>- directory where output will be stored</p></td>
-    </tr>
-    <tr>
-      <th>in.path</th>
-      <td><p>- path of coarse model (e.g. GCM output)</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>- prefix of model string as character (e.g. IPSL.r1i1p1.rcp85)</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>- yyyy-mm-dd</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>- yyyy-mm-dd</p></td>
-    </tr>
-    <tr>
-      <th>upscale</th>
-      <td><p>- Upscale can either be set for FALSE (leave alone) or to the temporal resolution you want to aggregate to</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: replace output file if it already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical: should <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package'>ncdf4</a></code>
-functions print debugging information as they run?</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>nc.merge
-Parses multiple netCDF files into one central document for temporal downscaling procedure</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other tdm - Temporally Downscale Meteorology: <code><a href='gen.subdaily.models.html'>gen.subdaily.models</a></code>,
-  <code><a href='lm_ensemble_sims.html'>lm_ensemble_sims</a></code>,
-  <code><a href='model.train.html'>model.train</a></code>,
-  <code><a href='predict_subdaily_met.html'>predict_subdaily_met</a></code>,
-  <code><a href='save.betas.html'>save.betas</a></code>, <code><a href='save.model.html'>save.model</a></code>,
-  <code><a href='subdaily_pred.html'>subdaily_pred</a></code>,
-  <code><a href='temporal.downscale.functions.html'>temporal.downscale.functions</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>- directory where output will be stored</p></td>
+            </tr>
+            <tr>
+              <th>in.path</th>
+              <td><p>- path of coarse model (e.g. GCM output)</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td>
+                <p>
+                  - prefix of model string as character (e.g. IPSL.r1i1p1.rcp85)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>- yyyy-mm-dd</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>- yyyy-mm-dd</p></td>
+            </tr>
+            <tr>
+              <th>upscale</th>
+              <td>
+                <p>
+                  - Upscale can either be set for FALSE (leave alone) or to the
+                  temporal resolution you want to aggregate to
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical: replace output file if it already exists?</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical: should
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package"
+                      >ncdf4</a
+                    ></code
+                  >
+                  functions print debugging information as they run?
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            nc.merge Parses multiple netCDF files into one central document for
+            temporal downscaling procedure
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other tdm - Temporally Downscale Meteorology:
+              <code
+                ><a href="gen.subdaily.models.html"
+                  >gen.subdaily.models</a
+                ></code
+              >,
+              <code><a href="lm_ensemble_sims.html">lm_ensemble_sims</a></code
+              >, <code><a href="model.train.html">model.train</a></code
+              >,
+              <code
+                ><a href="predict_subdaily_met.html"
+                  >predict_subdaily_met</a
+                ></code
+              >, <code><a href="save.betas.html">save.betas</a></code
+              >, <code><a href="save.model.html">save.model</a></code
+              >, <code><a href="subdaily_pred.html">subdaily_pred</a></code
+              >,
+              <code
+                ><a href="temporal.downscale.functions.html"
+                  >temporal.downscale.functions</a
+                ></code
+              >
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-James Simkins, Christy Rollinson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          James Simkins, Christy Rollinson
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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index b8c3e48..75a1723 100644
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+++ b/modules/data.atmosphere/docs/reference/par2ppfd.html
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+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                        >UNKNOWN TITLE</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>par2ppfd</h1>
-    
-    <div class="hidden name"><code>par2ppfd.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>convert PAR to PPFD</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>par2ppfd</span>(<span class='no'>watts</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>watts</th>
-      <td><p>PAR (W / m2)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>PPFD (umol / m2 / s)</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Converts photosynthetically active radiation (PAR, units of Watts / m2) to
-photosynthetic photon flux density (PPFD) in units of umol / m2 / s
-From Campbell and Norman p151
-PPFD = PAR * (J/m2/s) * (1 mol / 2.35e5 J)
-2.35e5 J / mol is the energy content of solar radiation in the PAR waveband</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>par2ppfd</h1>
+
+            <div class="hidden name"><code>par2ppfd.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>convert PAR to PPFD</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>par2ppfd</span>(<span class='no'>watts</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>watts</th>
+              <td><p>PAR (W / m2)</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>PPFD (umol / m2 / s)</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Converts photosynthetically active radiation (PAR, units of Watts /
+            m2) to photosynthetic photon flux density (PPFD) in units of umol /
+            m2 / s From Campbell and Norman p151 PPFD = PAR * (J/m2/s) * (1 mol
+            / 2.35e5 J) 2.35e5 J / mol is the energy content of solar radiation
+            in the PAR waveband
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-David LeBauer
-
-  </div>
-</div>
+          David LeBauer David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/data.atmosphere/docs/reference/pecan_standard_met_table.html b/modules/data.atmosphere/docs/reference/pecan_standard_met_table.html
index c9a11bc..1a9f48a 100644
--- a/modules/data.atmosphere/docs/reference/pecan_standard_met_table.html
+++ b/modules/data.atmosphere/docs/reference/pecan_standard_met_table.html
@@ -2,160 +2,215 @@
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+                  >PEcAn.data.atmosphere</a
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
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+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
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+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Conversion table for PEcAn standard meteorology</h1>
-    
-    <div class="hidden name"><code>pecan_standard_met_table.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Conversion table for PEcAn standard meteorology</p>
-    
-    </div>
-
-    <pre class="usage"><span class='no'>pecan_standard_met_table</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 18 rows and 8 columns.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Conversion table for PEcAn standard meteorology</h1>
+
+            <div class="hidden name">
+              <code>pecan_standard_met_table.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Conversion table for PEcAn standard meteorology</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='no'>pecan_standard_met_table</span></pre>
+
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
+
+          <p>
+            An object of class <code>tbl_df</code> (inherits from
+            <code>tbl</code>, <code>data.frame</code>) with 18 rows and 8
+            columns.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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diff --git a/modules/data.atmosphere/docs/reference/permute.nc.html b/modules/data.atmosphere/docs/reference/permute.nc.html
index 67da2e4..afb10d6 100644
--- a/modules/data.atmosphere/docs/reference/permute.nc.html
+++ b/modules/data.atmosphere/docs/reference/permute.nc.html
@@ -2,193 +2,247 @@
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+      crossorigin="anonymous"
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+
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+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
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+                        >UNKNOWN TITLE</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>permute.nc</h1>
-    
-    <div class="hidden name"><code>permute.nc.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>permute.nc</h1>
 
-    <div class="ref-description">
-    
-    <p>Permute netCDF files</p>
-    
-    </div>
+            <div class="hidden name"><code>permute.nc.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>permute.nc</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
-  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>location on disk where inputs are stored</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of input and output files</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>location on disk where outputs will be stored</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>the start date of the data to be permuted (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>the end date of the data to be permuted (will only use the year part of the date)</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>should existing files be overwritten</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>should ouput of function be extra verbose</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Elizabeth Cowdery, Rob Kooper
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Permute netCDF files</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>permute.nc</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>location on disk where inputs are stored</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of input and output files</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>location on disk where outputs will be stored</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  the start date of the data to be permuted (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  the end date of the data to be permuted (will only use the
+                  year part of the date)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>should existing files be overwritten</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>should ouput of function be extra verbose</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Elizabeth Cowdery, Rob Kooper
+        </div>
+      </div>
 
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+        <div class="copyright">
+          <p>Developed by .</p>
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+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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diff --git a/modules/data.atmosphere/docs/reference/post_process.html b/modules/data.atmosphere/docs/reference/post_process.html
index 24c7a1f..44bed68 100644
--- a/modules/data.atmosphere/docs/reference/post_process.html
+++ b/modules/data.atmosphere/docs/reference/post_process.html
@@ -2,164 +2,217 @@
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+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
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+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
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+                  </ul>
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+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Post process raw NARR downloaded data frame</h1>
-    
-    <div class="hidden name"><code>post_process.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Post process raw NARR downloaded data frame</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>post_process</span>(<span class='no'>dat</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>Nested `tibble` from mapped call to [get_narr_url]</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Post process raw NARR downloaded data frame</h1>
+
+            <div class="hidden name"><code>post_process.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Post process raw NARR downloaded data frame</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>post_process</span>(<span class='no'>dat</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td><p>Nested `tibble` from mapped call to [get_narr_url]</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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index 6d16ec9..13ab5c3 100644
--- a/modules/data.atmosphere/docs/reference/predict_subdaily_met.html
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+      content="This is the main function of the tdm family workflow. This function predicts subdaily meteorology
              from daily means using a linear regression modeling approach. It takes a dataset with
              daily resolution and temporally downscales it to hourly resolution using the statistics
              generated by gen.subdaily.models(). It references the predict.subdaily.function
              located in lm_ensemble_sims() which uses a linear regression based approach to downscale.
              We generate multiple ensembles of possible hourly values dictated from the models and betas
              generated in gen.subdaily.models. Each ensemble member is saved as a netCDF file
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>predict_subdaily_met</h1>
-    
-    <div class="hidden name"><code>predict_subdaily_met.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This is the main function of the tdm family workflow. This function predicts subdaily meteorology
-             from daily means using a linear regression modeling approach. It takes a dataset with
-             daily resolution and temporally downscales it to hourly resolution using the statistics
-             generated by gen.subdaily.models(). It references the predict.subdaily.function
-             located in lm_ensemble_sims() which uses a linear regression based approach to downscale.
-             We generate multiple ensembles of possible hourly values dictated from the models and betas
-             generated in gen.subdaily.models. Each ensemble member is saved as a netCDF file
-             in CF conventions and these files are ready to be used in the general PEcAn workflow.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>predict_subdaily_met</span>(<span class='no'>outfolder</span>, <span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>path.train</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>predict_subdaily_met</h1>
+
+            <div class="hidden name"><code>predict_subdaily_met.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This is the main function of the tdm family workflow. This
+              function predicts subdaily meteorology from daily means using a
+              linear regression modeling approach. It takes a dataset with daily
+              resolution and temporally downscales it to hourly resolution using
+              the statistics generated by gen.subdaily.models(). It references
+              the predict.subdaily.function located in lm_ensemble_sims() which
+              uses a linear regression based approach to downscale. We generate
+              multiple ensembles of possible hourly values dictated from the
+              models and betas generated in gen.subdaily.models. Each ensemble
+              member is saved as a netCDF file in CF conventions and these files
+              are ready to be used in the general PEcAn workflow.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>predict_subdaily_met</span>(<span class='no'>outfolder</span>, <span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>path.train</span>,
   <span class='kw'>direction.filter</span> <span class='kw'>=</span> <span class='st'>"forward"</span>, <span class='no'>lm.models.base</span>, <span class='kw'>yrs.predict</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>ens.labs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>3</span>, <span class='kw'>resids</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>force.sanity</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>sanity.tries</span> <span class='kw'>=</span> <span class='fl'>25</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fu'>format</span>(<span class='fu'>Sys.time</span>(), <span class='st'>"%m%d"</span>), <span class='kw'>print.progress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>- directory where output file will be stored</p></td>
-    </tr>
-    <tr>
-      <th>in.path</th>
-      <td><p>- base path to dataset you wish to temporally downscale; Note: in order for parallelization 
-to work, the in.prefix will need to be appended as the final level of the file structure.  
-For example, if prefix is GFDL.CM3.rcp45.r1i1p1, there should be a directory with that title in in.path.</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>- prefix of model dataset, i.e. if file is GFDL.CM3.rcp45.r1i1p1.2006 the prefix is 'GFDL.CM3.rcp45.r1i1p1'</p></td>
-    </tr>
-    <tr>
-      <th>path.train</th>
-      <td><p>- path to CF/PEcAn style training data where each year is in a separate file.</p></td>
-    </tr>
-    <tr>
-      <th>direction.filter</th>
-      <td><p>- Whether the model will be filtered backward or forwards in time. options = c("backward", "forwards")
-(default is forward; PalEON will go backward, anybody interested in the future will go forwards)</p></td>
-    </tr>
-    <tr>
-      <th>lm.models.base</th>
-      <td><p>- path to linear regression model folders generated using gen.subdaily.models</p></td>
-    </tr>
-    <tr>
-      <th>yrs.predict</th>
-      <td><p>- years for which you want to generate met.  if NULL, all years in in.path will be done</p></td>
-    </tr>
-    <tr>
-      <th>ens.labs</th>
-      <td><p>- vector containing the labels (suffixes) for each ensemble member; this allows you to add to your 
-ensemble rather than overwriting with a default naming scheme</p></td>
-    </tr>
-    <tr>
-      <th>resids</th>
-      <td><p>- logical stating whether to pass on residual data or not</p></td>
-    </tr>
-    <tr>
-      <th>force.sanity</th>
-      <td><p>- (logical) do we force the data to meet sanity checks?</p></td>
-    </tr>
-    <tr>
-      <th>sanity.tries</th>
-      <td><p>- how many time should we try to predict a reasonable value before giving up?  We don't want to end up in an infinite loop</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: replace output file if it already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical: should <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package'>ncdf4</a></code> functions print debugging information as they run?</p></td>
-    </tr>
-    <tr>
-      <th>seed</th>
-      <td><p>- manually set seed for results to be reproducible</p></td>
-    </tr>
-    <tr>
-      <th>print.progress</th>
-      <td><p>- print the progress bar?</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Predict Subdaily Meteorology
-Predict Subdaily Meteorology based off of statistics created in gen.subdaily.models()</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other tdm - Temporally Downscale Meteorology: <code><a href='gen.subdaily.models.html'>gen.subdaily.models</a></code>,
-  <code><a href='lm_ensemble_sims.html'>lm_ensemble_sims</a></code>,
-  <code><a href='model.train.html'>model.train</a></code>, <code><a href='nc.merge.html'>nc.merge</a></code>,
-  <code><a href='save.betas.html'>save.betas</a></code>, <code><a href='save.model.html'>save.model</a></code>,
-  <code><a href='subdaily_pred.html'>subdaily_pred</a></code>,
-  <code><a href='temporal.downscale.functions.html'>temporal.downscale.functions</a></code></p></div>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>- directory where output file will be stored</p></td>
+            </tr>
+            <tr>
+              <th>in.path</th>
+              <td>
+                <p>
+                  - base path to dataset you wish to temporally downscale; Note:
+                  in order for parallelization to work, the in.prefix will need
+                  to be appended as the final level of the file structure. For
+                  example, if prefix is GFDL.CM3.rcp45.r1i1p1, there should be a
+                  directory with that title in in.path.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td>
+                <p>
+                  - prefix of model dataset, i.e. if file is
+                  GFDL.CM3.rcp45.r1i1p1.2006 the prefix is
+                  'GFDL.CM3.rcp45.r1i1p1'
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>path.train</th>
+              <td>
+                <p>
+                  - path to CF/PEcAn style training data where each year is in a
+                  separate file.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>direction.filter</th>
+              <td>
+                <p>
+                  - Whether the model will be filtered backward or forwards in
+                  time. options = c("backward", "forwards") (default is forward;
+                  PalEON will go backward, anybody interested in the future will
+                  go forwards)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lm.models.base</th>
+              <td>
+                <p>
+                  - path to linear regression model folders generated using
+                  gen.subdaily.models
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>yrs.predict</th>
+              <td>
+                <p>
+                  - years for which you want to generate met. if NULL, all years
+                  in in.path will be done
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ens.labs</th>
+              <td>
+                <p>
+                  - vector containing the labels (suffixes) for each ensemble
+                  member; this allows you to add to your ensemble rather than
+                  overwriting with a default naming scheme
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>resids</th>
+              <td>
+                <p>- logical stating whether to pass on residual data or not</p>
+              </td>
+            </tr>
+            <tr>
+              <th>force.sanity</th>
+              <td>
+                <p>- (logical) do we force the data to meet sanity checks?</p>
+              </td>
+            </tr>
+            <tr>
+              <th>sanity.tries</th>
+              <td>
+                <p>
+                  - how many time should we try to predict a reasonable value
+                  before giving up? We don't want to end up in an infinite loop
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical: replace output file if it already exists?</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical: should
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package"
+                      >ncdf4</a
+                    ></code
+                  >
+                  functions print debugging information as they run?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>seed</th>
+              <td><p>- manually set seed for results to be reproducible</p></td>
+            </tr>
+            <tr>
+              <th>print.progress</th>
+              <td><p>- print the progress bar?</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Predict Subdaily Meteorology Predict Subdaily Meteorology based off
+            of statistics created in gen.subdaily.models()
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other tdm - Temporally Downscale Meteorology:
+              <code
+                ><a href="gen.subdaily.models.html"
+                  >gen.subdaily.models</a
+                ></code
+              >,
+              <code><a href="lm_ensemble_sims.html">lm_ensemble_sims</a></code
+              >, <code><a href="model.train.html">model.train</a></code
+              >, <code><a href="nc.merge.html">nc.merge</a></code
+              >, <code><a href="save.betas.html">save.betas</a></code
+              >, <code><a href="save.model.html">save.model</a></code
+              >, <code><a href="subdaily_pred.html">subdaily_pred</a></code
+              >,
+              <code
+                ><a href="temporal.downscale.functions.html"
+                  >temporal.downscale.functions</a
+                ></code
+              >
+            </p>
+          </div>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>library</span>(<span class='no'>PEcAn.data.atmosphere</span>)
 <span class='no'>outfolder</span> <span class='kw'>=</span> <span class='st'>'~/Downscaled_GCM'</span>
 <span class='no'>in.path</span> <span class='kw'>=</span> <span class='st'>'~/raw_GCM'</span>
@@ -241,40 +385,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='no'>cores.max</span> <span class='kw'>=</span> <span class='fl'>12</span>
 <span class='no'>n.ens</span> <span class='kw'>=</span> <span class='fl'>3</span>
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Christy Rollinson, James Simkins
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#see-also">See also</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+
+          <h2>Author</h2>
 
-  
+          Christy Rollinson, James Simkins
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
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-
diff --git a/modules/data.atmosphere/docs/reference/prepare_narr_year.html b/modules/data.atmosphere/docs/reference/prepare_narr_year.html
index 0d533aa..f0159e5 100644
--- a/modules/data.atmosphere/docs/reference/prepare_narr_year.html
+++ b/modules/data.atmosphere/docs/reference/prepare_narr_year.html
@@ -2,187 +2,246 @@
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+                        station</a
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+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write NetCDF file for a single year of data</h1>
-    
-    <div class="hidden name"><code>prepare_narr_year.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Write NetCDF file for a single year of data</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>prepare_narr_year</span>(<span class='no'>dat</span>, <span class='no'>file</span>, <span class='no'>lat_nc</span>, <span class='no'>lon_nc</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>NARR tabular data for a single year ([get_NARR_thredds])</p></td>
-    </tr>
-    <tr>
-      <th>file</th>
-      <td><p>Full path to target file</p></td>
-    </tr>
-    <tr>
-      <th>lat_nc</th>
-      <td><p>`ncdim` object for latitude</p></td>
-    </tr>
-    <tr>
-      <th>lon_nc</th>
-      <td><p>`ncdim` object for longitude</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>List of NetCDF variables in data. Creates NetCDF file containing 
-data as a side effect</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write NetCDF file for a single year of data</h1>
+
+            <div class="hidden name"><code>prepare_narr_year.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Write NetCDF file for a single year of data</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>prepare_narr_year</span>(<span class='no'>dat</span>, <span class='no'>file</span>, <span class='no'>lat_nc</span>, <span class='no'>lon_nc</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td>
+                <p>NARR tabular data for a single year ([get_NARR_thredds])</p>
+              </td>
+            </tr>
+            <tr>
+              <th>file</th>
+              <td><p>Full path to target file</p></td>
+            </tr>
+            <tr>
+              <th>lat_nc</th>
+              <td><p>`ncdim` object for latitude</p></td>
+            </tr>
+            <tr>
+              <th>lon_nc</th>
+              <td><p>`ncdim` object for longitude</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            List of NetCDF variables in data. Creates NetCDF file containing
+            data as a side effect
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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diff --git a/modules/data.atmosphere/docs/reference/qair2rh.html b/modules/data.atmosphere/docs/reference/qair2rh.html
index 997618d..3b0c5cb 100644
--- a/modules/data.atmosphere/docs/reference/qair2rh.html
+++ b/modules/data.atmosphere/docs/reference/qair2rh.html
@@ -2,191 +2,255 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>qair2rh</h1>
-    
-    <div class="hidden name"><code>qair2rh.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert specific humidity to relative humidity</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>qair2rh</span>(<span class='no'>qair</span>, <span class='no'>temp</span>, <span class='kw'>press</span> <span class='kw'>=</span> <span class='fl'>1013.25</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>qair</th>
-      <td><p>specific humidity, dimensionless (e.g. kg/kg) ratio of water mass / total air mass</p></td>
-    </tr>
-    <tr>
-      <th>temp</th>
-      <td><p>degrees C</p></td>
-    </tr>
-    <tr>
-      <th>press</th>
-      <td><p>pressure in mb</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>rh relative humidity, ratio of actual water mixing ratio to saturation mixing ratio</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>converting specific humidity into relative humidity
-NCEP surface flux data does not have RH
-from Bolton 1980 Teh computation of Equivalent Potential Temperature
-<a href='http://www.eol.ucar.edu/projects/ceop/dm/documents/refdata_report/eqns.html'>http://www.eol.ucar.edu/projects/ceop/dm/documents/refdata_report/eqns.html</a></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>qair2rh</h1>
+
+            <div class="hidden name"><code>qair2rh.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert specific humidity to relative humidity</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>qair2rh</span>(<span class='no'>qair</span>, <span class='no'>temp</span>, <span class='kw'>press</span> <span class='kw'>=</span> <span class='fl'>1013.25</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>qair</th>
+              <td>
+                <p>
+                  specific humidity, dimensionless (e.g. kg/kg) ratio of water
+                  mass / total air mass
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>temp</th>
+              <td><p>degrees C</p></td>
+            </tr>
+            <tr>
+              <th>press</th>
+              <td><p>pressure in mb</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            rh relative humidity, ratio of actual water mixing ratio to
+            saturation mixing ratio
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            converting specific humidity into relative humidity NCEP surface
+            flux data does not have RH from Bolton 1980 Teh computation of
+            Equivalent Potential Temperature
+            <a
+              href="http://www.eol.ucar.edu/projects/ceop/dm/documents/refdata_report/eqns.html"
+              >http://www.eol.ucar.edu/projects/ceop/dm/documents/refdata_report/eqns.html</a
+            >
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>read.register</h1>
-    
-    <div class="hidden name"><code>read.register.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>read.register</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read.register</span>(<span class='no'>register.xml</span>, <span class='no'>con</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>register.xml</th>
-      <td><p>path of xml file</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>betydb connection</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Betsy Cowdery
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>read.register</h1>
+
+            <div class="hidden name"><code>read.register.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>read.register</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read.register</span>(<span class='no'>register.xml</span>, <span class='no'>con</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>register.xml</th>
+              <td><p>path of xml file</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>betydb connection</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Betsy Cowdery
+        </div>
+      </div>
 
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diff --git a/modules/data.atmosphere/docs/reference/read_narr_var.html b/modules/data.atmosphere/docs/reference/read_narr_var.html
index 1fa4832..fbbdddd 100644
--- a/modules/data.atmosphere/docs/reference/read_narr_var.html
+++ b/modules/data.atmosphere/docs/reference/read_narr_var.html
@@ -2,189 +2,246 @@
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+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read a specific variable from a NARR NetCDF file</h1>
-    
-    <div class="hidden name"><code>read_narr_var.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Read a specific variable from a NARR NetCDF file</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_narr_var</span>(<span class='no'>nc</span>, <span class='no'>xy</span>, <span class='no'>variable</span>, <span class='no'>unit</span>, <span class='no'>flx</span>, <span class='kw'>pb</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>nc</th>
-      <td><p>`ncdf4` connection object</p></td>
-    </tr>
-    <tr>
-      <th>xy</th>
-      <td><p>Vector length 2 containing NARR coordinates</p></td>
-    </tr>
-    <tr>
-      <th>variable</th>
-      <td><p>NARR name of variable to retrieve</p></td>
-    </tr>
-    <tr>
-      <th>unit</th>
-      <td><p>Output unit of variable to retrieve</p></td>
-    </tr>
-    <tr>
-      <th>flx</th>
-      <td><p>(Logical) If `TRUE`, format for `flx` variables. Otherwise, 
-format for `sfc` variables. See [narr_flx_vars].</p></td>
-    </tr>
-    <tr>
-      <th>pb</th>
-      <td><p>Progress bar R6 object (default = `NULL`)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read a specific variable from a NARR NetCDF file</h1>
+
+            <div class="hidden name"><code>read_narr_var.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Read a specific variable from a NARR NetCDF file</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_narr_var</span>(<span class='no'>nc</span>, <span class='no'>xy</span>, <span class='no'>variable</span>, <span class='no'>unit</span>, <span class='no'>flx</span>, <span class='kw'>pb</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>nc</th>
+              <td><p>`ncdf4` connection object</p></td>
+            </tr>
+            <tr>
+              <th>xy</th>
+              <td><p>Vector length 2 containing NARR coordinates</p></td>
+            </tr>
+            <tr>
+              <th>variable</th>
+              <td><p>NARR name of variable to retrieve</p></td>
+            </tr>
+            <tr>
+              <th>unit</th>
+              <td><p>Output unit of variable to retrieve</p></td>
+            </tr>
+            <tr>
+              <th>flx</th>
+              <td>
+                <p>
+                  (Logical) If `TRUE`, format for `flx` variables. Otherwise,
+                  format for `sfc` variables. See [narr_flx_vars].
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pb</th>
+              <td><p>Progress bar R6 object (default = `NULL`)</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
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+          <p>Developed by .</p>
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diff --git a/modules/data.atmosphere/docs/reference/rh2qair.html b/modules/data.atmosphere/docs/reference/rh2qair.html
index 4dafdb3..27b11a5 100644
--- a/modules/data.atmosphere/docs/reference/rh2qair.html
+++ b/modules/data.atmosphere/docs/reference/rh2qair.html
@@ -2,176 +2,223 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>RH to SH</h1>
-    
-    <div class="hidden name"><code>rh2qair.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>converts relative humidity to specific humidity</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>rh2qair</span>(<span class='no'>rh</span>, <span class='no'>T</span>, <span class='kw'>press</span> <span class='kw'>=</span> <span class='fl'>101325</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>rh</th>
-      <td><p>relative humidity (proportion, not %)</p></td>
-    </tr>
-    <tr>
-      <th>T</th>
-      <td><p>absolute temperature (Kelvin)</p></td>
-    </tr>
-    <tr>
-      <th>press</th>
-      <td><p>air pressure (Pascals)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze, Ankur Desai
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>RH to SH</h1>
+
+            <div class="hidden name"><code>rh2qair.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>converts relative humidity to specific humidity</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>rh2qair</span>(<span class='no'>rh</span>, <span class='no'>T</span>, <span class='kw'>press</span> <span class='kw'>=</span> <span class='fl'>101325</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>rh</th>
+              <td><p>relative humidity (proportion, not %)</p></td>
+            </tr>
+            <tr>
+              <th>T</th>
+              <td><p>absolute temperature (Kelvin)</p></td>
+            </tr>
+            <tr>
+              <th>press</th>
+              <td><p>air pressure (Pascals)</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze, Ankur Desai
+        </div>
+      </div>
 
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+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
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+                    href="#"
+                    class="dropdown-toggle"
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+                    role="button"
+                    aria-expanded="false"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Adverb to try calling a function `n` times before giving up</h1>
-    
-    <div class="hidden name"><code>robustly.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Adverb to try calling a function `n` times before giving up</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>robustly</span>(<span class='no'>.f</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>timeout</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>silent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>.f</th>
-      <td><p>Function to call.</p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>Number of attempts to try</p></td>
-    </tr>
-    <tr>
-      <th>timeout</th>
-      <td><p>Timeout between attempts, in seconds</p></td>
-    </tr>
-    <tr>
-      <th>silent</th>
-      <td><p>Silence error messages?</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Modified version of input function</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Adverb to try calling a function `n` times before giving up</h1>
+
+            <div class="hidden name"><code>robustly.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Adverb to try calling a function `n` times before giving up</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>robustly</span>(<span class='no'>.f</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>timeout</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>silent</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>.f</th>
+              <td><p>Function to call.</p></td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td><p>Number of attempts to try</p></td>
+            </tr>
+            <tr>
+              <th>timeout</th>
+              <td><p>Timeout between attempts, in seconds</p></td>
+            </tr>
+            <tr>
+              <th>silent</th>
+              <td><p>Silence error messages?</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Modified version of input function</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>rlog</span> <span class='kw'>&lt;-</span> <span class='fu'>robustly</span>(<span class='no'>log</span>, <span class='kw'>timeout</span> <span class='kw'>=</span> <span class='fl'>0.3</span>)
 <span class='fu'>try</span>(<span class='fu'>rlog</span>(<span class='st'>"fail"</span>))
 <span class='co'># }</span><span class='co'># NOT RUN {</span>
@@ -164,34 +226,30 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
  <span class='co'># Useful in `purrr` maps</span>
  <span class='no'>many_vars</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>purrr</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/purrr/topics/map'>map</a></span>(<span class='no'>varnames</span>, <span class='fu'>robustly</span>(<span class='kw pkg'>ncdf4</span><span class='kw ns'>::</span><span class='no'><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncvar_get'>ncvar_get</a></span>), <span class='kw'>nc</span> <span class='kw'>=</span> <span class='no'>nc</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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+    </div>
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 </html>
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diff --git a/modules/data.atmosphere/docs/reference/save.betas.html b/modules/data.atmosphere/docs/reference/save.betas.html
index 4229a27..a13965e 100644
--- a/modules/data.atmosphere/docs/reference/save.betas.html
+++ b/modules/data.atmosphere/docs/reference/save.betas.html
@@ -2,196 +2,276 @@
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 <html>
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+             gen.subdaily.models() when linear regression models are created"
+    />
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+                    data-toggle="dropdown"
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+
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
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+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
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+                      <a href="../articles/tdm_downscaling.html"
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+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>save.betas</h1>
-    
-    <div class="hidden name"><code>save.betas.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to save betas as a .nc file. This is utilized in
-             gen.subdaily.models() when linear regression models are created</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>save.betas</span>(<span class='no'>model.out</span>, <span class='no'>betas</span>, <span class='no'>outfile</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>model.out</th>
-      <td><p>list linear regression model output</p></td>
-    </tr>
-    <tr>
-      <th>betas</th>
-      <td><p>name of the layer of betas to save (e.g. 'betas' or 'betas.resid')</p></td>
-    </tr>
-    <tr>
-      <th>outfile</th>
-      <td><p>location where output will be stored</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>TDM Save Betas
-Saves betas that are calculated during gen.subdaily.models()</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other tdm - Temporally Downscale Meteorology: <code><a href='gen.subdaily.models.html'>gen.subdaily.models</a></code>,
-  <code><a href='lm_ensemble_sims.html'>lm_ensemble_sims</a></code>,
-  <code><a href='model.train.html'>model.train</a></code>, <code><a href='nc.merge.html'>nc.merge</a></code>,
-  <code><a href='predict_subdaily_met.html'>predict_subdaily_met</a></code>,
-  <code><a href='save.model.html'>save.model</a></code>, <code><a href='subdaily_pred.html'>subdaily_pred</a></code>,
-  <code><a href='temporal.downscale.functions.html'>temporal.downscale.functions</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>save.betas</h1>
+
+            <div class="hidden name"><code>save.betas.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to save betas as a .nc file. This is utilized in
+              gen.subdaily.models() when linear regression models are created
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>save.betas</span>(<span class='no'>model.out</span>, <span class='no'>betas</span>, <span class='no'>outfile</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>model.out</th>
+              <td><p>list linear regression model output</p></td>
+            </tr>
+            <tr>
+              <th>betas</th>
+              <td>
+                <p>
+                  name of the layer of betas to save (e.g. 'betas' or
+                  'betas.resid')
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfile</th>
+              <td><p>location where output will be stored</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            TDM Save Betas Saves betas that are calculated during
+            gen.subdaily.models()
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other tdm - Temporally Downscale Meteorology:
+              <code
+                ><a href="gen.subdaily.models.html"
+                  >gen.subdaily.models</a
+                ></code
+              >,
+              <code><a href="lm_ensemble_sims.html">lm_ensemble_sims</a></code
+              >, <code><a href="model.train.html">model.train</a></code
+              >, <code><a href="nc.merge.html">nc.merge</a></code
+              >,
+              <code
+                ><a href="predict_subdaily_met.html"
+                  >predict_subdaily_met</a
+                ></code
+              >, <code><a href="save.model.html">save.model</a></code
+              >, <code><a href="subdaily_pred.html">subdaily_pred</a></code
+              >,
+              <code
+                ><a href="temporal.downscale.functions.html"
+                  >temporal.downscale.functions</a
+                ></code
+              >
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson, James Simkins
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson, James Simkins
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/data.atmosphere/docs/reference/save.model.html b/modules/data.atmosphere/docs/reference/save.model.html
index 1a0c226..306c8a9 100644
--- a/modules/data.atmosphere/docs/reference/save.model.html
+++ b/modules/data.atmosphere/docs/reference/save.model.html
@@ -2,196 +2,276 @@
 <!DOCTYPE html>
 <html>
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
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-             gen.subdaily.models() when linear regression models are created" />
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+
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+             gen.subdaily.models() when linear regression models are created"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+              </button>
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
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+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>save.model</h1>
-    
-    <div class="hidden name"><code>save.model.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to save models as a .nc file. This is utilized in
-             gen.subdaily.models() when linear regression models are created</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>save.model</span>(<span class='no'>model.out</span>, <span class='no'>model</span>, <span class='no'>outfile</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>model.out</th>
-      <td><p>list linear regression model output</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>name of the layer of model to save (e.g. 'model' or 'model.resid')</p></td>
-    </tr>
-    <tr>
-      <th>outfile</th>
-      <td><p>location where output will be stored</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>TDM Save Models
-Saves models that are created during gen.subdaily.models()</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other tdm - Temporally Downscale Meteorology: <code><a href='gen.subdaily.models.html'>gen.subdaily.models</a></code>,
-  <code><a href='lm_ensemble_sims.html'>lm_ensemble_sims</a></code>,
-  <code><a href='model.train.html'>model.train</a></code>, <code><a href='nc.merge.html'>nc.merge</a></code>,
-  <code><a href='predict_subdaily_met.html'>predict_subdaily_met</a></code>,
-  <code><a href='save.betas.html'>save.betas</a></code>, <code><a href='subdaily_pred.html'>subdaily_pred</a></code>,
-  <code><a href='temporal.downscale.functions.html'>temporal.downscale.functions</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>save.model</h1>
+
+            <div class="hidden name"><code>save.model.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to save models as a .nc file. This is utilized in
+              gen.subdaily.models() when linear regression models are created
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>save.model</span>(<span class='no'>model.out</span>, <span class='no'>model</span>, <span class='no'>outfile</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>model.out</th>
+              <td><p>list linear regression model output</p></td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td>
+                <p>
+                  name of the layer of model to save (e.g. 'model' or
+                  'model.resid')
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfile</th>
+              <td><p>location where output will be stored</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            TDM Save Models Saves models that are created during
+            gen.subdaily.models()
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other tdm - Temporally Downscale Meteorology:
+              <code
+                ><a href="gen.subdaily.models.html"
+                  >gen.subdaily.models</a
+                ></code
+              >,
+              <code><a href="lm_ensemble_sims.html">lm_ensemble_sims</a></code
+              >, <code><a href="model.train.html">model.train</a></code
+              >, <code><a href="nc.merge.html">nc.merge</a></code
+              >,
+              <code
+                ><a href="predict_subdaily_met.html"
+                  >predict_subdaily_met</a
+                ></code
+              >, <code><a href="save.betas.html">save.betas</a></code
+              >, <code><a href="subdaily_pred.html">subdaily_pred</a></code
+              >,
+              <code
+                ><a href="temporal.downscale.functions.html"
+                  >temporal.downscale.functions</a
+                ></code
+              >
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson, James Simkins
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson, James Simkins
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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   </body>
 </html>
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diff --git a/modules/data.atmosphere/docs/reference/site.lst.html b/modules/data.atmosphere/docs/reference/site.lst.html
index 0ff6a0d..330cbc8 100644
--- a/modules/data.atmosphere/docs/reference/site.lst.html
+++ b/modules/data.atmosphere/docs/reference/site.lst.html
@@ -2,158 +2,196 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="site.lst — site.lst" />
+
+    <meta property="og:description" content="Find time zone for a site" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
-    </li>
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-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="../articles/compare_narr_cruncep_met.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="../articles/tdm_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>site.lst</h1>
-    
-    <div class="hidden name"><code>site.lst.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>site.lst</h1>
 
-    <div class="ref-description">
-    
-    <p>Find time zone for a site</p>
-    
-    </div>
+            <div class="hidden name"><code>site.lst.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>site.lst</span>(<span class='no'>site.id</span>, <span class='no'>con</span>)</pre>
-        
+          <div class="ref-description">
+            <p>Find time zone for a site</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>site.lst</span>(<span class='no'>site.id</span>, <span class='no'>con</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Betsy Cowdery
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Betsy Cowdery
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/site_from_tag.html b/modules/data.atmosphere/docs/reference/site_from_tag.html
index c0ae705..94c0955 100644
--- a/modules/data.atmosphere/docs/reference/site_from_tag.html
+++ b/modules/data.atmosphere/docs/reference/site_from_tag.html
@@ -2,165 +2,199 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>site_from_tag — site_from_tag • PEcAn.data.atmosphere</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="site_from_tag — site_from_tag" />
-
-<meta property="og:description" content="site_from_tag" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>site_from_tag — site_from_tag • PEcAn.data.atmosphere</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="site_from_tag — site_from_tag" />
+
+    <meta property="og:description" content="site_from_tag" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.atmosphere</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
-    </li>
-    <li>
-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="../articles/compare_narr_cruncep_met.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
-      <a href="../articles/tdm_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>site_from_tag</h1>
-    
-    <div class="hidden name"><code>site_from_tag.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>site_from_tag</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>site_from_tag</h1>
 
-    <pre class="usage"><span class='fu'>site_from_tag</span>(<span class='no'>sitename</span>, <span class='no'>tag</span>)</pre>
-        
+            <div class="hidden name"><code>site_from_tag.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>site_from_tag</p>
+          </div>
 
-    <h2>Author</h2>
-    
-Betsy Cowdery
+          <pre
+            class="usage"
+          ><span class='fu'>site_from_tag</span>(<span class='no'>sitename</span>, <span class='no'>tag</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-Function to find the site code for a specific tag
-Example:
-  sitename = 'Rhinelander Aspen FACE Experiment (FACE-RHIN)'
-  tag = 'FACE'
-  site_from_tag(sitename,tag) = 'RHIN'
-Requires that site names be set up specifically with (tag-sitecode) - this may change
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Betsy Cowdery Function to find the site code for a specific tag
+          Example: sitename = 'Rhinelander Aspen FACE Experiment (FACE-RHIN)'
+          tag = 'FACE' site_from_tag(sitename,tag) = 'RHIN' Requires that site
+          names be set up specifically with (tag-sitecode) - this may change
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/solarMJ2ppfd.html b/modules/data.atmosphere/docs/reference/solarMJ2ppfd.html
index 7becc9f..629d71c 100644
--- a/modules/data.atmosphere/docs/reference/solarMJ2ppfd.html
+++ b/modules/data.atmosphere/docs/reference/solarMJ2ppfd.html
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>MJ to PPFD</h1>
-    
-    <div class="hidden name"><code>solarMJ2ppfd.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Solar Radiation to PPFD</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>solarMJ2ppfd</span>(<span class='no'>solarMJ</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>solarMJ</th>
-      <td><p>MJ per day</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>PPFD umol /m2 / s</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>There is no easy straight way to convert MJ/m2 to mu mol photons / m2 / s (PAR).
-Note: 1 Watt = 1J/s
-The above conversion is based on the following reasoning
-0.12 is about how much of the total radiation is expected to ocurr during the hour of maximum insolation (it is a guesstimate)
-2.07 is a coefficient which converts from MJ to mol photons (it is approximate and it is taken from ...
-Campbell and Norman (1998). Introduction to Environmental Biophysics. pg 151 'the energy content of solar radiation in the PAR waveband is 2.35 x 10^5 J/mol'
-See also the chapter radiation basics (10)
-Here the input is the total solar radiation so to obtain in the PAR spectrum need to multiply by 0.486
-This last value 0.486 is based on the approximation that PAR is 0.45-0.50 of the total radiation
-This means that 1e6 / (2.35e6) * 0.486 = 2.07
-1e6 converts from mol to mu mol
-1/3600 divides the values in hours to seconds</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>MJ to PPFD</h1>
+
+            <div class="hidden name"><code>solarMJ2ppfd.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Solar Radiation to PPFD</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>solarMJ2ppfd</span>(<span class='no'>solarMJ</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>solarMJ</th>
+              <td><p>MJ per day</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>PPFD umol /m2 / s</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            There is no easy straight way to convert MJ/m2 to mu mol photons /
+            m2 / s (PAR). Note: 1 Watt = 1J/s The above conversion is based on
+            the following reasoning 0.12 is about how much of the total
+            radiation is expected to ocurr during the hour of maximum insolation
+            (it is a guesstimate) 2.07 is a coefficient which converts from MJ
+            to mol photons (it is approximate and it is taken from ... Campbell
+            and Norman (1998). Introduction to Environmental Biophysics. pg 151
+            'the energy content of solar radiation in the PAR waveband is 2.35 x
+            10^5 J/mol' See also the chapter radiation basics (10) Here the
+            input is the total solar radiation so to obtain in the PAR spectrum
+            need to multiply by 0.486 This last value 0.486 is based on the
+            approximation that PAR is 0.45-0.50 of the total radiation This
+            means that 1e6 / (2.35e6) * 0.486 = 2.07 1e6 converts from mol to mu
+            mol 1/3600 divides the values in hours to seconds
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Fernando Miguez
+          <h2>Author</h2>
 
-David LeBauer
-
-  </div>
-</div>
+          Fernando Miguez David LeBauer
+        </div>
+      </div>
 
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index 69bd93d..1fc053a 100644
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-</li>
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-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
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-    <li>
-      <a href="../articles/ameriflux_demo.html">PEcAn: Importing Met data from Bondville, IL Ameriflux station</a>
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-      <a href="../articles/cfmet_downscaling.html">UNKNOWN TITLE</a>
-    </li>
-    <li>
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-    <li>
-      <a href="../articles/tdm_downscaling.html">UNKNOWN TITLE</a>
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-  </ul>
-</li>
-      </ul>
-      
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-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Spin-up meteorology</h1>
-    
-    <div class="hidden name"><code>spin.met.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Spin-up meteorology</h1>
 
-    <div class="ref-description">
-    
-    <p>Spin-up meteorology</p>
-    
-    </div>
+            <div class="hidden name"><code>spin.met.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>spin.met</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>nyear</span> <span class='kw'>=</span> <span class='fl'>1000</span>,
+          <div class="ref-description">
+            <p>Spin-up meteorology</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>spin.met</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>nyear</span> <span class='kw'>=</span> <span class='fl'>1000</span>,
   <span class='kw'>nsample</span> <span class='kw'>=</span> <span class='fl'>50</span>, <span class='kw'>resample</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>run_start_date</span> <span class='kw'>=</span> <span class='no'>start_date</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>met input folder path</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>met input file prefix (shared by all annual files, can be "")</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>start of met</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>end of met</p></td>
-    </tr>
-    <tr>
-      <th>nyear</th>
-      <td><p>number of years of spin-up, default 1000</p></td>
-    </tr>
-    <tr>
-      <th>nsample</th>
-      <td><p>sample the first nsample years of met, default 50</p></td>
-    </tr>
-    <tr>
-      <th>resample</th>
-      <td><p>resample (TRUE, default) or cycle (FALSE) meteorology</p></td>
-    </tr>
-    <tr>
-      <th>run_start_date</th>
-      <td><p>date the run itself starts, which can be different than the start of met</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>whether to replace previous resampling</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>updated start date</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>spin.met works by creating symbolic links to the sampled met file, 
-rather than copying the whole file. Be aware that the internal dates in 
-those files are not modified. Right now this is designed to be called within
-met2model.[MODEL] before the met is processed (it's designed to work with annual CF
-files not model-specific files) for example with models that process met
-into one large file</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>met input folder path</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td>
+                <p>
+                  met input file prefix (shared by all annual files, can be "")
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>start of met</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>end of met</p></td>
+            </tr>
+            <tr>
+              <th>nyear</th>
+              <td><p>number of years of spin-up, default 1000</p></td>
+            </tr>
+            <tr>
+              <th>nsample</th>
+              <td><p>sample the first nsample years of met, default 50</p></td>
+            </tr>
+            <tr>
+              <th>resample</th>
+              <td>
+                <p>resample (TRUE, default) or cycle (FALSE) meteorology</p>
+              </td>
+            </tr>
+            <tr>
+              <th>run_start_date</th>
+              <td>
+                <p>
+                  date the run itself starts, which can be different than the
+                  start of met
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>whether to replace previous resampling</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>updated start date</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            spin.met works by creating symbolic links to the sampled met file,
+            rather than copying the whole file. Be aware that the internal dates
+            in those files are not modified. Right now this is designed to be
+            called within met2model.[MODEL] before the met is processed (it's
+            designed to work with annual CF files not model-specific files) for
+            example with models that process met into one large file
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>start_date</span> <span class='kw'>&lt;-</span> <span class='st'>"0850-01-01 00:00:00"</span>
 <span class='no'>end_date</span>   <span class='kw'>&lt;-</span> <span class='st'>"2010-12-31 23:59:59"</span>
 <span class='no'>nyear</span>      <span class='kw'>&lt;-</span> <span class='fl'>10</span>
@@ -200,36 +268,32 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
      <span class='no'>nyear</span>, <span class='no'>nsample</span>, <span class='no'>resample</span>)
 }
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#details">Details</a></li>
 
-  
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diff --git a/modules/data.atmosphere/docs/reference/split_wind.html b/modules/data.atmosphere/docs/reference/split_wind.html
index be2ca81..e729baa 100644
--- a/modules/data.atmosphere/docs/reference/split_wind.html
+++ b/modules/data.atmosphere/docs/reference/split_wind.html
@@ -2,171 +2,247 @@
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+      PEcAn.data.atmosphere
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+
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+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Split wind_speed into eastward_wind and northward_wind</h1>
-    
-    <div class="hidden name"><code>split_wind.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Split wind_speed into eastward_wind and northward_wind</h1>
 
-    <div class="ref-description">
-    
-    <p>Split wind_speed into eastward_wind and northward_wind</p>
-    
-    </div>
+            <div class="hidden name"><code>split_wind.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Split wind_speed into eastward_wind and northward_wind</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>split_wind</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>split_wind</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>path to original data</p></td>
-    </tr>
-    <tr>
-      <th>in.prefix</th>
-      <td><p>prefix of original data</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: replace output file if it already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical: should <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package'>ncdf4</a></code> functions print debugging information as they run?</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>other arguments, currently ignored</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Currently modifies the files IN PLACE rather than creating a new copy of the files an a new DB record.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>path to original data</p></td>
+            </tr>
+            <tr>
+              <th>in.prefix</th>
+              <td><p>prefix of original data</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical: replace output file if it already exists?</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical: should
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package"
+                      >ncdf4</a
+                    ></code
+                  >
+                  functions print debugging information as they run?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>other arguments, currently ignored</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Currently modifies the files IN PLACE rather than creating a new
+            copy of the files an a new DB record.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>in.path</span>    <span class='kw'>&lt;-</span> <span class='st'>"~/paleon/PalEONregional_CF_site_1-24047/"</span>
 <span class='no'>in.prefix</span>  <span class='kw'>&lt;-</span> <span class='st'>""</span>
 <span class='no'>outfolder</span>  <span class='kw'>&lt;-</span> <span class='st'>"~/paleon/metTest/"</span>
@@ -177,34 +253,30 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 
 <span class='fu'>split_wind</span>(<span class='no'>in.path</span>, <span class='no'>in.prefix</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>merge.file</span>, <span class='no'>overwrite</span>, <span class='no'>verbose</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.atmosphere/docs/reference/step_means.html b/modules/data.atmosphere/docs/reference/step_means.html
index ea2a56a..cb2549b 100644
--- a/modules/data.atmosphere/docs/reference/step_means.html
+++ b/modules/data.atmosphere/docs/reference/step_means.html
@@ -2,180 +2,237 @@
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+      take mean at fixed intervals along a vector — step_means •
+      PEcAn.data.atmosphere
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+              </button>
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
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+              <ul class="nav navbar-nav">
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+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>take mean at fixed intervals along a vector</h1>
-    
-    <div class="hidden name"><code>step_means.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>take mean at fixed intervals along a vector</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>step_means</span>(<span class='no'>x</span>, <span class='no'>step</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>numeric vector</p></td>
-    </tr>
-    <tr>
-      <th>step</th>
-      <td><p>integer step size</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>numeric of length length(x)/step</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>User should check that length(x) is an even multiple of step</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>take mean at fixed intervals along a vector</h1>
+
+            <div class="hidden name"><code>step_means.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>take mean at fixed intervals along a vector</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>step_means</span>(<span class='no'>x</span>, <span class='no'>step</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>numeric vector</p></td>
+            </tr>
+            <tr>
+              <th>step</th>
+              <td><p>integer step size</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>numeric of length length(x)/step</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>User should check that length(x) is an even multiple of step</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/data.atmosphere/docs/reference/subdaily_pred.html b/modules/data.atmosphere/docs/reference/subdaily_pred.html
index 122a758..7267be7 100644
--- a/modules/data.atmosphere/docs/reference/subdaily_pred.html
+++ b/modules/data.atmosphere/docs/reference/subdaily_pred.html
@@ -2,217 +2,294 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>subdaily_pred — subdaily_pred • PEcAn.data.atmosphere</title>
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+
+    <meta
+      property="og:description"
+      content="Function to pull objects created in linear regression models
              and are used to predict subdaily meteorology. This function is called in
              lm_ensemble_sims() to downscale a meteorology product.
-             Linear regression models are created in gen.subdaily.models()" />
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+             Linear regression models are created in gen.subdaily.models()"
+    />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>subdaily_pred</h1>
-    
-    <div class="hidden name"><code>subdaily_pred.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to pull objects created in linear regression models
-             and are used to predict subdaily meteorology. This function is called in
-             lm_ensemble_sims() to downscale a meteorology product.
-             Linear regression models are created in gen.subdaily.models()</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>subdaily_pred</span>(<span class='no'>newdata</span>, <span class='no'>model.predict</span>, <span class='no'>Rbeta</span>, <span class='kw'>resid.err</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>subdaily_pred</h1>
+
+            <div class="hidden name"><code>subdaily_pred.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to pull objects created in linear regression models and
+              are used to predict subdaily meteorology. This function is called
+              in lm_ensemble_sims() to downscale a meteorology product. Linear
+              regression models are created in gen.subdaily.models()
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>subdaily_pred</span>(<span class='no'>newdata</span>, <span class='no'>model.predict</span>, <span class='no'>Rbeta</span>, <span class='kw'>resid.err</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>model.resid</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>Rbeta.resid</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>n.ens</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>newdata</th>
-      <td><p>dataframe with data to be downscaled</p></td>
-    </tr>
-    <tr>
-      <th>model.predict</th>
-      <td><p>saved linear regression model</p></td>
-    </tr>
-    <tr>
-      <th>Rbeta</th>
-      <td><p>matrix with Rbetas from saved linear regression model</p></td>
-    </tr>
-    <tr>
-      <th>resid.err</th>
-      <td><p>logical, whether to include residual error or not</p></td>
-    </tr>
-    <tr>
-      <th>model.resid</th>
-      <td><p>data.frame of model residuals</p></td>
-    </tr>
-    <tr>
-      <th>Rbeta.resid</th>
-      <td><p>data.frame of Rbeta residuals</p></td>
-    </tr>
-    <tr>
-      <th>n.ens</th>
-      <td><p>number of ensembles to create</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Subdaily Prediction
-Pulls information from linear regression models to predict subdaily meteorology</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other tdm - Temporally Downscale Meteorology: <code><a href='gen.subdaily.models.html'>gen.subdaily.models</a></code>,
-  <code><a href='lm_ensemble_sims.html'>lm_ensemble_sims</a></code>,
-  <code><a href='model.train.html'>model.train</a></code>, <code><a href='nc.merge.html'>nc.merge</a></code>,
-  <code><a href='predict_subdaily_met.html'>predict_subdaily_met</a></code>,
-  <code><a href='save.betas.html'>save.betas</a></code>, <code><a href='save.model.html'>save.model</a></code>,
-  <code><a href='temporal.downscale.functions.html'>temporal.downscale.functions</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>newdata</th>
+              <td><p>dataframe with data to be downscaled</p></td>
+            </tr>
+            <tr>
+              <th>model.predict</th>
+              <td><p>saved linear regression model</p></td>
+            </tr>
+            <tr>
+              <th>Rbeta</th>
+              <td>
+                <p>matrix with Rbetas from saved linear regression model</p>
+              </td>
+            </tr>
+            <tr>
+              <th>resid.err</th>
+              <td><p>logical, whether to include residual error or not</p></td>
+            </tr>
+            <tr>
+              <th>model.resid</th>
+              <td><p>data.frame of model residuals</p></td>
+            </tr>
+            <tr>
+              <th>Rbeta.resid</th>
+              <td><p>data.frame of Rbeta residuals</p></td>
+            </tr>
+            <tr>
+              <th>n.ens</th>
+              <td><p>number of ensembles to create</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Subdaily Prediction Pulls information from linear regression models
+            to predict subdaily meteorology
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other tdm - Temporally Downscale Meteorology:
+              <code
+                ><a href="gen.subdaily.models.html"
+                  >gen.subdaily.models</a
+                ></code
+              >,
+              <code><a href="lm_ensemble_sims.html">lm_ensemble_sims</a></code
+              >, <code><a href="model.train.html">model.train</a></code
+              >, <code><a href="nc.merge.html">nc.merge</a></code
+              >,
+              <code
+                ><a href="predict_subdaily_met.html"
+                  >predict_subdaily_met</a
+                ></code
+              >, <code><a href="save.betas.html">save.betas</a></code
+              >, <code><a href="save.model.html">save.model</a></code
+              >,
+              <code
+                ><a href="temporal.downscale.functions.html"
+                  >temporal.downscale.functions</a
+                ></code
+              >
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson, James Simkins
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson, James Simkins
+        </div>
+      </div>
 
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index fbdd32a..e1a05b0 100644
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>SW to PAR</h1>
-    
-    <div class="hidden name"><code>sw2par.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Solar Radiation to PPFD</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sw2par</span>(<span class='no'>sw</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sw</th>
-      <td><p>shortwave radiation (W/m2 == J/m2/s)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>PAR W/m2</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Here the input is the total solar radiation
-so to obtain in the PAR spectrum need to multiply by 0.486 From Campbell and Norman p151
-This is based on the approximation that PAR is 0.45-0.50 of the total radiation</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>SW to PAR</h1>
+
+            <div class="hidden name"><code>sw2par.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Solar Radiation to PPFD</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sw2par</span>(<span class='no'>sw</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sw</th>
+              <td><p>shortwave radiation (W/m2 == J/m2/s)</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>PAR W/m2</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Here the input is the total solar radiation so to obtain in the PAR
+            spectrum need to multiply by 0.486 From Campbell and Norman p151
+            This is based on the approximation that PAR is 0.45-0.50 of the
+            total radiation
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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diff --git a/modules/data.atmosphere/docs/reference/sw2ppfd.html b/modules/data.atmosphere/docs/reference/sw2ppfd.html
index dca9a3b..210efc3 100644
--- a/modules/data.atmosphere/docs/reference/sw2ppfd.html
+++ b/modules/data.atmosphere/docs/reference/sw2ppfd.html
@@ -2,180 +2,230 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
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+                      <a href="../articles/tdm_downscaling.html"
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>SW to PPFD</h1>
-    
-    <div class="hidden name"><code>sw2ppfd.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>CF Shortwave to PPFD</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sw2ppfd</span>(<span class='no'>sw</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sw</th>
-      <td><p>CF surface_downwelling_shortwave_flux_in_air (W/m2)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>PPFD umol /m2 / s</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Cambell and Norman 1998 p 151, ch 10</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>SW to PPFD</h1>
+
+            <div class="hidden name"><code>sw2ppfd.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>CF Shortwave to PPFD</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sw2ppfd</span>(<span class='no'>sw</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sw</th>
+              <td>
+                <p>CF surface_downwelling_shortwave_flux_in_air (W/m2)</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>PPFD umol /m2 / s</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Cambell and Norman 1998 p 151, ch 10</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
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index 6348227..3ee125c 100644
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              and predict.subdaily.workflow(). Individual variable functions actually generate the models 
              and betas from the dat.train_file and save them in the output file. save.model() and 
              save.betas() are helper functions that save the linear regression model output to a 
              specific location. In the future, we should only save the data that we actually use from the 
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>temporal_downscale_functions</h1>
-    
-    <div class="hidden name"><code>temporal.downscale.functions.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function contains the functions that do the heavy lifting in gen.subdaily.models()
-             and predict.subdaily.workflow(). Individual variable functions actually generate the models 
-             and betas from the dat.train_file and save them in the output file. save.model() and 
-             save.betas() are helper functions that save the linear regression model output to a 
-             specific location. In the future, we should only save the data that we actually use from the 
-             linear regression model because this is a large file. predict.met() is called from
-             predict.subdaily.workflow() and references the linear regression model output to 
-             predict the ensemble data.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>temporal.downscale.functions</span>(<span class='no'>dat.train</span>, <span class='no'>n.beta</span>, <span class='no'>day.window</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>temporal_downscale_functions</h1>
+
+            <div class="hidden name">
+              <code>temporal.downscale.functions.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function contains the functions that do the heavy lifting in
+              gen.subdaily.models() and predict.subdaily.workflow(). Individual
+              variable functions actually generate the models and betas from the
+              dat.train_file and save them in the output file. save.model() and
+              save.betas() are helper functions that save the linear regression
+              model output to a specific location. In the future, we should only
+              save the data that we actually use from the linear regression
+              model because this is a large file. predict.met() is called from
+              predict.subdaily.workflow() and references the linear regression
+              model output to predict the ensemble data.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>temporal.downscale.functions</span>(<span class='no'>dat.train</span>, <span class='no'>n.beta</span>, <span class='no'>day.window</span>,
   <span class='kw'>resids</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>parallel</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>n.cores</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fu'>format</span>(<span class='fu'>Sys.time</span>(), <span class='st'>"%m%d"</span>), <span class='no'>outfolder</span>,
   <span class='kw'>print.progress</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat.train</th>
-      <td><p>- training data generated by tdm_nc2dat.train.R</p></td>
-    </tr>
-    <tr>
-      <th>n.beta</th>
-      <td><p>- number of betas to generate</p></td>
-    </tr>
-    <tr>
-      <th>day.window</th>
-      <td><p>- number of days surrounding current day we want to pull
-statistics from</p></td>
-    </tr>
-    <tr>
-      <th>resids</th>
-      <td><p>- whether or not to propogate residuals, set to FALSE</p></td>
-    </tr>
-    <tr>
-      <th>parallel</th>
-      <td><p>- whether or not to run in parallel. this is a feature
-still being worked on, set to FALSE</p></td>
-    </tr>
-    <tr>
-      <th>n.cores</th>
-      <td><p>- number of cores to use parallel processing on, set to NULL</p></td>
-    </tr>
-    <tr>
-      <th>seed</th>
-      <td><p>- allows this to be reproducible</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>= where the output should be stored</p></td>
-    </tr>
-    <tr>
-      <th>print.progress</th>
-      <td><p>- print progress of model generation?</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Temporal Downscale Functions
- Met variable functions that are called in gen.subdaily.models and predict.subdaily.workflow</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>Other tdm - Temporally Downscale Meteorology: <code><a href='gen.subdaily.models.html'>gen.subdaily.models</a></code>,
-  <code><a href='lm_ensemble_sims.html'>lm_ensemble_sims</a></code>,
-  <code><a href='model.train.html'>model.train</a></code>, <code><a href='nc.merge.html'>nc.merge</a></code>,
-  <code><a href='predict_subdaily_met.html'>predict_subdaily_met</a></code>,
-  <code><a href='save.betas.html'>save.betas</a></code>, <code><a href='save.model.html'>save.model</a></code>,
-  <code><a href='subdaily_pred.html'>subdaily_pred</a></code></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat.train</th>
+              <td><p>- training data generated by tdm_nc2dat.train.R</p></td>
+            </tr>
+            <tr>
+              <th>n.beta</th>
+              <td><p>- number of betas to generate</p></td>
+            </tr>
+            <tr>
+              <th>day.window</th>
+              <td>
+                <p>
+                  - number of days surrounding current day we want to pull
+                  statistics from
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>resids</th>
+              <td>
+                <p>- whether or not to propogate residuals, set to FALSE</p>
+              </td>
+            </tr>
+            <tr>
+              <th>parallel</th>
+              <td>
+                <p>
+                  - whether or not to run in parallel. this is a feature still
+                  being worked on, set to FALSE
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.cores</th>
+              <td>
+                <p>
+                  - number of cores to use parallel processing on, set to NULL
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>seed</th>
+              <td><p>- allows this to be reproducible</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>= where the output should be stored</p></td>
+            </tr>
+            <tr>
+              <th>print.progress</th>
+              <td><p>- print progress of model generation?</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Temporal Downscale Functions Met variable functions that are called
+            in gen.subdaily.models and predict.subdaily.workflow
+          </p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              Other tdm - Temporally Downscale Meteorology:
+              <code
+                ><a href="gen.subdaily.models.html"
+                  >gen.subdaily.models</a
+                ></code
+              >,
+              <code><a href="lm_ensemble_sims.html">lm_ensemble_sims</a></code
+              >, <code><a href="model.train.html">model.train</a></code
+              >, <code><a href="nc.merge.html">nc.merge</a></code
+              >,
+              <code
+                ><a href="predict_subdaily_met.html"
+                  >predict_subdaily_met</a
+                ></code
+              >, <code><a href="save.betas.html">save.betas</a></code
+              >, <code><a href="save.model.html">save.model</a></code
+              >, <code><a href="subdaily_pred.html">subdaily_pred</a></code>
+            </p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Christy Rollinson, James Simkins
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Christy Rollinson, James Simkins
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
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+        <div class="copyright">
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
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diff --git a/modules/data.atmosphere/docs/reference/upscale_met.html b/modules/data.atmosphere/docs/reference/upscale_met.html
index bd1e523..44556de 100644
--- a/modules/data.atmosphere/docs/reference/upscale_met.html
+++ b/modules/data.atmosphere/docs/reference/upscale_met.html
@@ -2,190 +2,252 @@
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 <html>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+    <![endif]-->
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/compare_narr_cruncep_met.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/tdm_downscaling.html"
+                        >UNKNOWN TITLE</a
+                      >
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+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>upscale_met</h1>
-    
-    <div class="hidden name"><code>upscale_met.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>upscale_met</h1>
 
-    <div class="ref-description">
-    
-    <p>upscale_met upscales the temporal resolution of a dataset</p>
-    
-    </div>
+            <div class="hidden name"><code>upscale_met.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>upscale_met</span>(<span class='no'>outfolder</span>, <span class='no'>input_met</span>, <span class='kw'>resolution</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>24</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-  <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>path to directory where output should be saved
-Output is netcdf named as &lt;input_met_filename&gt;.upscaled.nc</p></td>
-    </tr>
-    <tr>
-      <th>input_met</th>
-      <td><p>path to netcdf file containing met dataset</p></td>
-    </tr>
-    <tr>
-      <th>resolution</th>
-      <td><p>desired output resolution, in days</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical: replace output file if it already exists?</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>logical: should <code><a href='http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package'>ncdf4</a></code> functions print debugging information as they run?</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>other arguments, currently ignored</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-James Simkins, Chris Black
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>upscale_met upscales the temporal resolution of a dataset</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>upscale_met</span>(<span class='no'>outfolder</span>, <span class='no'>input_met</span>, <span class='kw'>resolution</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>24</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td>
+                <p>
+                  path to directory where output should be saved Output is
+                  netcdf named as &lt;input_met_filename&gt;.upscaled.nc
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>input_met</th>
+              <td><p>path to netcdf file containing met dataset</p></td>
+            </tr>
+            <tr>
+              <th>resolution</th>
+              <td><p>desired output resolution, in days</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical: replace output file if it already exists?</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  logical: should
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/ncdf4/topics/ncdf4-package"
+                      >ncdf4</a
+                    ></code
+                  >
+                  functions print debugging information as they run?
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>other arguments, currently ignored</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          James Simkins, Chris Black
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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       </footer>
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diff --git a/modules/data.atmosphere/docs/reference/wide2long.html b/modules/data.atmosphere/docs/reference/wide2long.html
index 1ee0874..8e2585d 100644
--- a/modules/data.atmosphere/docs/reference/wide2long.html
+++ b/modules/data.atmosphere/docs/reference/wide2long.html
@@ -2,186 +2,232 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.atmosphere</a
+                >
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+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ameriflux_demo.html"
+                        >PEcAn: Importing Met data from Bondville, IL Ameriflux
+                        station</a
+                      >
+                    </li>
+                    <li>
+                      <a href="../articles/cfmet_downscaling.html"
+                        >UNKNOWN TITLE</a
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+                        >UNKNOWN TITLE</a
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Wide to Long</h1>
-    
-    <div class="hidden name"><code>wide2long.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert raster to lat, lon, var</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>wide2long</span>(<span class='no'>data.wide</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>var</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data.wide</th>
-      <td><p>data</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>latitude for rows</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>longitude for columns</p></td>
-    </tr>
-    <tr>
-      <th>var</th>
-      <td><p>variable being measured</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data.frame with colnames (lat, lon, var)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Wide to Long</h1>
+
+            <div class="hidden name"><code>wide2long.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert raster to lat, lon, var</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>wide2long</span>(<span class='no'>data.wide</span>, <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='no'>var</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data.wide</th>
+              <td><p>data</p></td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>latitude for rows</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>longitude for columns</p></td>
+            </tr>
+            <tr>
+              <th>var</th>
+              <td><p>variable being measured</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>data.frame with colnames (lat, lon, var)</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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diff --git a/modules/data.hydrology/docs/LICENSE-text.html b/modules/data.hydrology/docs/LICENSE-text.html
index 15adc3d..cda68f6 100644
--- a/modules/data.hydrology/docs/LICENSE-text.html
+++ b/modules/data.hydrology/docs/LICENSE-text.html
@@ -2,97 +2,128 @@
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+                <a class="navbar-link" href="index.html"
+                  >PEcAn.data.hydrology</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
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-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +152,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
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diff --git a/modules/data.hydrology/docs/authors.html b/modules/data.hydrology/docs/authors.html
index cf637c1..8ce8623 100644
--- a/modules/data.hydrology/docs/authors.html
+++ b/modules/data.hydrology/docs/authors.html
@@ -2,142 +2,160 @@
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.hydrology</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html"
+                  >PEcAn.data.hydrology</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.hydrology/docs/docsearch.css b/modules/data.hydrology/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/data.hydrology/docs/docsearch.css
+++ b/modules/data.hydrology/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/data.hydrology/docs/docsearch.js b/modules/data.hydrology/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/data.hydrology/docs/docsearch.js
+++ b/modules/data.hydrology/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/data.hydrology/docs/index.html b/modules/data.hydrology/docs/index.html
index 22e1128..93a3314 100644
--- a/modules/data.hydrology/docs/index.html
+++ b/modules/data.hydrology/docs/index.html
@@ -1,111 +1,171 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
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-<title>PEcAn functions used for ecological forecasts and reanalysis • PEcAn.data.hydrology</title>
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-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis •
+      PEcAn.data.hydrology
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.">
-<meta name="twitter:card" content="summary">
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    efficacy of scientific investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.hydrology</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
-  </div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html"
+                  >PEcAn.data.hydrology</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-  </div>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/data.hydrology/docs/pkgdown.css b/modules/data.hydrology/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/data.hydrology/docs/pkgdown.css
+++ b/modules/data.hydrology/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/data.hydrology/docs/pkgdown.js b/modules/data.hydrology/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/data.hydrology/docs/pkgdown.js
+++ b/modules/data.hydrology/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/data.hydrology/docs/reference/index.html b/modules/data.hydrology/docs/reference/index.html
index 0a1b0ce..a81f3ed 100644
--- a/modules/data.hydrology/docs/reference/index.html
+++ b/modules/data.hydrology/docs/reference/index.html
@@ -2,129 +2,151 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title> • PEcAn.data.hydrology</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
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-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>• PEcAn.data.hydrology</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.hydrology</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.hydrology</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/LICENSE-text.html b/modules/data.land/docs/LICENSE-text.html
index 2a3e3ec..ce75ce7 100644
--- a/modules/data.land/docs/LICENSE-text.html
+++ b/modules/data.land/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>License • PEcAn.data.land</title>
-
-<!-- jquery -->
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
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-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+    <title>License • PEcAn.data.land</title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
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+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
+    <!-- sticky kit -->
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.land</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
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-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/authors.html b/modules/data.land/docs/authors.html
index 17a768b..402bed5 100644
--- a/modules/data.land/docs/authors.html
+++ b/modules/data.land/docs/authors.html
@@ -2,150 +2,164 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.data.land</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.data.land</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.land</a>
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-      </span>
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-      <ul class="nav navbar-nav">
-        <li>
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-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Alexey Shiklomanov</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Alexey Shiklomanov</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/docsearch.css b/modules/data.land/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/data.land/docs/docsearch.css
+++ b/modules/data.land/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/data.land/docs/docsearch.js b/modules/data.land/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/data.land/docs/docsearch.js
+++ b/modules/data.land/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/data.land/docs/index.html b/modules/data.land/docs/index.html
index 8d0a666..20e7bd0 100644
--- a/modules/data.land/docs/index.html
+++ b/modules/data.land/docs/index.html
@@ -1,111 +1,169 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for ecological forecasts and reanalysis • PEcAn.data.land</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis •
+      PEcAn.data.land
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    efficacy of scientific investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.land</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation.
-  </div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-  </div>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/data.land/docs/pkgdown.css b/modules/data.land/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/data.land/docs/pkgdown.css
+++ b/modules/data.land/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/data.land/docs/pkgdown.js b/modules/data.land/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/data.land/docs/pkgdown.js
+++ b/modules/data.land/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/data.land/docs/reference/Clean_Tucson.html b/modules/data.land/docs/reference/Clean_Tucson.html
index 9206b11..711a3ae 100644
--- a/modules/data.land/docs/reference/Clean_Tucson.html
+++ b/modules/data.land/docs/reference/Clean_Tucson.html
@@ -2,133 +2,154 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-
-<meta property="og:title" content="Clean_Tucson — Clean_Tucson" />
-
-<meta property="og:description" content="tree core QAQC" />
-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Clean_Tucson — Clean_Tucson • PEcAn.data.land</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Clean_Tucson — Clean_Tucson" />
+
+    <meta property="og:description" content="tree core QAQC" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-        <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Clean_Tucson</h1>
-    
-    <div class="hidden name"><code>Clean_Tucson.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>tree core QAQC</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Clean_Tucson</h1>
 
-    <pre class="usage"><span class='fu'>Clean_Tucson</span>(<span class='no'>file</span>)</pre>
-        
+            <div class="hidden name"><code>Clean_Tucson.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>tree core QAQC</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>Clean_Tucson</span>(<span class='no'>file</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/InventoryGrowthFusion.html b/modules/data.land/docs/reference/InventoryGrowthFusion.html
index 701218d..2e54e44 100644
--- a/modules/data.land/docs/reference/InventoryGrowthFusion.html
+++ b/modules/data.land/docs/reference/InventoryGrowthFusion.html
@@ -2,181 +2,242 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>InventoryGrowthFusion — InventoryGrowthFusion • PEcAn.data.land</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="InventoryGrowthFusion — InventoryGrowthFusion" />
-
-<meta property="og:description" content="this code fuses forest inventory data with tree growth data (tree ring or dendrometer band)
-for the same plots. Code is a rewrite of Clark et al 2007 Ecol Appl into JAGS" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      InventoryGrowthFusion — InventoryGrowthFusion • PEcAn.data.land
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="InventoryGrowthFusion — InventoryGrowthFusion"
+    />
+
+    <meta
+      property="og:description"
+      content="this code fuses forest inventory data with tree growth data (tree ring or dendrometer band)
+for the same plots. Code is a rewrite of Clark et al 2007 Ecol Appl into JAGS"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              >
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>InventoryGrowthFusion</h1>
-    
-    <div class="hidden name"><code>InventoryGrowthFusion.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>this code fuses forest inventory data with tree growth data (tree ring or dendrometer band)
-for the same plots. Code is a rewrite of Clark et al 2007 Ecol Appl into JAGS</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>InventoryGrowthFusion</span>(<span class='no'>data</span>, <span class='kw'>cov.data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>time_data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>InventoryGrowthFusion</h1>
+
+            <div class="hidden name"><code>InventoryGrowthFusion.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              this code fuses forest inventory data with tree growth data (tree
+              ring or dendrometer band) for the same plots. Code is a rewrite of
+              Clark et al 2007 Ecol Appl into JAGS
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>InventoryGrowthFusion</span>(<span class='no'>data</span>, <span class='kw'>cov.data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>time_data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>n.iter</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>n.chunk</span> <span class='kw'>=</span> <span class='no'>n.iter</span>, <span class='kw'>n.burn</span> <span class='kw'>=</span> <span class='fu'>min</span>(<span class='no'>n.chunk</span>, <span class='fl'>2000</span>),
   <span class='kw'>random</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>time_varying</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>burnin_plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>save.jags</span> <span class='kw'>=</span> <span class='st'>"IGF.txt"</span>, <span class='kw'>z0</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>save.state</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>restart</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data</th>
-      <td><p>list of data inputs</p></td>
-    </tr>
-    <tr>
-      <th>n.chunk</th>
-      <td><p>number of MCMC steps to evaluate at a time. Will only return LAST. If restarting, second number in vector is chunk to start from</p></td>
-    </tr>
-    <tr>
-      <th>n.burn</th>
-      <td><p>number of steps to automatically discard as burn-in</p></td>
-    </tr>
-    <tr>
-      <th>random</th>
-      <td><p>= whether or not to include random effects</p></td>
-    </tr>
-    <tr>
-      <th>save.state</th>
-      <td><p>whether or not to include inferred DBH in output (can be large). Enter numeric value to save.state periodically (in terms of n.chunk)</p></td>
-    </tr>
-    <tr>
-      <th>restart</th>
-      <td><p>final mcmc.list from previous execution. NULL for new run. TRUE to save final state for new run.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>an mcmc.list object</p>
-    
-    <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
-
-    <p>Requires JAGS</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#note">Note</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data</th>
+              <td><p>list of data inputs</p></td>
+            </tr>
+            <tr>
+              <th>n.chunk</th>
+              <td>
+                <p>
+                  number of MCMC steps to evaluate at a time. Will only return
+                  LAST. If restarting, second number in vector is chunk to start
+                  from
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.burn</th>
+              <td>
+                <p>number of steps to automatically discard as burn-in</p>
+              </td>
+            </tr>
+            <tr>
+              <th>random</th>
+              <td><p>= whether or not to include random effects</p></td>
+            </tr>
+            <tr>
+              <th>save.state</th>
+              <td>
+                <p>
+                  whether or not to include inferred DBH in output (can be
+                  large). Enter numeric value to save.state periodically (in
+                  terms of n.chunk)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>restart</th>
+              <td>
+                <p>
+                  final mcmc.list from previous execution. NULL for new run.
+                  TRUE to save final state for new run.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>an mcmc.list object</p>
+
+          <h2 class="hasAnchor" id="note">
+            <a class="anchor" href="#note"></a>Note
+          </h2>
+
+          <p>Requires JAGS</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#note">Note</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/data.land/docs/reference/InventoryGrowthFusionDiagnostics.html b/modules/data.land/docs/reference/InventoryGrowthFusionDiagnostics.html
index 713591c..aa706f5 100644
--- a/modules/data.land/docs/reference/InventoryGrowthFusionDiagnostics.html
+++ b/modules/data.land/docs/reference/InventoryGrowthFusionDiagnostics.html
@@ -2,151 +2,189 @@
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+      PEcAn.data.land
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+    />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>InventoryGrowthFusionDiagnostics</h1>
-    
-    <div class="hidden name"><code>InventoryGrowthFusionDiagnostics.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>InventoryGrowthFusionDiagnostics</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>InventoryGrowthFusionDiagnostics</span>(<span class='no'>jags.out</span>, <span class='kw'>combined</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>jags.out</th>
-      <td><p>output mcmc.list from InventoryGrowthFusion</p></td>
-    </tr>
-    <tr>
-      <th>combined</th>
-      <td><p>data output from matchInventoryRings</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>InventoryGrowthFusionDiagnostics</h1>
+
+            <div class="hidden name">
+              <code>InventoryGrowthFusionDiagnostics.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>InventoryGrowthFusionDiagnostics</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>InventoryGrowthFusionDiagnostics</span>(<span class='no'>jags.out</span>, <span class='kw'>combined</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>jags.out</th>
+              <td><p>output mcmc.list from InventoryGrowthFusion</p></td>
+            </tr>
+            <tr>
+              <th>combined</th>
+              <td><p>data output from matchInventoryRings</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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diff --git a/modules/data.land/docs/reference/Read_Tucson.html b/modules/data.land/docs/reference/Read_Tucson.html
index f076999..6f8445b 100644
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@@ -2,137 +2,164 @@
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-    
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-        
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read_Tucson</h1>
+
+            <div class="hidden name"><code>Read_Tucson.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              wrapper around read.tucson that loads a whole directory of tree
+              ring files and calls a 'clean' function that removes redundant
+              records (WinDendro can sometimes create duplicate records when
+              editing)
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>Read_Tucson</span>(<span class='no'>folder</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
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+        <div class="copyright">
+          <p>Developed by .</p>
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diff --git a/modules/data.land/docs/reference/buildJAGSdata_InventoryRings.html b/modules/data.land/docs/reference/buildJAGSdata_InventoryRings.html
index 3fae47f..4e2d358 100644
--- a/modules/data.land/docs/reference/buildJAGSdata_InventoryRings.html
+++ b/modules/data.land/docs/reference/buildJAGSdata_InventoryRings.html
@@ -2,159 +2,210 @@
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 <html>
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+      PEcAn.data.land
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
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+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    <script src="../pkgdown.js"></script>
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+      content="Format ring &amp; plot data for JAGA — buildJAGSdata_InventoryRings"
+    />
+
+    <meta
+      property="og:description"
+      content="builds the JAGS data object for the tree ring / inventory fusion code
+also sets all the priors"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Format ring &amp; plot data for JAGA</h1>
-    
-    <div class="hidden name"><code>buildJAGSdata_InventoryRings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>builds the JAGS data object for the tree ring / inventory fusion code
-also sets all the priors</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>buildJAGSdata_InventoryRings</span>(<span class='no'>combined</span>, <span class='kw'>inc.unit.conv</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>combined</th>
-      <td><p>object returned from matchInventoryRings. Matrix with both increment and plot data</p></td>
-    </tr>
-    <tr>
-      <th>inc.unit.conv</th>
-      <td><p>conversion factor from loaded increments to cm (of radius)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Format ring &amp; plot data for JAGA</h1>
+
+            <div class="hidden name">
+              <code>buildJAGSdata_InventoryRings.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              builds the JAGS data object for the tree ring / inventory fusion
+              code also sets all the priors
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>buildJAGSdata_InventoryRings</span>(<span class='no'>combined</span>, <span class='kw'>inc.unit.conv</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>combined</th>
+              <td>
+                <p>
+                  object returned from matchInventoryRings. Matrix with both
+                  increment and plot data
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>inc.unit.conv</th>
+              <td>
+                <p>
+                  conversion factor from loaded increments to cm (of radius)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/cohort2pool.html b/modules/data.land/docs/reference/cohort2pool.html
index 13cdc20..5225d0d 100644
--- a/modules/data.land/docs/reference/cohort2pool.html
+++ b/modules/data.land/docs/reference/cohort2pool.html
@@ -2,163 +2,210 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>cohort2pool function
-Calculates total biomass using veg cohort file. — cohort2pool • PEcAn.data.land</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
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+Calculates total biomass using veg cohort file. — cohort2pool"
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+Calculates total biomass using veg cohort file."
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-<div class="row">
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-    <h1>cohort2pool function
-Calculates total biomass using veg cohort file.</h1>
-    
-    <div class="hidden name"><code>cohort2pool.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>cohort2pool function
-Calculates total biomass using veg cohort file.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>cohort2pool</span>(<span class='no'>veg_file</span>, <span class='kw'>allom_param</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>veg_file</th>
-      <td><p>path to standard cohort veg_file</p></td>
-    </tr>
-    <tr>
-      <th>allom_param</th>
-      <td><p>parameters for allometric equation, a and b. Based on base-10 log-log linear model (power law)</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              cohort2pool function Calculates total biomass using veg cohort
+              file.
+            </h1>
+
+            <div class="hidden name"><code>cohort2pool.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              cohort2pool function Calculates total biomass using veg cohort
+              file.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>cohort2pool</span>(<span class='no'>veg_file</span>, <span class='kw'>allom_param</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>veg_file</th>
+              <td><p>path to standard cohort veg_file</p></td>
+            </tr>
+            <tr>
+              <th>allom_param</th>
+              <td>
+                <p>
+                  parameters for allometric equation, a and b. Based on base-10
+                  log-log linear model (power law)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>veg_file</span> <span class='kw'>&lt;-</span> <span class='st'>"~/downloads/FFT_site_1-25665/FFT.2008.veg.rds"</span>
 <span class='fu'>cohort2pool</span>(<span class='kw'>veg_File</span> <span class='kw'>=</span> <span class='no'>veg_file</span>, <span class='kw'>allom_param</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
 <span class='co'># }</span></pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Saloni Shah
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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diff --git a/modules/data.land/docs/reference/dataone_download.html b/modules/data.land/docs/reference/dataone_download.html
index a546ecc..333f089 100644
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+++ b/modules/data.land/docs/reference/dataone_download.html
@@ -2,170 +2,223 @@
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>DataONE download</h1>
-    
-    <div class="hidden name"><code>dataone_download.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Adapts the dataone::getDataPackage workflow to allow users to download data from the DataONE federation by simply entering the doi or associated package id</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>dataone_download</span>(<span class='no'>id</span>, <span class='kw'>filepath</span> <span class='kw'>=</span> <span class='st'>"/fs/data1/pecan.data/dbfiles"</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>DataONE download</h1>
+
+            <div class="hidden name"><code>dataone_download.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Adapts the dataone::getDataPackage workflow to allow users to
+              download data from the DataONE federation by simply entering the
+              doi or associated package id
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dataone_download</span>(<span class='no'>id</span>, <span class='kw'>filepath</span> <span class='kw'>=</span> <span class='st'>"/fs/data1/pecan.data/dbfiles"</span>,
   <span class='kw'>CNode</span> <span class='kw'>=</span> <span class='st'>"PROD"</span>, <span class='kw'>lazyLoad</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>id</th>
-      <td><p>"The identifier of a package, package metadata or other package member" -- dataone r</p></td>
-    </tr>
-    <tr>
-      <th>filepath</th>
-      <td><p>path to where files will be stored</p></td>
-    </tr>
-    <tr>
-      <th>CNode</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>lazyLoad</th>
-      <td><p>"A logical value. If TRUE, then only package member system metadata is downloaded and not data. The default is FALSE." -- dataone R</p></td>
-    </tr>
-    <tr>
-      <th>quiet</th>
-      <td><p>"A 'logical'. If TRUE (the default) then informational messages will not be printed." -- dataone R</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>id</th>
+              <td>
+                <p>
+                  "The identifier of a package, package metadata or other
+                  package member" -- dataone r
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>filepath</th>
+              <td><p>path to where files will be stored</p></td>
+            </tr>
+            <tr>
+              <th>CNode</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>lazyLoad</th>
+              <td>
+                <p>
+                  "A logical value. If TRUE, then only package member system
+                  metadata is downloaded and not data. The default is FALSE." --
+                  dataone R
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>quiet</th>
+              <td>
+                <p>
+                  "A 'logical'. If TRUE (the default) then informational
+                  messages will not be printed." -- dataone R
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>dataone_download</span>(<span class='kw'>id</span> <span class='kw'>=</span> <span class='st'>"doi:10.6073/pasta/63ad7159306bc031520f09b2faefcf87"</span>, <span class='kw'>filepath</span> <span class='kw'>=</span> <span class='st'>"/fs/data1/pecan.data/dbfiles"</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Liam P Burke, <a href='mailto:lpburke@bu.edu'>lpburke@bu.edu</a>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Liam P Burke, <a href="mailto:lpburke@bu.edu">lpburke@bu.edu</a>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/data.land/docs/reference/download_package_rm.html b/modules/data.land/docs/reference/download_package_rm.html
index 6f72dac..3d49c4d 100644
--- a/modules/data.land/docs/reference/download_package_rm.html
+++ b/modules/data.land/docs/reference/download_package_rm.html
@@ -2,167 +2,220 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    />
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+    />
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+      property="og:description"
+      content="Uses resource_map and dataone::getPackage to download the data into a BagItFile. Then utils::unzip unzips the data and stores in the user's directory."
+    />
+    <meta name="twitter:card" content="summary" />
+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download_packages</h1>
-    
-    <div class="hidden name"><code>download_package_rm.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Uses resource_map and dataone::getPackage to download the data into a BagItFile. Then utils::unzip unzips the data and stores in the user's directory.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>download_package_rm</span>(<span class='no'>resource_map</span>, <span class='no'>directory</span>, <span class='kw'>CNode</span> <span class='kw'>=</span> <span class='st'>"PROD"</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download_packages</h1>
+
+            <div class="hidden name"><code>download_package_rm.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Uses resource_map and dataone::getPackage to download the data
+              into a BagItFile. Then utils::unzip unzips the data and stores in
+              the user's directory.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>download_package_rm</span>(<span class='no'>resource_map</span>, <span class='no'>directory</span>, <span class='kw'>CNode</span> <span class='kw'>=</span> <span class='st'>"PROD"</span>,
   <span class='kw'>download_format</span> <span class='kw'>=</span> <span class='st'>"application/bagit-097"</span>,
   <span class='kw'>overwrite_directory</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>resource_map</th>
-      <td><p>the resource map that corresponds to the given data package</p></td>
-    </tr>
-    <tr>
-      <th>directory</th>
-      <td><p>location that download.packages places the data</p></td>
-    </tr>
-    <tr>
-      <th>CNode</th>
-      <td><p>defaults to "PROD"</p></td>
-    </tr>
-    <tr>
-      <th>download_format</th>
-      <td><p>typically "application/bagit-097". Other possible formats currently unknown.</p></td>
-    </tr>
-    <tr>
-      <th>overwrite_directory</th>
-      <td><p>boolean that indicates whether or not the function should overwrite the directory</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>results of download</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>resource_map</th>
+              <td>
+                <p>
+                  the resource map that corresponds to the given data package
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>directory</th>
+              <td><p>location that download.packages places the data</p></td>
+            </tr>
+            <tr>
+              <th>CNode</th>
+              <td><p>defaults to "PROD"</p></td>
+            </tr>
+            <tr>
+              <th>download_format</th>
+              <td>
+                <p>
+                  typically "application/bagit-097". Other possible formats
+                  currently unknown.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite_directory</th>
+              <td>
+                <p>
+                  boolean that indicates whether or not the function should
+                  overwrite the directory
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>results of download</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+
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diff --git a/modules/data.land/docs/reference/ens_veg_module.html b/modules/data.land/docs/reference/ens_veg_module.html
index cc7e87e..d289e6a 100644
--- a/modules/data.land/docs/reference/ens_veg_module.html
+++ b/modules/data.land/docs/reference/ens_veg_module.html
@@ -2,184 +2,250 @@
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+
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Sampling/ensemble module</h1>
-    
-    <div class="hidden name"><code>ens_veg_module.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Sampling/ensemble module</h1>
 
-    <div class="ref-description">
-    
-    <p>Sampling/ensemble module</p>
-    
-    </div>
+            <div class="hidden name"><code>ens_veg_module.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>ens_veg_module</span>(<span class='no'>getveg.id</span>, <span class='no'>dbparms</span>, <span class='no'>input_veg</span>, <span class='no'>outfolder</span>, <span class='no'>machine</span>,
-  <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>n.ensemble</span>, <span class='no'>new_site</span>, <span class='no'>host</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>getveg.id</th>
-      <td><p>list, input.id and dbfile.id of the IC file in intermediate pecan standard</p></td>
-    </tr>
-    <tr>
-      <th>dbparms</th>
-      <td><p>list, settings$database info reqired for opening a connection to DB</p></td>
-    </tr>
-    <tr>
-      <th>input_veg</th>
-      <td><p>list, this is a sublist of settings$run$inputs that has info about source, id, metadata of the requested IC file</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>path to where the processed files will be written</p></td>
-    </tr>
-    <tr>
-      <th>machine</th>
-      <td><p>data frame, DB info regarding localhost machine id/hostname etc.</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$start.date, otherwise start_date of the IC file in DB</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$end.date, otherwise end_date of the IC file in DB</p></td>
-    </tr>
-    <tr>
-      <th>n.ensemble</th>
-      <td><p>integer, ensemble member number</p></td>
-    </tr>
-    <tr>
-      <th>new_site</th>
-      <td><p>data frame, id/lat/lon/name info about the site</p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>list, host info as in settings$host, host$name forced to be "localhost" upstream</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Sampling/ensemble module</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>ens_veg_module</span>(<span class='no'>getveg.id</span>, <span class='no'>dbparms</span>, <span class='no'>input_veg</span>, <span class='no'>outfolder</span>, <span class='no'>machine</span>,
+  <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>n.ensemble</span>, <span class='no'>new_site</span>, <span class='no'>host</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>getveg.id</th>
+              <td>
+                <p>
+                  list, input.id and dbfile.id of the IC file in intermediate
+                  pecan standard
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>dbparms</th>
+              <td>
+                <p>
+                  list, settings$database info reqired for opening a connection
+                  to DB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>input_veg</th>
+              <td>
+                <p>
+                  list, this is a sublist of settings$run$inputs that has info
+                  about source, id, metadata of the requested IC file
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>path to where the processed files will be written</p></td>
+            </tr>
+            <tr>
+              <th>machine</th>
+              <td>
+                <p>
+                  data frame, DB info regarding localhost machine id/hostname
+                  etc.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  date in "YYYY-MM-DD" format, in case of source==FIA it's the
+                  settings$run$start.date, otherwise start_date of the IC file
+                  in DB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  date in "YYYY-MM-DD" format, in case of source==FIA it's the
+                  settings$run$end.date, otherwise end_date of the IC file in DB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>n.ensemble</th>
+              <td><p>integer, ensemble member number</p></td>
+            </tr>
+            <tr>
+              <th>new_site</th>
+              <td><p>data frame, id/lat/lon/name info about the site</p></td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td>
+                <p>
+                  list, host info as in settings$host, host$name forced to be
+                  "localhost" upstream
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
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diff --git a/modules/data.land/docs/reference/extract.stringCode.html b/modules/data.land/docs/reference/extract.stringCode.html
index 0458bf4..9dd6cf9 100644
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>extract.string.code</h1>
-    
-    <div class="hidden name"><code>extract.stringCode.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>extract.string.code</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>extract.string.code</h1>
 
-    <pre class="usage"><span class='fu'>extract.stringCode</span>(<span class='no'>x</span>, <span class='kw'>extractor</span> <span class='kw'>=</span> <span class='no'>from.TreeCode</span>)</pre>
-        
+            <div class="hidden name"><code>extract.stringCode.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>extract.string.code</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>extract.stringCode</span>(<span class='no'>x</span>, <span class='kw'>extractor</span> <span class='kw'>=</span> <span class='no'>from.TreeCode</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/data.land/docs/reference/extract_FIA.html b/modules/data.land/docs/reference/extract_FIA.html
index 9566979..7420dd1 100644
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>extract_FIA</h1>
-    
-    <div class="hidden name"><code>extract_FIA.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>extract_FIA</h1>
 
-    <div class="ref-description">
-    
-    <p>extract_FIA</p>
-    
-    </div>
+            <div class="hidden name"><code>extract_FIA.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>extract_FIA</span>(<span class='no'>lon</span>, <span class='no'>lat</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>gridres</span> <span class='kw'>=</span> <span class='fl'>0.075</span>, <span class='no'>dbparms</span>)</pre>
-        
+          <div class="ref-description">
+            <p>extract_FIA</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>extract_FIA</span>(<span class='no'>lon</span>, <span class='no'>lat</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='kw'>gridres</span> <span class='kw'>=</span> <span class='fl'>0.075</span>, <span class='no'>dbparms</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
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diff --git a/modules/data.land/docs/reference/extract_soil_gssurgo.html b/modules/data.land/docs/reference/extract_soil_gssurgo.html
index 8b23317..4a0bd81 100644
--- a/modules/data.land/docs/reference/extract_soil_gssurgo.html
+++ b/modules/data.land/docs/reference/extract_soil_gssurgo.html
@@ -2,171 +2,208 @@
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+    </title>
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Extract soil data from gssurgo</h1>
-    
-    <div class="hidden name"><code>extract_soil_gssurgo.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Extract soil data from gssurgo</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>extract_soil_gssurgo</span>(<span class='no'>outdir</span>, <span class='no'>lat</span>, <span class='no'>lon</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Output directory for writing down the netcdf file</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>Latitude</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>Longitude</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>It returns the address for the generated soil netcdf file</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Extract soil data from gssurgo</h1>
+
+            <div class="hidden name"><code>extract_soil_gssurgo.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Extract soil data from gssurgo</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>extract_soil_gssurgo</span>(<span class='no'>outdir</span>, <span class='no'>lat</span>, <span class='no'>lon</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Output directory for writing down the netcdf file</p></td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>Latitude</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>Longitude</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>It returns the address for the generated soil netcdf file</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>outdir</span>  <span class='kw'>&lt;-</span> <span class='st'>"~/paleon/envTest"</span>
 <span class='no'>lat</span>     <span class='kw'>&lt;-</span> <span class='fl'>40</span>
 <span class='no'>lon</span>     <span class='kw'>&lt;-</span> -<span class='fl'>80</span>
 <span class='co'># }</span><span class='co'># NOT RUN {</span>
    <span class='kw pkg'>PEcAn.data.land</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.data.land/topics/extract_soil_gssurgo'>extract_soil_gssurgo</a></span>(<span class='no'>outdir</span>,<span class='no'>lat</span>,<span class='no'>lon</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Hamze Dokoohaki
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Hamze Dokoohaki
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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-
diff --git a/modules/data.land/docs/reference/extract_soil_nc.html b/modules/data.land/docs/reference/extract_soil_nc.html
index b076f08..c3416ac 100644
--- a/modules/data.land/docs/reference/extract_soil_nc.html
+++ b/modules/data.land/docs/reference/extract_soil_nc.html
@@ -2,133 +2,167 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Extract soil data</h1>
-    
-    <div class="hidden name"><code>extract_soil_nc.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Extract soil data</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>extract_soil_nc</span>(<span class='no'>in.file</span>, <span class='no'>outdir</span>, <span class='no'>lat</span>, <span class='no'>lon</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.file</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Extract soil data</h1>
+
+            <div class="hidden name"><code>extract_soil_nc.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Extract soil data</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>extract_soil_nc</span>(<span class='no'>in.file</span>, <span class='no'>outdir</span>, <span class='no'>lat</span>, <span class='no'>lon</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.file</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>in.file</span> <span class='kw'>&lt;-</span> <span class='st'>"~/paleon/env_paleon/soil/paleon_soil.nc"</span>
 <span class='no'>outdir</span>  <span class='kw'>&lt;-</span> <span class='st'>"~/paleon/envTest"</span>
 <span class='no'>lat</span>     <span class='kw'>&lt;-</span> <span class='fl'>40</span>
@@ -136,32 +170,28 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span><span class='co'># NOT RUN {</span>
    <span class='kw pkg'>PEcAn.data.land</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.data.land/topics/extract_soil_nc'>extract_soil_nc</a></span>(<span class='no'>in.file</span>,<span class='no'>outdir</span>,<span class='no'>lat</span>,<span class='no'>lon</span>)
 <span class='co'># }</span></pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
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-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
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diff --git a/modules/data.land/docs/reference/extract_veg.html b/modules/data.land/docs/reference/extract_veg.html
index cf1f2d5..444e848 100644
--- a/modules/data.land/docs/reference/extract_veg.html
+++ b/modules/data.land/docs/reference/extract_veg.html
@@ -2,139 +2,163 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>load_veg</h1>
-    
-    <div class="hidden name"><code>extract_veg.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load_veg</h1>
 
-    <div class="ref-description">
-    
-    <p>Function queries a DB to extract veg info downstream</p>
-    
-    </div>
+            <div class="hidden name"><code>extract_veg.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Function queries a DB to extract veg info downstream</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>extract_veg</span>(<span class='no'>new_site</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>source</span>, <span class='no'>gridres</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>extract_veg</span>(<span class='no'>new_site</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>source</span>, <span class='no'>gridres</span>,
   <span class='kw'>format_name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>machine_host</span>, <span class='no'>dbparms</span>, <span class='no'>outfolder</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-        
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <h2>Author</h2>
 
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/fia.to.psscss.html b/modules/data.land/docs/reference/fia.to.psscss.html
index 0ebe2ba..00b2278 100644
--- a/modules/data.land/docs/reference/fia.to.psscss.html
+++ b/modules/data.land/docs/reference/fia.to.psscss.html
@@ -2,156 +2,185 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<script src="../pkgdown.js"></script>
-
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="fia.to.psscss — fia.to.psscss" />
+
+    <meta property="og:description" content="convert x into a table" />
+    <meta name="twitter:card" content="summary" />
+
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+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>fia.to.psscss</h1>
-    
-    <div class="hidden name"><code>fia.to.psscss.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>fia.to.psscss</h1>
 
-    <div class="ref-description">
-    
-    <p>convert x into a table</p>
-    
-    </div>
+            <div class="hidden name"><code>fia.to.psscss.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>convert x into a table</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>fia.to.psscss</span>(<span class='no'>settings</span>, <span class='kw'>lat</span> <span class='kw'>=</span> <span class='fu'>as.numeric</span>(<span class='no'>settings</span>$<span class='no'>run</span>$<span class='no'>site</span>$<span class='no'>lat</span>),
+          <pre
+            class="usage"
+          ><span class='fu'>fia.to.psscss</span>(<span class='no'>settings</span>, <span class='kw'>lat</span> <span class='kw'>=</span> <span class='fu'>as.numeric</span>(<span class='no'>settings</span>$<span class='no'>run</span>$<span class='no'>site</span>$<span class='no'>lat</span>),
   <span class='kw'>lon</span> <span class='kw'>=</span> <span class='fu'>as.numeric</span>(<span class='no'>settings</span>$<span class='no'>run</span>$<span class='no'>site</span>$<span class='no'>lon</span>),
   <span class='kw'>year</span> <span class='kw'>=</span> <span class='kw pkg'>lubridate</span><span class='kw ns'>::</span><span class='fu'><a href='http://lubridate.tidyverse.org/reference/year.html'>year</a></span>(<span class='no'>settings</span>$<span class='no'>run</span>$<span class='no'>start.date</span>), <span class='kw'>gridres</span> <span class='kw'>=</span> <span class='fl'>0.075</span>,
   <span class='kw'>min.year</span> <span class='kw'>=</span> <span class='no'>year</span> - <span class='fl'>5</span>, <span class='kw'>max.year</span> <span class='kw'>=</span> <span class='no'>year</span> + <span class='fl'>5</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>create</th>
-      <td><p>pss/css files based on data in the fia database</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>create</th>
+              <td><p>pss/css files based on data in the fia database</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze, Rob Kooper, Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze, Rob Kooper, Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/find.land.html b/modules/data.land/docs/reference/find.land.html
index 6eb7daf..86f8348 100644
--- a/modules/data.land/docs/reference/find.land.html
+++ b/modules/data.land/docs/reference/find.land.html
@@ -2,163 +2,194 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="find.land — find.land" />
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-<meta property="og:description" content="find land" />
-<meta name="twitter:card" content="summary" />
-
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-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>find.land — find.land • PEcAn.data.land</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
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+    <script src="../pkgdown.js"></script>
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+    <meta property="og:description" content="find land" />
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+                <span
+                  class="label label-default"
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+                  >1.6.0</span
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+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>find.land</h1>
-    
-    <div class="hidden name"><code>find.land.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>find land</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>find.land</span>(<span class='no'>lat</span>, <span class='no'>lon</span>, <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>lat</th>
-      <td><p>vector of latitudes</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>vector of longitudes</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data frame with numeric lat, lon and logical value 'land'</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>extract terrestrial lat and lon coordinates from a grid</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>find.land</h1>
+
+            <div class="hidden name"><code>find.land.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>find land</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>find.land</span>(<span class='no'>lat</span>, <span class='no'>lon</span>, <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>lat</th>
+              <td><p>vector of latitudes</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>vector of longitudes</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>data frame with numeric lat, lon and logical value 'land'</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>extract terrestrial lat and lon coordinates from a grid</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/format_identifier.html b/modules/data.land/docs/reference/format_identifier.html
index d525b37..4e073b7 100644
--- a/modules/data.land/docs/reference/format_identifier.html
+++ b/modules/data.land/docs/reference/format_identifier.html
@@ -2,153 +2,197 @@
 <!DOCTYPE html>
 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="format_identifier — format_identifier" />
+
+    <meta
+      property="og:description"
+      content="This function is for formatting purposes. It simply inserts the doi or id that the user wishes to query into Solr format so that it is compatible with the dataoneR query functionality in the PEcAn function"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+                type="button"
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
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+                <li>
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+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>format_identifier</h1>
-    
-    <div class="hidden name"><code>format_identifier.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function is for formatting purposes. It simply inserts the doi or id that the user wishes to query into Solr format so that it is compatible with the dataoneR query functionality in the PEcAn function</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>format_identifier</span>(<span class='no'>id</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>id</th>
-      <td><p>the doi or other identifier linked to the package in DataONE</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>returns the id in the proper format for querying the DataONE Federation (using solrQuery syntax)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>format_identifier</h1>
+
+            <div class="hidden name"><code>format_identifier.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function is for formatting purposes. It simply inserts the
+              doi or id that the user wishes to query into Solr format so that
+              it is compatible with the dataoneR query functionality in the
+              PEcAn function
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>format_identifier</span>(<span class='no'>id</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>id</th>
+              <td>
+                <p>
+                  the doi or other identifier linked to the package in DataONE
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            returns the id in the proper format for querying the DataONE
+            Federation (using solrQuery syntax)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Liam P Burke, <a href='mailto:lpburke@bu.edu'>lpburke@bu.edu</a>
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Liam P Burke, <a href="mailto:lpburke@bu.edu">lpburke@bu.edu</a>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/from.Tag.html b/modules/data.land/docs/reference/from.Tag.html
index e916ec8..55885f3 100644
--- a/modules/data.land/docs/reference/from.Tag.html
+++ b/modules/data.land/docs/reference/from.Tag.html
@@ -2,133 +2,154 @@
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+      crossorigin="anonymous"
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-<div class="row">
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-    <div class="page-header">
-    <h1>from.Tag</h1>
-    
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-    </div>
-
-    <div class="ref-description">
-    
-    <p>from.Tag</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>from.Tag</h1>
 
-    <pre class="usage"><span class='fu'>from.Tag</span>(<span class='no'>x</span>)</pre>
-        
+            <div class="hidden name"><code>from.Tag.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>from.Tag</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>from.Tag</span>(<span class='no'>x</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
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diff --git a/modules/data.land/docs/reference/from.TreeCode.html b/modules/data.land/docs/reference/from.TreeCode.html
index a22ed86..4e57154 100644
--- a/modules/data.land/docs/reference/from.TreeCode.html
+++ b/modules/data.land/docs/reference/from.TreeCode.html
@@ -2,133 +2,154 @@
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+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    <script
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+              <button
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+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
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+              <ul class="nav navbar-nav">
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-    <div class="page-header">
-    <h1>from.TreeCode</h1>
-    
-    <div class="hidden name"><code>from.TreeCode.Rd</code></div>
-    </div>
-
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-    
-    <p>from.TreeCode</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>from.TreeCode</h1>
 
-    <pre class="usage"><span class='fu'>from.TreeCode</span>(<span class='no'>x</span>)</pre>
-        
+            <div class="hidden name"><code>from.TreeCode.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>from.TreeCode</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>from.TreeCode</span>(<span class='no'>x</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
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+      </div>
 
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-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/data.land/docs/reference/gSSURGO.Query.html b/modules/data.land/docs/reference/gSSURGO.Query.html
index 73daeab..f17cf09 100644
--- a/modules/data.land/docs/reference/gSSURGO.Query.html
+++ b/modules/data.land/docs/reference/gSSURGO.Query.html
@@ -2,157 +2,213 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+      gSSURGO.Query • PEcAn.data.land
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>This function queries the gSSURGO database for a series of map unit keys</h1>
-    
-    <div class="hidden name"><code>gSSURGO.Query.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function queries the gSSURGO database for a series of map unit keys</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>gSSURGO.Query</span>(<span class='kw'>mukeys</span> <span class='kw'>=</span> <span class='fl'>2747727</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mukeys</th>
-      <td><p>map unit key from gssurgo</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a dataframe with soil properties. units can be looked up from database documentation</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Full documention of available tables and their relationships can be found here <a href='www.sdmdataaccess.nrcs.usda.gov/QueryHelp.aspx'>www.sdmdataaccess.nrcs.usda.gov/QueryHelp.aspx</a>
-There have been occasions where NRCS made some minor changes to the structure of the API which this code is where those changes need
-to be implemneted here.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              This function queries the gSSURGO database for a series of map
+              unit keys
+            </h1>
+
+            <div class="hidden name"><code>gSSURGO.Query.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function queries the gSSURGO database for a series of map
+              unit keys
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>gSSURGO.Query</span>(<span class='kw'>mukeys</span> <span class='kw'>=</span> <span class='fl'>2747727</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mukeys</th>
+              <td><p>map unit key from gssurgo</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            a dataframe with soil properties. units can be looked up from
+            database documentation
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Full documention of available tables and their relationships can be
+            found here
+            <a href="www.sdmdataaccess.nrcs.usda.gov/QueryHelp.aspx"
+              >www.sdmdataaccess.nrcs.usda.gov/QueryHelp.aspx</a
+            >
+            There have been occasions where NRCS made some minor changes to the
+            structure of the API which this code is where those changes need to
+            be implemneted here.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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index 1b3593d..67af9c2 100644
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+      get.attributes • PEcAn.data.land
+    </title>
+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Retrieve attribute information from a vector or raster layer</h1>
-    
-    <div class="hidden name"><code>get.attributes.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to extract attribute information from vector or raster data layer.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.attributes</span>(<span class='no'>file</span>, <span class='no'>coords</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>file</th>
-      <td><p>vector or raster layer</p></td>
-    </tr>
-    <tr>
-      <th>coords</th>
-      <td><p>vector containin xmin,ymin,xmax,ymax defing the bounding box for subset</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Retrieve attribute information from a vector or raster layer
+            </h1>
+
+            <div class="hidden name"><code>get.attributes.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to extract attribute information from vector or raster
+              data layer.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.attributes</span>(<span class='no'>file</span>, <span class='no'>coords</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>file</th>
+              <td><p>vector or raster layer</p></td>
+            </tr>
+            <tr>
+              <th>coords</th>
+              <td>
+                <p>
+                  vector containin xmin,ymin,xmax,ymax defing the bounding box
+                  for subset
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>file</span> <span class='kw'>&lt;-</span> <span class='fu'>Sys.glob</span>(<span class='fu'>file.path</span>(<span class='fu'>R.home</span>(), <span class='st'>'library'</span>, <span class='st'>'PEcAn.data.land'</span>,<span class='st'>'data'</span>,<span class='st'>'*.kml'</span>))
 <span class='no'>out</span> <span class='kw'>&lt;-</span> <span class='fu'>get.attributes</span>(<span class='kw'>file</span><span class='kw'>=</span><span class='no'>file</span>,<span class='kw'>coords</span><span class='kw'>=</span><span class='fu'>c</span>(-<span class='fl'>95</span>,<span class='fl'>42</span>,-<span class='fl'>84</span>,<span class='fl'>47</span>))
 <span class='fu'>print</span>(<span class='no'>out</span>)
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Shawn P. Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Shawn P. Serbin
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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-
diff --git a/modules/data.land/docs/reference/get.soil.html b/modules/data.land/docs/reference/get.soil.html
index 2b6404a..11dd856 100644
--- a/modules/data.land/docs/reference/get.soil.html
+++ b/modules/data.land/docs/reference/get.soil.html
@@ -2,161 +2,190 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+    <meta property="og:description" content="Get Soil" />
+    <meta name="twitter:card" content="summary" />
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get.soil</h1>
-    
-    <div class="hidden name"><code>get.soil.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get Soil</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.soil</span>(<span class='no'>lat</span>, <span class='no'>lon</span>, <span class='kw'>soil.nc</span> <span class='kw'>=</span> <span class='no'>soil.nc</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>lat</th>
-      <td><p>latitude</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>longitude</p></td>
-    </tr>
-    <tr>
-      <th>soil.nc</th>
-      <td><p>netCDFe file with soil data</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>usda soil class</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get.soil</h1>
+
+            <div class="hidden name"><code>get.soil.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get Soil</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.soil</span>(<span class='no'>lat</span>, <span class='no'>lon</span>, <span class='kw'>soil.nc</span> <span class='kw'>=</span> <span class='no'>soil.nc</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>lat</th>
+              <td><p>latitude</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>longitude</p></td>
+            </tr>
+            <tr>
+              <th>soil.nc</th>
+              <td><p>netCDFe file with soil data</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>usda soil class</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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+    </div>
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-
diff --git a/modules/data.land/docs/reference/get_resource_map.html b/modules/data.land/docs/reference/get_resource_map.html
index b9bfc8b..03fb3d8 100644
--- a/modules/data.land/docs/reference/get_resource_map.html
+++ b/modules/data.land/docs/reference/get_resource_map.html
@@ -2,153 +2,196 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+
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+    />
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+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+
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+              <ul class="nav navbar-nav">
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
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+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get_resource_map</h1>
-    
-    <div class="hidden name"><code>get_resource_map.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Locates data in DataONE and returns the resource_map or a message indicating that there is no corresponding resource_map for the given id</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get_resource_map</span>(<span class='no'>id</span>, <span class='kw'>CNode</span> <span class='kw'>=</span> <span class='st'>"PROD"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>id</th>
-      <td><p>the doi or other identifier linked to the package in DataONE</p></td>
-    </tr>
-    <tr>
-      <th>CNode</th>
-      <td><p>default is "PROD"</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>return the resource_map or a message indicating that there is no corresponding resource_map for the given id</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get_resource_map</h1>
+
+            <div class="hidden name"><code>get_resource_map.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Locates data in DataONE and returns the resource_map or a message
+              indicating that there is no corresponding resource_map for the
+              given id
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get_resource_map</span>(<span class='no'>id</span>, <span class='kw'>CNode</span> <span class='kw'>=</span> <span class='st'>"PROD"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>id</th>
+              <td>
+                <p>
+                  the doi or other identifier linked to the package in DataONE
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>CNode</th>
+              <td><p>default is "PROD"</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            return the resource_map or a message indicating that there is no
+            corresponding resource_map for the given id
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/data.land/docs/reference/get_veg_module.html b/modules/data.land/docs/reference/get_veg_module.html
index ed93bef..d177640 100644
--- a/modules/data.land/docs/reference/get_veg_module.html
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@@ -2,180 +2,241 @@
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+        <!--/.navbar -->
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Load/extract + match species module</h1>
-    
-    <div class="hidden name"><code>get_veg_module.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Load/extract + match species module</h1>
 
-    <div class="ref-description">
-    
-    <p>Load/extract + match species module</p>
-    
-    </div>
+            <div class="hidden name"><code>get_veg_module.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>get_veg_module</span>(<span class='no'>input_veg</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>dbparms</span>,
-  <span class='no'>new_site</span>, <span class='no'>host</span>, <span class='no'>machine_host</span>, <span class='no'>overwrite</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>input_veg</th>
-      <td><p>list, this is a sublist of settings$run$inputs that has info about source, id, metadata of the requested IC file</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>path to where the processed files will be written</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$start.date, otherwise start_date of the IC file in DB</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$end.date, otherwise end_date of the IC file in DB</p></td>
-    </tr>
-    <tr>
-      <th>dbparms</th>
-      <td><p>list, settings$database info reqired for opening a connection to DB</p></td>
-    </tr>
-    <tr>
-      <th>new_site</th>
-      <td><p>data frame, id/lat/lon/name info about the site</p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>list, host info as in settings$host, host$name forced to be "localhost" upstream</p></td>
-    </tr>
-    <tr>
-      <th>machine_host</th>
-      <td><p>local machine hostname, e.g. "pecan2.bu.edu"</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical flag for convert.input</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Load/extract + match species module</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>get_veg_module</span>(<span class='no'>input_veg</span>, <span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>dbparms</span>,
+  <span class='no'>new_site</span>, <span class='no'>host</span>, <span class='no'>machine_host</span>, <span class='no'>overwrite</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>input_veg</th>
+              <td>
+                <p>
+                  list, this is a sublist of settings$run$inputs that has info
+                  about source, id, metadata of the requested IC file
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>path to where the processed files will be written</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  date in "YYYY-MM-DD" format, in case of source==FIA it's the
+                  settings$run$start.date, otherwise start_date of the IC file
+                  in DB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  date in "YYYY-MM-DD" format, in case of source==FIA it's the
+                  settings$run$end.date, otherwise end_date of the IC file in DB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>dbparms</th>
+              <td>
+                <p>
+                  list, settings$database info reqired for opening a connection
+                  to DB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>new_site</th>
+              <td><p>data frame, id/lat/lon/name info about the site</p></td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td>
+                <p>
+                  list, host info as in settings$host, host$name forced to be
+                  "localhost" upstream
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>machine_host</th>
+              <td><p>local machine hostname, e.g. "pecan2.bu.edu"</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical flag for convert.input</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/ic_process.html b/modules/data.land/docs/reference/ic_process.html
index 3f3a6f5..0a0dc91 100644
--- a/modules/data.land/docs/reference/ic_process.html
+++ b/modules/data.land/docs/reference/ic_process.html
@@ -2,155 +2,182 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>ic_process</h1>
-    
-    <div class="hidden name"><code>ic_process.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>ic_process</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>ic_process</span>(<span class='no'>settings</span>, <span class='no'>input</span>, <span class='no'>dir</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>pecan settings list</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>whether to force ic_process to proceed</p></td>
-    </tr>
-    <tr>
-      <th>dbfiles</th>
-      <td><p>where to write files</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>ic_process</h1>
+
+            <div class="hidden name"><code>ic_process.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>ic_process</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>ic_process</span>(<span class='no'>settings</span>, <span class='no'>input</span>, <span class='no'>dir</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>pecan settings list</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>whether to force ic_process to proceed</p></td>
+            </tr>
+            <tr>
+              <th>dbfiles</th>
+              <td><p>where to write files</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
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diff --git a/modules/data.land/docs/reference/id_resolveable.html b/modules/data.land/docs/reference/id_resolveable.html
index 2dfc843..f7786d8 100644
--- a/modules/data.land/docs/reference/id_resolveable.html
+++ b/modules/data.land/docs/reference/id_resolveable.html
@@ -2,157 +2,204 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>id_resolveable</h1>
-    
-    <div class="hidden name"><code>id_resolveable.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Uses dataone::query from dataoneR to query DataONE. Prints result if data exists</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>id_resolveable</span>(<span class='no'>id</span>, <span class='kw'>return_result</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>CNode</span> <span class='kw'>=</span> <span class='st'>"PROD"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>id</th>
-      <td><p>the doi or other identifier linked to the package in DataONE</p></td>
-    </tr>
-    <tr>
-      <th>return_result</th>
-      <td><p>boolean that returns or suppresses result of query. defaults to TRUE.</p></td>
-    </tr>
-    <tr>
-      <th>CNode</th>
-      <td><p>CNode="PROD"</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>returns message indicating wether or not the id resolves to data in the DataONE federation and information about said data.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>id_resolveable</h1>
+
+            <div class="hidden name"><code>id_resolveable.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Uses dataone::query from dataoneR to query DataONE. Prints result
+              if data exists
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>id_resolveable</span>(<span class='no'>id</span>, <span class='kw'>return_result</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>CNode</span> <span class='kw'>=</span> <span class='st'>"PROD"</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>id</th>
+              <td>
+                <p>
+                  the doi or other identifier linked to the package in DataONE
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>return_result</th>
+              <td>
+                <p>
+                  boolean that returns or suppresses result of query. defaults
+                  to TRUE.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>CNode</th>
+              <td><p>CNode="PROD"</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            returns message indicating wether or not the id resolves to data in
+            the DataONE federation and information about said data.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+          <p>Developed by .</p>
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+    <!-- Font Awesome icons -->
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+    <!-- sticky kit -->
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+      crossorigin="anonymous"
+    ></script>
 
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+    <!-- pkgdown -->
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+    <!-- mathjax -->
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-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="Clean_Tucson.html">Clean_Tucson()</a></code> </p>
-        </td>
-        <td><p>Clean_Tucson</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="InventoryGrowthFusion.html">InventoryGrowthFusion()</a></code> </p>
-        </td>
-        <td><p>InventoryGrowthFusion</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="InventoryGrowthFusionDiagnostics.html">InventoryGrowthFusionDiagnostics()</a></code> </p>
-        </td>
-        <td><p>InventoryGrowthFusionDiagnostics</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="Read_Tucson.html">Read_Tucson()</a></code> </p>
-        </td>
-        <td><p>Read_Tucson</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="buildJAGSdata_InventoryRings.html">buildJAGSdata_InventoryRings()</a></code> </p>
-        </td>
-        <td><p>Format ring &amp; plot data for JAGA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="cohort2pool.html">cohort2pool()</a></code> </p>
-        </td>
-        <td><p>cohort2pool function
-Calculates total biomass using veg cohort file.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dataone_download.html">dataone_download()</a></code> </p>
-        </td>
-        <td><p>DataONE download</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="download_package_rm.html">download_package_rm()</a></code> </p>
-        </td>
-        <td><p>download_packages</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ens_veg_module.html">ens_veg_module()</a></code> </p>
-        </td>
-        <td><p>Sampling/ensemble module</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="extract.stringCode.html">extract.stringCode()</a></code> </p>
-        </td>
-        <td><p>extract.string.code</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="extract_FIA.html">extract_FIA()</a></code> </p>
-        </td>
-        <td><p>extract_FIA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="extract_soil_gssurgo.html">extract_soil_gssurgo()</a></code> </p>
-        </td>
-        <td><p>Extract soil data from gssurgo</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="extract_soil_nc.html">extract_soil_nc()</a></code> </p>
-        </td>
-        <td><p>Extract soil data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="extract_veg.html">extract_veg()</a></code> </p>
-        </td>
-        <td><p>load_veg</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="fia.to.psscss.html">fia.to.psscss()</a></code> </p>
-        </td>
-        <td><p>fia.to.psscss</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="find.land.html">find.land()</a></code> </p>
-        </td>
-        <td><p>find.land</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="format_identifier.html">format_identifier()</a></code> </p>
-        </td>
-        <td><p>format_identifier</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="from.Tag.html">from.Tag()</a></code> </p>
-        </td>
-        <td><p>from.Tag</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="from.TreeCode.html">from.TreeCode()</a></code> </p>
-        </td>
-        <td><p>from.TreeCode</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="gSSURGO.Query.html">gSSURGO.Query()</a></code> </p>
-        </td>
-        <td><p>This function queries the gSSURGO database for a series of map unit keys</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.attributes.html">get.attributes()</a></code> </p>
-        </td>
-        <td><p>Retrieve attribute information from a vector or raster layer</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.soil.html">get.soil()</a></code> </p>
-        </td>
-        <td><p>get.soil</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_resource_map.html">get_resource_map()</a></code> </p>
-        </td>
-        <td><p>get_resource_map</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_veg_module.html">get_veg_module()</a></code> </p>
-        </td>
-        <td><p>Load/extract + match species module</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ic_process.html">ic_process()</a></code> </p>
-        </td>
-        <td><p>ic_process</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="id_resolveable.html">id_resolveable()</a></code> </p>
-        </td>
-        <td><p>id_resolveable</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load_veg.html">load_veg()</a></code> </p>
-        </td>
-        <td><p>load_veg</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="matchInventoryRings.html">matchInventoryRings()</a></code> </p>
-        </td>
-        <td><p>matchInventoryRings</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="match_pft.html">match_pft()</a></code> </p>
-        </td>
-        <td><p>Match model PFTs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="match_species_id.html">match_species_id()</a></code> </p>
-        </td>
-        <td><p>Match BETY species ID.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="mpot2smoist.html">mpot2smoist()</a></code> </p>
-        </td>
-        <td><p>Convert a matric potential to a soil moisture</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="parse.MatrixNames.html">parse.MatrixNames()</a></code> </p>
-        </td>
-        <td><p>parse.MatrixNames</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="partition_roots.html">partition_roots()</a></code> </p>
-        </td>
-        <td><p>partition_roots</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot2AGB.html">plot2AGB()</a></code> </p>
-        </td>
-        <td><p>plot2AGB</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pool_ic_list2netcdf.html">pool_ic_list2netcdf()</a></code> </p>
-        </td>
-        <td><p>pool_ic_list2netcdf</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pool_ic_netcdf2list.html">pool_ic_netcdf2list()</a></code> </p>
-        </td>
-        <td><p>pool_ic_netcdf2list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="prepare_pools.html">prepare_pools()</a></code> </p>
-        </td>
-        <td><p>prepare_pools</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="put_veg_module.html">put_veg_module()</a></code> </p>
-        </td>
-        <td><p>Match species to PFTs + veg2model module</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sample_ic.html">sample_ic()</a></code> </p>
-        </td>
-        <td><p>sample_ic</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sclass.html">sclass()</a></code> </p>
-        </td>
-        <td><p>This function determines the soil class number based on the fraction of sand, clay, and silt</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="shp2kml.html">shp2kml()</a></code> </p>
-        </td>
-        <td><p>Convert shapefile to KML</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="soil.units.html">soil.units()</a></code> </p>
-        </td>
-        <td><p>Get standard units for a soil variable</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="soil2netcdf.html">soil2netcdf()</a></code> </p>
-        </td>
-        <td><p>Save soil texture &amp; parameters in PEcAn standard netCDF CF</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="soil_params.html">soil_params()</a></code> </p>
-        </td>
-        <td><p>Estimate soil parameters from texture class or sand/silt/clay</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="soil_process.html">soil_process()</a></code> </p>
-        </td>
-        <td><p>Module for managing soil texture extraction</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="subset.layer.html">subset(<i>&lt;layer&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Function to subset and clip a GIS vector or raster layer by a bounding box
-or clip/subset layer (e.g. shapefile/KML)</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="to.Tag.html">to.Tag()</a></code> </p>
-        </td>
-        <td><p>to.Tag</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="to.TreeCode.html">to.TreeCode()</a></code> </p>
-        </td>
-        <td><p>to.TreeCode</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_ic.html">write_ic()</a></code> </p>
-        </td>
-        <td><p>write_ic</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write_veg.html">write_veg()</a></code> </p>
-        </td>
-        <td><p>write_veg</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="Clean_Tucson.html">Clean_Tucson()</a></code>
+                  </p>
+                </td>
+                <td><p>Clean_Tucson</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="InventoryGrowthFusion.html"
+                        >InventoryGrowthFusion()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>InventoryGrowthFusion</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="InventoryGrowthFusionDiagnostics.html"
+                        >InventoryGrowthFusionDiagnostics()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>InventoryGrowthFusionDiagnostics</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="Read_Tucson.html">Read_Tucson()</a></code>
+                  </p>
+                </td>
+                <td><p>Read_Tucson</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="buildJAGSdata_InventoryRings.html"
+                        >buildJAGSdata_InventoryRings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Format ring &amp; plot data for JAGA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="cohort2pool.html">cohort2pool()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    cohort2pool function Calculates total biomass using veg
+                    cohort file.
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="dataone_download.html"
+                        >dataone_download()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>DataONE download</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download_package_rm.html"
+                        >download_package_rm()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>download_packages</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="ens_veg_module.html">ens_veg_module()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Sampling/ensemble module</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="extract.stringCode.html"
+                        >extract.stringCode()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>extract.string.code</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="extract_FIA.html">extract_FIA()</a></code>
+                  </p>
+                </td>
+                <td><p>extract_FIA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="extract_soil_gssurgo.html"
+                        >extract_soil_gssurgo()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Extract soil data from gssurgo</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="extract_soil_nc.html"
+                        >extract_soil_nc()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Extract soil data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="extract_veg.html">extract_veg()</a></code>
+                  </p>
+                </td>
+                <td><p>load_veg</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="fia.to.psscss.html">fia.to.psscss()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>fia.to.psscss</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="find.land.html">find.land()</a></code>
+                  </p>
+                </td>
+                <td><p>find.land</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="format_identifier.html"
+                        >format_identifier()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>format_identifier</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="from.Tag.html">from.Tag()</a></code>
+                  </p>
+                </td>
+                <td><p>from.Tag</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="from.TreeCode.html">from.TreeCode()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>from.TreeCode</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="gSSURGO.Query.html">gSSURGO.Query()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    This function queries the gSSURGO database for a series of
+                    map unit keys
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.attributes.html">get.attributes()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Retrieve attribute information from a vector or raster layer
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.soil.html">get.soil()</a></code>
+                  </p>
+                </td>
+                <td><p>get.soil</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_resource_map.html"
+                        >get_resource_map()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>get_resource_map</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get_veg_module.html">get_veg_module()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Load/extract + match species module</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ic_process.html">ic_process()</a></code>
+                  </p>
+                </td>
+                <td><p>ic_process</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="id_resolveable.html">id_resolveable()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>id_resolveable</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="load_veg.html">load_veg()</a></code>
+                  </p>
+                </td>
+                <td><p>load_veg</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="matchInventoryRings.html"
+                        >matchInventoryRings()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>matchInventoryRings</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="match_pft.html">match_pft()</a></code>
+                  </p>
+                </td>
+                <td><p>Match model PFTs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="match_species_id.html"
+                        >match_species_id()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Match BETY species ID.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="mpot2smoist.html">mpot2smoist()</a></code>
+                  </p>
+                </td>
+                <td><p>Convert a matric potential to a soil moisture</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="parse.MatrixNames.html"
+                        >parse.MatrixNames()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>parse.MatrixNames</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="partition_roots.html"
+                        >partition_roots()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>partition_roots</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="plot2AGB.html">plot2AGB()</a></code>
+                  </p>
+                </td>
+                <td><p>plot2AGB</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pool_ic_list2netcdf.html"
+                        >pool_ic_list2netcdf()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>pool_ic_list2netcdf</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pool_ic_netcdf2list.html"
+                        >pool_ic_netcdf2list()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>pool_ic_netcdf2list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="prepare_pools.html">prepare_pools()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>prepare_pools</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="put_veg_module.html">put_veg_module()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Match species to PFTs + veg2model module</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sample_ic.html">sample_ic()</a></code>
+                  </p>
+                </td>
+                <td><p>sample_ic</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sclass.html">sclass()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    This function determines the soil class number based on the
+                    fraction of sand, clay, and silt
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="shp2kml.html">shp2kml()</a></code>
+                  </p>
+                </td>
+                <td><p>Convert shapefile to KML</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="soil.units.html">soil.units()</a></code>
+                  </p>
+                </td>
+                <td><p>Get standard units for a soil variable</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="soil2netcdf.html">soil2netcdf()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Save soil texture &amp; parameters in PEcAn standard netCDF
+                    CF
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="soil_params.html">soil_params()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Estimate soil parameters from texture class or
+                    sand/silt/clay
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="soil_process.html">soil_process()</a></code>
+                  </p>
+                </td>
+                <td><p>Module for managing soil texture extraction</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="subset.layer.html"
+                        >subset(<i>&lt;layer&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function to subset and clip a GIS vector or raster layer by
+                    a bounding box or clip/subset layer (e.g. shapefile/KML)
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="to.Tag.html">to.Tag()</a></code>
+                  </p>
+                </td>
+                <td><p>to.Tag</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="to.TreeCode.html">to.TreeCode()</a></code>
+                  </p>
+                </td>
+                <td><p>to.TreeCode</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="write_ic.html">write_ic()</a></code>
+                  </p>
+                </td>
+                <td><p>write_ic</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="write_veg.html">write_veg()</a></code>
+                  </p>
+                </td>
+                <td><p>write_veg</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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 </html>
-
diff --git a/modules/data.land/docs/reference/load_veg.html b/modules/data.land/docs/reference/load_veg.html
index f61a9fa..4ab9bee 100644
--- a/modules/data.land/docs/reference/load_veg.html
+++ b/modules/data.land/docs/reference/load_veg.html
@@ -2,139 +2,163 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
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+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    />
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="load_veg — load_veg" />
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
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-  </div><!--/.container -->
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-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>load_veg</h1>
-    
-    <div class="hidden name"><code>load_veg.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>load_veg</h1>
 
-    <div class="ref-description">
-    
-    <p>Function uses load_databenchmark to get veg data</p>
-    
-    </div>
+            <div class="hidden name"><code>load_veg.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Function uses load_databenchmark to get veg data</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>load_veg</span>(<span class='no'>new_site</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>source_id</span>, <span class='no'>source</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>load_veg</span>(<span class='no'>new_site</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>source_id</span>, <span class='no'>source</span>,
   <span class='kw'>icmeta</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>format_name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>machine_host</span>, <span class='no'>dbparms</span>, <span class='no'>outfolder</span>,
   <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-        
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <h2>Author</h2>
 
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/matchInventoryRings.html b/modules/data.land/docs/reference/matchInventoryRings.html
index c34e81b..eefea88 100644
--- a/modules/data.land/docs/reference/matchInventoryRings.html
+++ b/modules/data.land/docs/reference/matchInventoryRings.html
@@ -2,134 +2,158 @@
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 <html>
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-  <meta charset="utf-8">
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-
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-
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-
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+    <meta charset="utf-8" />
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      content="matchInventoryRings — matchInventoryRings"
+    />
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+    <meta name="twitter:card" content="summary" />
+
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+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>matchInventoryRings</h1>
-    
-    <div class="hidden name"><code>matchInventoryRings.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>matchInventoryRings</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>matchInventoryRings</h1>
 
-    <pre class="usage"><span class='fu'>matchInventoryRings</span>(<span class='no'>trees</span>, <span class='no'>rings</span>, <span class='kw'>extractor</span> <span class='kw'>=</span> <span class='st'>"TreeCode"</span>, <span class='kw'>nyears</span> <span class='kw'>=</span> <span class='fl'>30</span>,
-  <span class='kw'>coredOnly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-        
+            <div class="hidden name"><code>matchInventoryRings.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>matchInventoryRings</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>matchInventoryRings</span>(<span class='no'>trees</span>, <span class='no'>rings</span>, <span class='kw'>extractor</span> <span class='kw'>=</span> <span class='st'>"TreeCode"</span>, <span class='kw'>nyears</span> <span class='kw'>=</span> <span class='fl'>30</span>,
+  <span class='kw'>coredOnly</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/match_pft.html b/modules/data.land/docs/reference/match_pft.html
index 39001dc..b55d548 100644
--- a/modules/data.land/docs/reference/match_pft.html
+++ b/modules/data.land/docs/reference/match_pft.html
@@ -2,166 +2,208 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Match model PFTs — match_pft" />
-
-<meta property="og:description" content="Matches BETYdb species IDs to model-specific PFTs" />
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Match model PFTs — match_pft • PEcAn.data.land</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+
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+      property="og:description"
+      content="Matches BETYdb species IDs to model-specific PFTs"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
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+    <![endif]-->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Match model PFTs</h1>
-    
-    <div class="hidden name"><code>match_pft.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Match model PFTs</h1>
 
-    <div class="ref-description">
-    
-    <p>Matches BETYdb species IDs to model-specific PFTs</p>
-    
-    </div>
+            <div class="hidden name"><code>match_pft.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Matches BETYdb species IDs to model-specific PFTs</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>match_pft</span>(<span class='no'>bety_species_id</span>, <span class='no'>pfts</span>, <span class='kw'>query</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>match_pft</span>(<span class='no'>bety_species_id</span>, <span class='no'>pfts</span>, <span class='kw'>query</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>allow_missing</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>bety_species_id</th>
-      <td><p>vector of BETYdb species IDs</p></td>
-    </tr>
-    <tr>
-      <th>pfts</th>
-      <td><p>settings$pfts.  List of pfts with database matching based on name</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>database connection, if NULL use traits package</p></td>
-    </tr>
-    <tr>
-      <th>allow_missing</th>
-      <td><p>flag to indicate that settings file does not need to match exactly</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>table of BETYdb PFT IDs matched to species IDs</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>bety_species_id</th>
+              <td><p>vector of BETYdb species IDs</p></td>
+            </tr>
+            <tr>
+              <th>pfts</th>
+              <td>
+                <p>
+                  settings$pfts. List of pfts with database matching based on
+                  name
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td><p>database connection, if NULL use traits package</p></td>
+            </tr>
+            <tr>
+              <th>allow_missing</th>
+              <td>
+                <p>
+                  flag to indicate that settings file does not need to match
+                  exactly
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>table of BETYdb PFT IDs matched to species IDs</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze, Istem Fer
+        </div>
+      </div>
 
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diff --git a/modules/data.land/docs/reference/match_species_id.html b/modules/data.land/docs/reference/match_species_id.html
index a5721fd..c4b8fba 100644
--- a/modules/data.land/docs/reference/match_species_id.html
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Match BETY species ID.</h1>
-    
-    <div class="hidden name"><code>match_species_id.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Match BETY species ID.</h1>
 
-    <div class="ref-description">
-    
-    <p>Parses species codes in input data and matches them with the BETY species ID.</p>
-    
-    </div>
+            <div class="hidden name"><code>match_species_id.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>match_species_id</span>(<span class='no'>input_codes</span>, <span class='kw'>format_name</span> <span class='kw'>=</span> <span class='st'>"custom"</span>, <span class='kw'>bety</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>
+              Parses species codes in input data and matches them with the BETY
+              species ID.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>match_species_id</span>(<span class='no'>input_codes</span>, <span class='kw'>format_name</span> <span class='kw'>=</span> <span class='st'>"custom"</span>, <span class='kw'>bety</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>translation_table</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>input_codes</th>
-      <td><p>Character vector of species codes</p></td>
-    </tr>
-    <tr>
-      <th>format_name</th>
-      <td><p>Species code format name (see details)</p></td>
-    </tr>
-    <tr>
-      <th>bety</th>
-      <td><p><code>dplyr</code> <code>src</code> object containing BETY connection</p></td>
-    </tr>
-    <tr>
-      <th>translation_table</th>
-      <td><p>Data frame with custom translation table (see details).</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p><code>data.frame</code> containing the following columns:</p><dl class='dl-horizontal'>
- <dt><code>input_code</code></dt><dd><p>Character provided as input</p></dd>
- <dt><code>bety_species_id</code></dt><dd><p>Big integer species ID, unique and specific to BETY</p></dd>
- <dt><code>genus</code></dt><dd><p>Genus part of Latin name, from BETY</p></dd>
- <dt><code>species</code></dt><dd><p>Species part of Latin name, from BETY</p></dd>
-</dl>
-
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><code>format_name</code> can be one of the following:</p><dl class='dl-horizontal'>
- <dt><code>usda</code></dt><dd><p>USDA Plants database symbol (e.g. QURU, TSCA)</p></dd>
- <dt><code>fia</code></dt><dd><p>FIA species code</p></dd>
- <dt><code>latin_name</code></dt><dd><p>Scientific name, as "Genus species"; must match exactly and unambiguously to <code>scientificname</code> field in BETY</p></dd>
- <dt><code>custom</code></dt><dd><p>A data frame matching BETY IDs (column name <code>bety_species_id</code>) to input codes (column name <code>input_code</code>). This data frame must be passed via the <code>translation_table</code> argument.</p></dd>
-</dl>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>input_codes</th>
+              <td><p>Character vector of species codes</p></td>
+            </tr>
+            <tr>
+              <th>format_name</th>
+              <td><p>Species code format name (see details)</p></td>
+            </tr>
+            <tr>
+              <th>bety</th>
+              <td>
+                <p>
+                  <code>dplyr</code> <code>src</code> object containing BETY
+                  connection
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>translation_table</th>
+              <td>
+                <p>Data frame with custom translation table (see details).</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p><code>data.frame</code> containing the following columns:</p>
+          <dl class="dl-horizontal">
+            <dt><code>input_code</code></dt>
+            <dd><p>Character provided as input</p></dd>
+            <dt><code>bety_species_id</code></dt>
+            <dd><p>Big integer species ID, unique and specific to BETY</p></dd>
+            <dt><code>genus</code></dt>
+            <dd><p>Genus part of Latin name, from BETY</p></dd>
+            <dt><code>species</code></dt>
+            <dd><p>Species part of Latin name, from BETY</p></dd>
+          </dl>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p><code>format_name</code> can be one of the following:</p>
+          <dl class="dl-horizontal">
+            <dt><code>usda</code></dt>
+            <dd><p>USDA Plants database symbol (e.g. QURU, TSCA)</p></dd>
+            <dt><code>fia</code></dt>
+            <dd><p>FIA species code</p></dd>
+            <dt><code>latin_name</code></dt>
+            <dd>
+              <p>
+                Scientific name, as "Genus species"; must match exactly and
+                unambiguously to <code>scientificname</code> field in BETY
+              </p>
+            </dd>
+            <dt><code>custom</code></dt>
+            <dd>
+              <p>
+                A data frame matching BETY IDs (column name
+                <code>bety_species_id</code>) to input codes (column name
+                <code>input_code</code>). This data frame must be passed via the
+                <code>translation_table</code> argument.
+              </p>
+            </dd>
+          </dl>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>bety</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>dplyr</span><span class='kw ns'>::</span><span class='fu'><a href='http://dplyr.tidyverse.org/reference/src_dbi.html'>src_postgres</a></span>(<span class='kw'>dbname</span> <span class='kw'>=</span> <span class='st'>'bety'</span>,
                        <span class='kw'>user</span> <span class='kw'>=</span> <span class='st'>'bety'</span>,
                        <span class='kw'>password</span> <span class='kw'>=</span> <span class='st'>'bety'</span>,
@@ -160,40 +235,36 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
                  <span class='kw'>bety</span> <span class='kw'>=</span> <span class='no'>bety</span>)
 
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov &lt;ashiklom@bu.edu&gt;, Istem Fer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          Alexey Shiklomanov &lt;ashiklom@bu.edu&gt;, Istem Fer
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/mpot2smoist.html b/modules/data.land/docs/reference/mpot2smoist.html
index 03e9539..e955e1e 100644
--- a/modules/data.land/docs/reference/mpot2smoist.html
+++ b/modules/data.land/docs/reference/mpot2smoist.html
@@ -2,148 +2,184 @@
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 <html>
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-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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+      PEcAn.data.land
+    </title>
+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
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+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="Convert a matric potential to a soil moisture — mpot2smoist"
+    />
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+      content="Convert a matric potential to a soil moisture"
+    />
+    <meta name="twitter:card" content="summary" />
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+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert a matric potential to a soil moisture</h1>
-    
-    <div class="hidden name"><code>mpot2smoist.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert a matric potential to a soil moisture</h1>
 
-    <div class="ref-description">
-    
-    <p>Convert a matric potential to a soil moisture</p>
-    
-    </div>
+            <div class="hidden name"><code>mpot2smoist.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>mpot2smoist</span>(<span class='no'>mpot</span>, <span class='no'>soil_water_potential_at_saturation</span>, <span class='no'>soil_hydraulic_b</span>,
-  <span class='no'>volume_fraction_of_water_in_soil_at_saturation</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mpot</th>
-      <td><p>water potential</p></td>
-    </tr>
-    <tr>
-      <th>mysoil</th>
-      <td><p>soil property list</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Convert a matric potential to a soil moisture</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>mpot2smoist</span>(<span class='no'>mpot</span>, <span class='no'>soil_water_potential_at_saturation</span>, <span class='no'>soil_hydraulic_b</span>,
+  <span class='no'>volume_fraction_of_water_in_soil_at_saturation</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mpot</th>
+              <td><p>water potential</p></td>
+            </tr>
+            <tr>
+              <th>mysoil</th>
+              <td><p>soil property list</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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diff --git a/modules/data.land/docs/reference/parse.MatrixNames.html b/modules/data.land/docs/reference/parse.MatrixNames.html
index 6090f9b..2f58ff5 100644
--- a/modules/data.land/docs/reference/parse.MatrixNames.html
+++ b/modules/data.land/docs/reference/parse.MatrixNames.html
@@ -2,161 +2,194 @@
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 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>parse.MatrixNames</h1>
-    
-    <div class="hidden name"><code>parse.MatrixNames.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>parse.MatrixNames</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>parse.MatrixNames</span>(<span class='no'>w</span>, <span class='kw'>pre</span> <span class='kw'>=</span> <span class='st'>"x"</span>, <span class='kw'>numeric</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>w</th>
-      <td><p>mcmc object containing matrix outputs</p></td>
-    </tr>
-    <tr>
-      <th>pre</th>
-      <td><p>prefix (variable name) for the matrix variable to be extracted</p></td>
-    </tr>
-    <tr>
-      <th>numeric</th>
-      <td><p>boolean, whether to coerce class to numeric</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>matrix</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>parse.MatrixNames</h1>
+
+            <div class="hidden name"><code>parse.MatrixNames.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>parse.MatrixNames</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>parse.MatrixNames</span>(<span class='no'>w</span>, <span class='kw'>pre</span> <span class='kw'>=</span> <span class='st'>"x"</span>, <span class='kw'>numeric</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>w</th>
+              <td><p>mcmc object containing matrix outputs</p></td>
+            </tr>
+            <tr>
+              <th>pre</th>
+              <td>
+                <p>
+                  prefix (variable name) for the matrix variable to be extracted
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>numeric</th>
+              <td><p>boolean, whether to coerce class to numeric</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>matrix</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/data.land/docs/reference/partition_roots.html b/modules/data.land/docs/reference/partition_roots.html
index f6fa4e8..96e136d 100644
--- a/modules/data.land/docs/reference/partition_roots.html
+++ b/modules/data.land/docs/reference/partition_roots.html
@@ -2,157 +2,206 @@
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+
+    <meta property="og:title" content="partition_roots — partition_roots" />
+
+    <meta
+      property="og:description"
+      content="Given a vector of root size thresholds (lower bound of each) and a vector of corresponding root carbon values, partition_roots checks if the input can be partitioned along the .002 m threshold between fine and coarse roots and returns a list containing the summed values for fine and coarse. If there are fewer than two thresholds or none within .0005 m of .002 m, returns NULL. Meant to be used in conjunction with standard variable root_carbon_content with rtsize dimension, extracted from netcdf."
+    />
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>partition_roots</h1>
-    
-    <div class="hidden name"><code>partition_roots.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Given a vector of root size thresholds (lower bound of each) and a vector of corresponding root carbon values, partition_roots checks if the input can be partitioned along the .002 m threshold between fine and coarse roots and returns a list containing the summed values for fine and coarse. If there are fewer than two thresholds or none within .0005 m of .002 m, returns NULL. Meant to be used in conjunction with standard variable root_carbon_content with rtsize dimension, extracted from netcdf.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>partition_roots</span>(<span class='no'>roots</span>, <span class='no'>rtsize</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>roots</th>
-      <td><p>vector of root carbon values in kg C m-2</p></td>
-    </tr>
-    <tr>
-      <th>rtsize</th>
-      <td><p>vector of lower bounds of root size class thresholds in m, length greater than one and equal to roots. Must contain threshold within .0005 m of .002 m</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list containing summed fine root and coarse root carbon (2 values)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>partition_roots</h1>
+
+            <div class="hidden name"><code>partition_roots.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Given a vector of root size thresholds (lower bound of each) and a
+              vector of corresponding root carbon values, partition_roots checks
+              if the input can be partitioned along the .002 m threshold between
+              fine and coarse roots and returns a list containing the summed
+              values for fine and coarse. If there are fewer than two thresholds
+              or none within .0005 m of .002 m, returns NULL. Meant to be used
+              in conjunction with standard variable root_carbon_content with
+              rtsize dimension, extracted from netcdf.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>partition_roots</span>(<span class='no'>roots</span>, <span class='no'>rtsize</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>roots</th>
+              <td><p>vector of root carbon values in kg C m-2</p></td>
+            </tr>
+            <tr>
+              <th>rtsize</th>
+              <td>
+                <p>
+                  vector of lower bounds of root size class thresholds in m,
+                  length greater than one and equal to roots. Must contain
+                  threshold within .0005 m of .002 m
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            list containing summed fine root and coarse root carbon (2 values)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Anne Thomas
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Anne Thomas
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-</div>
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+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/data.land/docs/reference/plot2AGB.html b/modules/data.land/docs/reference/plot2AGB.html
index 4594dcc..8a534e6 100644
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>plot2AGB</h1>
-    
-    <div class="hidden name"><code>plot2AGB.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>convert composite ring &amp; census data into AGB</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>plot2AGB</span>(<span class='no'>combined</span>, <span class='no'>out</span>, <span class='no'>outfolder</span>, <span class='no'>allom.stats</span>, <span class='kw'>unit.conv</span> <span class='kw'>=</span> <span class='fl'>0.02</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>combined</th>
-      <td><p>data frame merging plot inventory and tree ring data</p></td>
-    </tr>
-    <tr>
-      <th>out</th>
-      <td><p>MCMC samples for diameter (sample x tree)</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>output folder for graphs &amp; data</p></td>
-    </tr>
-    <tr>
-      <th>unit.conv</th>
-      <td><p>area conversion from sum(kg/tree) to kg/area</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze <a href='mailto:dietze@bu.edu'>dietze@bu.edu</a>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>plot2AGB</h1>
+
+            <div class="hidden name"><code>plot2AGB.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>convert composite ring &amp; census data into AGB</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>plot2AGB</span>(<span class='no'>combined</span>, <span class='no'>out</span>, <span class='no'>outfolder</span>, <span class='no'>allom.stats</span>, <span class='kw'>unit.conv</span> <span class='kw'>=</span> <span class='fl'>0.02</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>combined</th>
+              <td>
+                <p>data frame merging plot inventory and tree ring data</p>
+              </td>
+            </tr>
+            <tr>
+              <th>out</th>
+              <td><p>MCMC samples for diameter (sample x tree)</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>output folder for graphs &amp; data</p></td>
+            </tr>
+            <tr>
+              <th>unit.conv</th>
+              <td><p>area conversion from sum(kg/tree) to kg/area</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze <a href="mailto:dietze@bu.edu">dietze@bu.edu</a>
+        </div>
+      </div>
 
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diff --git a/modules/data.land/docs/reference/pool_ic_list2netcdf.html b/modules/data.land/docs/reference/pool_ic_list2netcdf.html
index 3d46b86..805d0ff 100644
--- a/modules/data.land/docs/reference/pool_ic_list2netcdf.html
+++ b/modules/data.land/docs/reference/pool_ic_list2netcdf.html
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>pool_ic_list2netcdf</h1>
-    
-    <div class="hidden name"><code>pool_ic_list2netcdf.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Converts input list containing standard dimensions and variables (named values) for initial conditions to a netcdf file, input to pool-based models.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pool_ic_list2netcdf</span>(<span class='no'>input</span>, <span class='no'>outdir</span>, <span class='no'>siteid</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>input</th>
-      <td><p>list with two elements: list of netcdf dimensions (dims, with named values) and list of variables (vals, with named values)</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>directory to write netcdf file</p></td>
-    </tr>
-    <tr>
-      <th>siteid</th>
-      <td><p>site id</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Anne Thomas
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>pool_ic_list2netcdf</h1>
+
+            <div class="hidden name"><code>pool_ic_list2netcdf.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Converts input list containing standard dimensions and variables
+              (named values) for initial conditions to a netcdf file, input to
+              pool-based models.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pool_ic_list2netcdf</span>(<span class='no'>input</span>, <span class='no'>outdir</span>, <span class='no'>siteid</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>input</th>
+              <td>
+                <p>
+                  list with two elements: list of netcdf dimensions (dims, with
+                  named values) and list of variables (vals, with named values)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>directory to write netcdf file</p></td>
+            </tr>
+            <tr>
+              <th>siteid</th>
+              <td><p>site id</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Anne Thomas
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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diff --git a/modules/data.land/docs/reference/pool_ic_netcdf2list.html b/modules/data.land/docs/reference/pool_ic_netcdf2list.html
index 1a41be7..b9f4655 100644
--- a/modules/data.land/docs/reference/pool_ic_netcdf2list.html
+++ b/modules/data.land/docs/reference/pool_ic_netcdf2list.html
@@ -2,153 +2,200 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>pool_ic_netcdf2list</h1>
-    
-    <div class="hidden name"><code>pool_ic_netcdf2list.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Converts netcdf containing standard dimensions and variables for pool-based initial conditions, created by pool_ic_list2netcdf, back into list format</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pool_ic_netcdf2list</span>(<span class='no'>nc.path</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>nc.path</th>
-      <td><p>path to netcdf file containing standard dimensions and variables</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list with two elements: list of netcdf dimensions (dims, with named values) and list of variables (vals, with named values)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>pool_ic_netcdf2list</h1>
+
+            <div class="hidden name"><code>pool_ic_netcdf2list.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Converts netcdf containing standard dimensions and variables for
+              pool-based initial conditions, created by pool_ic_list2netcdf,
+              back into list format
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pool_ic_netcdf2list</span>(<span class='no'>nc.path</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>nc.path</th>
+              <td>
+                <p>
+                  path to netcdf file containing standard dimensions and
+                  variables
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            list with two elements: list of netcdf dimensions (dims, with named
+            values) and list of variables (vals, with named values)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Anne Thomas
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Anne Thomas
+        </div>
+      </div>
 
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   </body>
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-
diff --git a/modules/data.land/docs/reference/prepare_pools.html b/modules/data.land/docs/reference/prepare_pools.html
index 6216d01..8f092c5 100644
--- a/modules/data.land/docs/reference/prepare_pools.html
+++ b/modules/data.land/docs/reference/prepare_pools.html
@@ -2,157 +2,206 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    />
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-    <h1>prepare_pools</h1>
-    
-    <div class="hidden name"><code>prepare_pools.Rd</code></div>
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-
-    <div class="ref-description">
-    
-    <p>Calculates pools from given initial condition values, deriving complements where necessary/possible if given TotLivBiomass</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>prepare_pools</span>(<span class='no'>nc.path</span>, <span class='kw'>constants</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>nc.path</th>
-      <td><p>path to netcdf file containing standard dimensions and variables; currently supports these variables: TotLivBiom, leaf_carbon_content, LAI, AbvGrndWood, root_carbon_content, fine_root_carbon_content, coarse_root_carbon_content, litter_carbon_content, soil_organic_carbon_content, soil_carbon_content, wood_debris_carbon_content</p></td>
-    </tr>
-    <tr>
-      <th>constants</th>
-      <td><p>list of constants; must include SLA in m2 / kg C if providing LAI for leaf carbon</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list of pool values in kg C / m2 with generic names</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>prepare_pools</h1>
+
+            <div class="hidden name"><code>prepare_pools.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Calculates pools from given initial condition values, deriving
+              complements where necessary/possible if given TotLivBiomass
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>prepare_pools</span>(<span class='no'>nc.path</span>, <span class='kw'>constants</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>nc.path</th>
+              <td>
+                <p>
+                  path to netcdf file containing standard dimensions and
+                  variables; currently supports these variables: TotLivBiom,
+                  leaf_carbon_content, LAI, AbvGrndWood, root_carbon_content,
+                  fine_root_carbon_content, coarse_root_carbon_content,
+                  litter_carbon_content, soil_organic_carbon_content,
+                  soil_carbon_content, wood_debris_carbon_content
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>constants</th>
+              <td>
+                <p>
+                  list of constants; must include SLA in m2 / kg C if providing
+                  LAI for leaf carbon
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list of pool values in kg C / m2 with generic names</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Anne Thomas
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Anne Thomas
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/put_veg_module.html b/modules/data.land/docs/reference/put_veg_module.html
index f3b7d3b..92f9dca 100644
--- a/modules/data.land/docs/reference/put_veg_module.html
+++ b/modules/data.land/docs/reference/put_veg_module.html
@@ -2,200 +2,272 @@
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+      Match species to PFTs + veg2model module — put_veg_module •
+      PEcAn.data.land
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+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+    ></script>
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+    />
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Match species to PFTs + veg2model module</h1>
-    
-    <div class="hidden name"><code>put_veg_module.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Match species to PFTs + veg2model module</h1>
 
-    <div class="ref-description">
-    
-    <p>Match species to PFTs + veg2model module</p>
-    
-    </div>
+            <div class="hidden name"><code>put_veg_module.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>put_veg_module</span>(<span class='no'>getveg.id</span>, <span class='no'>dbparms</span>, <span class='no'>input_veg</span>, <span class='no'>pfts</span>, <span class='no'>outfolder</span>, <span class='no'>n.ensemble</span>,
-  <span class='no'>dir</span>, <span class='no'>machine</span>, <span class='no'>model</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>new_site</span>, <span class='no'>host</span>, <span class='no'>overwrite</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>getveg.id</th>
-      <td><p>list, input.id and dbfile.id of the IC file in intermediate pecan standard</p></td>
-    </tr>
-    <tr>
-      <th>dbparms</th>
-      <td><p>list, settings$database info reqired for opening a connection to DB</p></td>
-    </tr>
-    <tr>
-      <th>input_veg</th>
-      <td><p>list, this is a sublist of settings$run$inputs that has info about source, id, metadata of the requested IC file</p></td>
-    </tr>
-    <tr>
-      <th>pfts</th>
-      <td><p>list, same as settings$pfts</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>path to where the processed files will be written</p></td>
-    </tr>
-    <tr>
-      <th>n.ensemble</th>
-      <td><p>integer, ensemble member number</p></td>
-    </tr>
-    <tr>
-      <th>dir</th>
-      <td><p>dir path to dbfiles on local machine</p></td>
-    </tr>
-    <tr>
-      <th>machine</th>
-      <td><p>data frame, DB info regarding localhost machine id/hostname etc.</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>model name, e.g. "ED2"</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$start.date, otherwise start_date of the IC file in DB</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>date in "YYYY-MM-DD" format, in case of source==FIA it's the settings$run$end.date, otherwise end_date of the IC file in DB</p></td>
-    </tr>
-    <tr>
-      <th>new_site</th>
-      <td><p>data frame, id/lat/lon/name info about the site</p></td>
-    </tr>
-    <tr>
-      <th>host</th>
-      <td><p>list, host info as in settings$host, host$name forced to be "localhost" upstream</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>logical flag for convert.input</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Match species to PFTs + veg2model module</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>put_veg_module</span>(<span class='no'>getveg.id</span>, <span class='no'>dbparms</span>, <span class='no'>input_veg</span>, <span class='no'>pfts</span>, <span class='no'>outfolder</span>, <span class='no'>n.ensemble</span>,
+  <span class='no'>dir</span>, <span class='no'>machine</span>, <span class='no'>model</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>new_site</span>, <span class='no'>host</span>, <span class='no'>overwrite</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>getveg.id</th>
+              <td>
+                <p>
+                  list, input.id and dbfile.id of the IC file in intermediate
+                  pecan standard
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>dbparms</th>
+              <td>
+                <p>
+                  list, settings$database info reqired for opening a connection
+                  to DB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>input_veg</th>
+              <td>
+                <p>
+                  list, this is a sublist of settings$run$inputs that has info
+                  about source, id, metadata of the requested IC file
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pfts</th>
+              <td><p>list, same as settings$pfts</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>path to where the processed files will be written</p></td>
+            </tr>
+            <tr>
+              <th>n.ensemble</th>
+              <td><p>integer, ensemble member number</p></td>
+            </tr>
+            <tr>
+              <th>dir</th>
+              <td><p>dir path to dbfiles on local machine</p></td>
+            </tr>
+            <tr>
+              <th>machine</th>
+              <td>
+                <p>
+                  data frame, DB info regarding localhost machine id/hostname
+                  etc.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td><p>model name, e.g. "ED2"</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  date in "YYYY-MM-DD" format, in case of source==FIA it's the
+                  settings$run$start.date, otherwise start_date of the IC file
+                  in DB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  date in "YYYY-MM-DD" format, in case of source==FIA it's the
+                  settings$run$end.date, otherwise end_date of the IC file in DB
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>new_site</th>
+              <td><p>data frame, id/lat/lon/name info about the site</p></td>
+            </tr>
+            <tr>
+              <th>host</th>
+              <td>
+                <p>
+                  list, host info as in settings$host, host$name forced to be
+                  "localhost" upstream
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>logical flag for convert.input</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/sample_ic.html b/modules/data.land/docs/reference/sample_ic.html
index 212f3a3..f40b1a4 100644
--- a/modules/data.land/docs/reference/sample_ic.html
+++ b/modules/data.land/docs/reference/sample_ic.html
@@ -2,176 +2,203 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>sample_ic — sample_ic • PEcAn.data.land</title>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>sample_ic</h1>
-    
-    <div class="hidden name"><code>sample_ic.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>sample_ic</h1>
 
-    <div class="ref-description">
-    
-    <p>sample_ic</p>
-    
-    </div>
+            <div class="hidden name"><code>sample_ic.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>sample_ic</span>(<span class='no'>in.path</span>, <span class='no'>in.name</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>outfolder</span>, <span class='no'>n.ensemble</span>,
-  <span class='no'>machine_host</span>, <span class='no'>source</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>in.path</th>
-      <td><p>path to folder of the file to be sampled</p></td>
-    </tr>
-    <tr>
-      <th>in.name</th>
-      <td><p>file name of the file to be sampled</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>date in "YYYY-MM-DD" format</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>date in "YYYY-MM-DD" format</p></td>
-    </tr>
-    <tr>
-      <th>outfolder</th>
-      <td><p>dir path, whete to write the file</p></td>
-    </tr>
-    <tr>
-      <th>n.ensemble</th>
-      <td><p>integer, ensemble member number</p></td>
-    </tr>
-    <tr>
-      <th>machine_host</th>
-      <td><p>localhost name, e.g. "pecan2.bu.edu"</p></td>
-    </tr>
-    <tr>
-      <th>source</th>
-      <td><p>string to appear in file names, e.g. "PalEON"</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Istem Fer
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>sample_ic</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>sample_ic</span>(<span class='no'>in.path</span>, <span class='no'>in.name</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>outfolder</span>, <span class='no'>n.ensemble</span>,
+  <span class='no'>machine_host</span>, <span class='no'>source</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>in.path</th>
+              <td><p>path to folder of the file to be sampled</p></td>
+            </tr>
+            <tr>
+              <th>in.name</th>
+              <td><p>file name of the file to be sampled</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td><p>date in "YYYY-MM-DD" format</p></td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td><p>date in "YYYY-MM-DD" format</p></td>
+            </tr>
+            <tr>
+              <th>outfolder</th>
+              <td><p>dir path, whete to write the file</p></td>
+            </tr>
+            <tr>
+              <th>n.ensemble</th>
+              <td><p>integer, ensemble member number</p></td>
+            </tr>
+            <tr>
+              <th>machine_host</th>
+              <td><p>localhost name, e.g. "pecan2.bu.edu"</p></td>
+            </tr>
+            <tr>
+              <th>source</th>
+              <td><p>string to appear in file names, e.g. "PalEON"</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-
diff --git a/modules/data.land/docs/reference/sclass.html b/modules/data.land/docs/reference/sclass.html
index 70be9ca..bb19e94 100644
--- a/modules/data.land/docs/reference/sclass.html
+++ b/modules/data.land/docs/reference/sclass.html
@@ -2,153 +2,198 @@
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 <html>
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+      This function determines the soil class number based on the fraction of
+      sand, clay, and silt — sclass • PEcAn.data.land
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      property="og:title"
+      content="This function determines the soil class number based on the fraction of sand, clay, and silt — sclass"
+    />
+
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+      property="og:description"
+      content="This function determines the soil class number based on the fraction of sand, clay, and silt"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+              <ul class="nav navbar-nav">
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>This function determines the soil class number based on the fraction of sand, clay, and silt</h1>
-    
-    <div class="hidden name"><code>sclass.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function determines the soil class number based on the fraction of sand, clay, and silt</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sclass</span>(<span class='no'>sandfrac</span>, <span class='no'>clayfrac</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sandfrac</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>clayfrac</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              This function determines the soil class number based on the
+              fraction of sand, clay, and silt
+            </h1>
+
+            <div class="hidden name"><code>sclass.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function determines the soil class number based on the
+              fraction of sand, clay, and silt
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sclass</span>(<span class='no'>sandfrac</span>, <span class='no'>clayfrac</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sandfrac</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>clayfrac</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>sclass</span>(<span class='fl'>0.3</span>,<span class='fl'>0.3</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/shp2kml.html b/modules/data.land/docs/reference/shp2kml.html
index f66e4af..20386bf 100644
--- a/modules/data.land/docs/reference/shp2kml.html
+++ b/modules/data.land/docs/reference/shp2kml.html
@@ -2,148 +2,207 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
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-<script src="../pkgdown.js"></script>
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-<meta property="og:title" content="Convert shapefile to KML — shp2kml" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Convert shapefile to KML — shp2kml • PEcAn.data.land</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Convert shapefile to KML — shp2kml" />
+
+    <meta
+      property="og:description"
+      content="Convert ESRI shapefile (*.shp) to keyhole markup language (KML) file format"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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-        
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-      
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert shapefile to KML</h1>
-    
-    <div class="hidden name"><code>shp2kml.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert shapefile to KML</h1>
 
-    <div class="ref-description">
-    
-    <p>Convert ESRI shapefile (*.shp) to keyhole markup language (KML) file format</p>
-    
-    </div>
+            <div class="hidden name"><code>shp2kml.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>shp2kml</span>(<span class='no'>dir</span>, <span class='no'>ext</span>, <span class='kw'>kmz</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>proj4</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>color</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>
+              Convert ESRI shapefile (*.shp) to keyhole markup language (KML)
+              file format
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>shp2kml</span>(<span class='no'>dir</span>, <span class='no'>ext</span>, <span class='kw'>kmz</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>proj4</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>color</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>NameField</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>out.dir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dir</th>
-      <td><p>Directory of GIS shapefiles to convert to kml/kmz</p></td>
-    </tr>
-    <tr>
-      <th>ext</th>
-      <td><p>File extension for files to convert to kml/kmz.  Defaults to ESRI shapefile,
-'.shp'.  [Place holder for other potential vector files to conver to kml]</p></td>
-    </tr>
-    <tr>
-      <th>kmz</th>
-      <td><p>TRUE/FALSE. Option to write out file as a compressed kml. Requires zip utility</p></td>
-    </tr>
-    <tr>
-      <th>proj4</th>
-      <td><p>OPTIONAL. Define output proj4 projection string.  If set, input vector will be 
-reprojected to desired projection.  Not yet implemented.</p></td>
-    </tr>
-    <tr>
-      <th>color</th>
-      <td><p>OPTIONAL. Fill color for output kml/kmz file</p></td>
-    </tr>
-    <tr>
-      <th>NameField</th>
-      <td><p>OPTIONAL. Define names for individual features in KML/KMZ file</p></td>
-    </tr>
-    <tr>
-      <th>out.dir</th>
-      <td><p>OPTIONAL. Output directory for converted files</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dir</th>
+              <td><p>Directory of GIS shapefiles to convert to kml/kmz</p></td>
+            </tr>
+            <tr>
+              <th>ext</th>
+              <td>
+                <p>
+                  File extension for files to convert to kml/kmz. Defaults to
+                  ESRI shapefile, '.shp'. [Place holder for other potential
+                  vector files to conver to kml]
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>kmz</th>
+              <td>
+                <p>
+                  TRUE/FALSE. Option to write out file as a compressed kml.
+                  Requires zip utility
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>proj4</th>
+              <td>
+                <p>
+                  OPTIONAL. Define output proj4 projection string. If set, input
+                  vector will be reprojected to desired projection. Not yet
+                  implemented.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>color</th>
+              <td><p>OPTIONAL. Fill color for output kml/kmz file</p></td>
+            </tr>
+            <tr>
+              <th>NameField</th>
+              <td>
+                <p>
+                  OPTIONAL. Define names for individual features in KML/KMZ file
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>out.dir</th>
+              <td><p>OPTIONAL. Output directory for converted files</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>dir</span> <span class='kw'>&lt;-</span> <span class='fu'>Sys.glob</span>(<span class='fu'>file.path</span>(<span class='fu'>R.home</span>(), <span class='st'>'library'</span>, <span class='st'>'PEcAn.data.land'</span>,<span class='st'>'data'</span>))
 <span class='no'>out.dir</span> <span class='kw'>&lt;-</span> <span class='fu'>path.expand</span>(<span class='st'>'~/temp'</span>)
 <span class='fu'>shp2kml</span>(<span class='no'>dir</span>,<span class='st'>'.shp'</span>,<span class='kw'>kmz</span><span class='kw'>=</span><span class='fl'>FALSE</span>,<span class='kw'>NameField</span><span class='kw'>=</span><span class='st'>'STATE'</span>,<span class='kw'>out.dir</span><span class='kw'>=</span><span class='no'>out.dir</span>)
@@ -151,36 +210,32 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Shawn P. Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Shawn P. Serbin
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/soil.units.html b/modules/data.land/docs/reference/soil.units.html
index 5656972..cd6638f 100644
--- a/modules/data.land/docs/reference/soil.units.html
+++ b/modules/data.land/docs/reference/soil.units.html
@@ -2,149 +2,187 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Get standard units for a soil variable — soil.units • PEcAn.data.land</title>
-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get standard units for a soil variable</h1>
-    
-    <div class="hidden name"><code>soil.units.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Get standard units for a soil variable</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>soil.units</span>(<span class='kw'>varname</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>varname</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get standard units for a soil variable</h1>
+
+            <div class="hidden name"><code>soil.units.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get standard units for a soil variable</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>soil.units</span>(<span class='kw'>varname</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>varname</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>soil.units</span>(<span class='st'>"soil_albedo"</span>)
 <span class='co'># }</span></pre>
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
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-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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diff --git a/modules/data.land/docs/reference/soil2netcdf.html b/modules/data.land/docs/reference/soil2netcdf.html
index f8a0dd8..1ee2b6a 100644
--- a/modules/data.land/docs/reference/soil2netcdf.html
+++ b/modules/data.land/docs/reference/soil2netcdf.html
@@ -2,173 +2,240 @@
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+      Save soil texture &amp; parameters in PEcAn standard netCDF CF —
+      soil2netcdf • PEcAn.data.land
+    </title>
+
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Save soil texture &amp; parameters in PEcAn standard netCDF CF</h1>
-    
-    <div class="hidden name"><code>soil2netcdf.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Save soil texture &amp; parameters in PEcAn standard netCDF CF</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>soil2netcdf</span>(<span class='no'>soil.data</span>, <span class='no'>new.file</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>soil.data</th>
-      <td><p>List of soil variables in standard names &amp; units. Minimum is soil_depth and two of [sand, silt, clay]. Bulk density encouraged.</p></td>
-    </tr>
-    <tr>
-      <th>new.file</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>none</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>A table of standard names and units can be displayed by running soil.units() without any arguements</p>
-<p>soil_params is called internally to estimate additional soil physical parameters from sand/silt/clay &amp; bulk density. Will not overwrite any provided values</p>
-<p>Need to expand to alternatively take soil_type (texture class) as an input</p>
-<p>On output, soil_type named class is converted to a number because netCDF is a pain for storing strings.
-Conversion back can be done by load(system.file("data/soil_class.RData",package = "PEcAn.data.land")) and then soil.name[soil_n]</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Save soil texture &amp; parameters in PEcAn standard netCDF CF
+            </h1>
+
+            <div class="hidden name"><code>soil2netcdf.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Save soil texture &amp; parameters in PEcAn standard netCDF CF
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>soil2netcdf</span>(<span class='no'>soil.data</span>, <span class='no'>new.file</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>soil.data</th>
+              <td>
+                <p>
+                  List of soil variables in standard names &amp; units. Minimum
+                  is soil_depth and two of [sand, silt, clay]. Bulk density
+                  encouraged.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>new.file</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>none</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            A table of standard names and units can be displayed by running
+            soil.units() without any arguements
+          </p>
+          <p>
+            soil_params is called internally to estimate additional soil
+            physical parameters from sand/silt/clay &amp; bulk density. Will not
+            overwrite any provided values
+          </p>
+          <p>
+            Need to expand to alternatively take soil_type (texture class) as an
+            input
+          </p>
+          <p>
+            On output, soil_type named class is converted to a number because
+            netCDF is a pain for storing strings. Conversion back can be done by
+            load(system.file("data/soil_class.RData",package =
+            "PEcAn.data.land")) and then soil.name[soil_n]
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>soil.data</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>fraction_of_sand_in_soil</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.3</span>,<span class='fl'>0.4</span>,<span class='fl'>0.5</span>),
                   <span class='kw'>fraction_of_clay_in_soil</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.3</span>,<span class='fl'>0.3</span>,<span class='fl'>0.3</span>),
                   <span class='kw'>soil_depth</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.2</span>,<span class='fl'>0.5</span>,<span class='fl'>1.0</span>))
 
 <span class='fu'>soil2netcdf</span>(<span class='no'>soil.data</span>,<span class='st'>"soil.nc"</span>)
 <span class='co'># }</span></pre>
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Estimate soil parameters from texture class or sand/silt/clay</h1>
-    
-    <div class="hidden name"><code>soil_params.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Estimate soil parameters from texture class or sand/silt/clay
+            </h1>
 
-    <div class="ref-description">
-    
-    <p>Estimate soil parameters from texture class or sand/silt/clay</p>
-    
-    </div>
+            <div class="hidden name"><code>soil_params.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>soil_params</span>(<span class='kw'>soil_type</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>sand</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>silt</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>Estimate soil parameters from texture class or sand/silt/clay</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>soil_params</span>(<span class='kw'>soil_type</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>sand</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>silt</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>clay</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>bulk</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>soil_type</th>
-      <td><p>USDA Soil Class. See Details</p></td>
-    </tr>
-    <tr>
-      <th>sand</th>
-      <td><p>percent sand</p></td>
-    </tr>
-    <tr>
-      <th>silt</th>
-      <td><p>percent silt</p></td>
-    </tr>
-    <tr>
-      <th>clay</th>
-      <td><p>percent clay</p></td>
-    </tr>
-    <tr>
-      <th>bulk</th>
-      <td><p>soil bulk density (optional, kg m-3)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list of soil hydraulic and thermal parameters</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>* Specify _either_ soil_type or sand/silt/clay. soil_type will be ignored if sand/silt/clay is provided
-* If only 2 out of sand/silt/clay are provided, it will be assumed they sum to 100<!-- % -->
-* Valid soil class options: "Sand","Loamy sand","Sandy loam","Silt loam","Loam",
-                            "Sandy clay loam","Silty clay loam","Clayey loam",
-                            "Sandy clay","Silty clay","Clay","Peat","Bedrock",
-                            "Silt","Heavy clay","Clayey sand","Clayey silt"
-* Based on ED2/R-utils/soilutils.r
-* Hydraulics based on Cosby et al 1984, using table 4 and equation 1 (which is incorrect it should be saturated moisture potential over moisture potential)</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>soil_type</th>
+              <td><p>USDA Soil Class. See Details</p></td>
+            </tr>
+            <tr>
+              <th>sand</th>
+              <td><p>percent sand</p></td>
+            </tr>
+            <tr>
+              <th>silt</th>
+              <td><p>percent silt</p></td>
+            </tr>
+            <tr>
+              <th>clay</th>
+              <td><p>percent clay</p></td>
+            </tr>
+            <tr>
+              <th>bulk</th>
+              <td><p>soil bulk density (optional, kg m-3)</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list of soil hydraulic and thermal parameters</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            * Specify _either_ soil_type or sand/silt/clay. soil_type will be
+            ignored if sand/silt/clay is provided * If only 2 out of
+            sand/silt/clay are provided, it will be assumed they sum to 100<!-- % -->
+            * Valid soil class options: "Sand","Loamy sand","Sandy loam","Silt
+            loam","Loam", "Sandy clay loam","Silty clay loam","Clayey loam",
+            "Sandy clay","Silty clay","Clay","Peat","Bedrock", "Silt","Heavy
+            clay","Clayey sand","Clayey silt" * Based on ED2/R-utils/soilutils.r
+            * Hydraulics based on Cosby et al 1984, using table 4 and equation 1
+            (which is incorrect it should be saturated moisture potential over
+            moisture potential)
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>sand</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.5</span>)
 <span class='no'>clay</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='fl'>0.3</span>, <span class='fl'>0.3</span>, <span class='fl'>0.3</span>)
 <span class='fu'>soil_params</span>(<span class='kw'>sand</span><span class='kw'>=</span><span class='no'>sand</span>,<span class='kw'>clay</span><span class='kw'>=</span><span class='no'>clay</span>)
 <span class='co'># }</span></pre>
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-      
-      <li><a href="#value">Value</a></li>
-
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-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
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-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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+            <li><a href="#value">Value</a></li>
 
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+            <li><a href="#details">Details</a></li>
 
-  
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-    <h1>Module for managing soil texture extraction</h1>
-    
-    <div class="hidden name"><code>soil_process.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Module for managing soil texture extraction</h1>
 
-    <div class="ref-description">
-    
-    <p>Module for managing soil texture extraction</p>
-    
-    </div>
+            <div class="hidden name"><code>soil_process.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>soil_process</span>(<span class='no'>settings</span>, <span class='no'>input</span>, <span class='no'>dbfiles</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+          <div class="ref-description">
+            <p>Module for managing soil texture extraction</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>soil_process</span>(<span class='no'>settings</span>, <span class='no'>input</span>, <span class='no'>dbfiles</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>run.local</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings list</p></td>
-    </tr>
-    <tr>
-      <th>input</th>
-      <td><p>PEcAn input list</p></td>
-    </tr>
-    <tr>
-      <th>dbfiles</th>
-      <td><p>directory to write database files</p></td>
-    </tr>
-    <tr>
-      <th>overwrite</th>
-      <td><p>overwrite previous results (boolean)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>path to soil file</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>PEcAn settings list</p></td>
+            </tr>
+            <tr>
+              <th>input</th>
+              <td><p>PEcAn input list</p></td>
+            </tr>
+            <tr>
+              <th>dbfiles</th>
+              <td><p>directory to write database files</p></td>
+            </tr>
+            <tr>
+              <th>overwrite</th>
+              <td><p>overwrite previous results (boolean)</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>path to soil file</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to subset and clip a GIS vector or raster layer by a bounding box
-or clip/subset layer (e.g. shapefile/KML)</h1>
-    
-    <div class="hidden name"><code>subset.layer.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to subset and clip a GIS vector or raster layer by a bounding box
-or clip/subset layer (e.g. shapefile/KML)</p>
-    
-    </div>
-
-    <pre class="usage"><span class='co'># S3 method for layer</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function to subset and clip a GIS vector or raster layer by a
+              bounding box or clip/subset layer (e.g. shapefile/KML)
+            </h1>
+
+            <div class="hidden name"><code>subset.layer.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to subset and clip a GIS vector or raster layer by a
+              bounding box or clip/subset layer (e.g. shapefile/KML)
+            </p>
+          </div>
+
+          <pre class="usage"><span class='co'># S3 method for layer</span>
 <span class='fu'>subset</span>(<span class='no'>file</span>, <span class='kw'>coords</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>sub.layer</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>clip</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>out.dir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>out.name</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>file</th>
-      <td><p>input file to be subset</p></td>
-    </tr>
-    <tr>
-      <th>coords</th>
-      <td><p>vector with xmin,ymin,xmax,ymax defing the bounding box for subset</p></td>
-    </tr>
-    <tr>
-      <th>sub.layer</th>
-      <td><p>Vector layer defining the subset region</p></td>
-    </tr>
-    <tr>
-      <th>clip</th>
-      <td><p>clip geometries to bounding box/subset layer? TRUE/FALSE</p></td>
-    </tr>
-    <tr>
-      <th>out.dir</th>
-      <td><p>output directory for subset layer. Defaults to location of
-input file.  Can also set to 'pwd'</p></td>
-    </tr>
-    <tr>
-      <th>out.name</th>
-      <td><p>filename for subset layer.  Defaults to original filename with the suffix
-*.sub</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>file</th>
+              <td><p>input file to be subset</p></td>
+            </tr>
+            <tr>
+              <th>coords</th>
+              <td>
+                <p>
+                  vector with xmin,ymin,xmax,ymax defing the bounding box for
+                  subset
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sub.layer</th>
+              <td><p>Vector layer defining the subset region</p></td>
+            </tr>
+            <tr>
+              <th>clip</th>
+              <td>
+                <p>clip geometries to bounding box/subset layer? TRUE/FALSE</p>
+              </td>
+            </tr>
+            <tr>
+              <th>out.dir</th>
+              <td>
+                <p>
+                  output directory for subset layer. Defaults to location of
+                  input file. Can also set to 'pwd'
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>out.name</th>
+              <td>
+                <p>
+                  filename for subset layer. Defaults to original filename with
+                  the suffix *.sub
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='co'># Test dataset</span>
 <span class='no'>file</span> <span class='kw'>&lt;-</span> <span class='fu'>Sys.glob</span>(<span class='fu'>file.path</span>(<span class='fu'>R.home</span>(), <span class='st'>'library'</span>, <span class='st'>'PEcAn.data.land'</span>,<span class='st'>'data'</span>,<span class='st'>'*.shp'</span>))
 <span class='no'>out.dir</span> <span class='kw'>&lt;-</span> <span class='fu'>path.expand</span>(<span class='st'>'~/temp'</span>)
@@ -157,36 +216,32 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Shawn P. Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Shawn P. Serbin
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/to.Tag.html b/modules/data.land/docs/reference/to.Tag.html
index 2f1ae8b..0d76124 100644
--- a/modules/data.land/docs/reference/to.Tag.html
+++ b/modules/data.land/docs/reference/to.Tag.html
@@ -2,133 +2,154 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="to.Tag — to.Tag" />
+
+    <meta property="og:description" content="to.Tag" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>to.Tag</h1>
-    
-    <div class="hidden name"><code>to.Tag.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>to.Tag</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>to.Tag</h1>
 
-    <pre class="usage"><span class='fu'>to.Tag</span>(<span class='no'>SITE</span>, <span class='no'>PLOT</span>, <span class='no'>SUBPLOT</span>, <span class='kw'>TAG</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-        
+            <div class="hidden name"><code>to.Tag.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>to.Tag</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>to.Tag</span>(<span class='no'>SITE</span>, <span class='no'>PLOT</span>, <span class='no'>SUBPLOT</span>, <span class='kw'>TAG</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/to.TreeCode.html b/modules/data.land/docs/reference/to.TreeCode.html
index a80ae03..60fb9dd 100644
--- a/modules/data.land/docs/reference/to.TreeCode.html
+++ b/modules/data.land/docs/reference/to.TreeCode.html
@@ -2,133 +2,154 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>to.TreeCode — to.TreeCode • PEcAn.data.land</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>to.TreeCode — to.TreeCode • PEcAn.data.land</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="to.TreeCode — to.TreeCode" />
+
+    <meta property="og:description" content="to.TreeCode" />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>to.TreeCode</h1>
-    
-    <div class="hidden name"><code>to.TreeCode.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>to.TreeCode</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>to.TreeCode</h1>
 
-    <pre class="usage"><span class='fu'>to.TreeCode</span>(<span class='no'>SITE</span>, <span class='no'>PLOT</span>, <span class='no'>SUBPLOT</span>, <span class='kw'>TAG</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-        
+            <div class="hidden name"><code>to.TreeCode.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>to.TreeCode</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>to.TreeCode</span>(<span class='no'>SITE</span>, <span class='no'>PLOT</span>, <span class='no'>SUBPLOT</span>, <span class='kw'>TAG</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/write_ic.html b/modules/data.land/docs/reference/write_ic.html
index 6a17d91..c564a97 100644
--- a/modules/data.land/docs/reference/write_ic.html
+++ b/modules/data.land/docs/reference/write_ic.html
@@ -2,138 +2,159 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>write_ic — write_ic • PEcAn.data.land</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-
-<meta property="og:title" content="write_ic — write_ic" />
-
-<meta property="og:description" content="write_ic" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>write_ic — write_ic • PEcAn.data.land</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="write_ic — write_ic" />
+
+    <meta property="og:description" content="write_ic" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>write_ic</h1>
-    
-    <div class="hidden name"><code>write_ic.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>write_ic</h1>
 
-    <div class="ref-description">
-    
-    <p>write_ic</p>
-    
-    </div>
+            <div class="hidden name"><code>write_ic.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>write_ic</span>(<span class='no'>in.path</span>, <span class='no'>in.name</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>outfolder</span>, <span class='no'>model</span>,
-  <span class='no'>new_site</span>, <span class='no'>pfts</span>, <span class='kw'>source</span> <span class='kw'>=</span> <span class='no'>input_veg</span>$<span class='no'>source</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
-        
+          <div class="ref-description">
+            <p>write_ic</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>write_ic</span>(<span class='no'>in.path</span>, <span class='no'>in.name</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>, <span class='no'>outfolder</span>, <span class='no'>model</span>,
+  <span class='no'>new_site</span>, <span class='no'>pfts</span>, <span class='kw'>source</span> <span class='kw'>=</span> <span class='no'>input_veg</span>$<span class='no'>source</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Istem Fer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.land/docs/reference/write_veg.html b/modules/data.land/docs/reference/write_veg.html
index 5314a1e..d1f5f4b 100644
--- a/modules/data.land/docs/reference/write_veg.html
+++ b/modules/data.land/docs/reference/write_veg.html
@@ -2,133 +2,157 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>write_veg — write_veg • PEcAn.data.land</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="write_veg — write_veg" />
-
-<meta property="og:description" content="Function to save intermediate rds file" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>write_veg — write_veg • PEcAn.data.land</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="write_veg — write_veg" />
+
+    <meta
+      property="og:description"
+      content="Function to save intermediate rds file"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
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-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
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-     
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.data.land</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>write_veg</h1>
-    
-    <div class="hidden name"><code>write_veg.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function to save intermediate rds file</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>write_veg</h1>
 
-    <pre class="usage"><span class='fu'>write_veg</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>veg_info</span>, <span class='no'>source</span>)</pre>
-        
+            <div class="hidden name"><code>write_veg.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Function to save intermediate rds file</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>write_veg</span>(<span class='no'>outfolder</span>, <span class='no'>start_date</span>, <span class='no'>veg_info</span>, <span class='no'>source</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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   </body>
 </html>
-
diff --git a/modules/data.mining/docs/LICENSE-text.html b/modules/data.mining/docs/LICENSE-text.html
index dd6d4eb..23541f5 100644
--- a/modules/data.mining/docs/LICENSE-text.html
+++ b/modules/data.mining/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- jquery -->
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-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+    <title>License • PEcAn.data.mining</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.mining</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
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-</li>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.data.mining</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.mining/docs/authors.html b/modules/data.mining/docs/authors.html
index d906cbb..c28ddcc 100644
--- a/modules/data.mining/docs/authors.html
+++ b/modules/data.mining/docs/authors.html
@@ -2,122 +2,143 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.data.mining</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
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-
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-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.data.mining</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
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+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.mining</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
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-</li>
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-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.data.mining</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
-
diff --git a/modules/data.mining/docs/docsearch.css b/modules/data.mining/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/data.mining/docs/docsearch.css
+++ b/modules/data.mining/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/data.mining/docs/docsearch.js b/modules/data.mining/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/data.mining/docs/docsearch.js
+++ b/modules/data.mining/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/data.mining/docs/index.html b/modules/data.mining/docs/index.html
index 5731c29..4746b27 100644
--- a/modules/data.mining/docs/index.html
+++ b/modules/data.mining/docs/index.html
@@ -1,103 +1,162 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for exploring model residuals and structures • PEcAn.data.mining</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for exploring model residuals and structures">
-<meta property="og:description" content="(Temporary description) PEcAn functions used for exploring model residuals and structures">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for exploring model residuals and structures •
+      PEcAn.data.mining
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for exploring model residuals and structures"
+    />
+    <meta
+      property="og:description"
+      content="(Temporary description) PEcAn functions used for exploring model residuals and structures"
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.mining</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    (Temporary description) PEcAn functions used for exploring model residuals and structures
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.data.mining</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          (Temporary description) PEcAn functions used for exploring model
+          residuals and structures
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/data.mining/docs/pkgdown.css b/modules/data.mining/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/data.mining/docs/pkgdown.css
+++ b/modules/data.mining/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/data.mining/docs/pkgdown.js b/modules/data.mining/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/data.mining/docs/pkgdown.js
+++ b/modules/data.mining/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/data.mining/docs/reference/index.html b/modules/data.mining/docs/reference/index.html
index 3854d21..f8f8825 100644
--- a/modules/data.mining/docs/reference/index.html
+++ b/modules/data.mining/docs/reference/index.html
@@ -2,129 +2,151 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title> • PEcAn.data.mining</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>• PEcAn.data.mining</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.mining</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.mining</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.remote/docs/LICENSE-text.html b/modules/data.remote/docs/LICENSE-text.html
index bdbd7fd..a04badc 100644
--- a/modules/data.remote/docs/LICENSE-text.html
+++ b/modules/data.remote/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>License • PEcAn.data.remote</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="License" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>License • PEcAn.data.remote</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.data.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -121,27 +150,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.remote/docs/authors.html b/modules/data.remote/docs/authors.html
index 581188d..5abc83c 100644
--- a/modules/data.remote/docs/authors.html
+++ b/modules/data.remote/docs/authors.html
@@ -2,122 +2,143 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.data.remote</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.data.remote</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.data.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.remote/docs/docsearch.css b/modules/data.remote/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/data.remote/docs/docsearch.css
+++ b/modules/data.remote/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/data.remote/docs/docsearch.js b/modules/data.remote/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/data.remote/docs/docsearch.js
+++ b/modules/data.remote/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/data.remote/docs/index.html b/modules/data.remote/docs/index.html
index 64bddb0..f6e5f9c 100644
--- a/modules/data.remote/docs/index.html
+++ b/modules/data.remote/docs/index.html
@@ -1,103 +1,158 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for remote sensing • PEcAn.data.remote</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for remote sensing">
-<meta property="og:description" content="PEcAn module for processing remote data">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn functions used for remote sensing • PEcAn.data.remote</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for remote sensing"
+    />
+    <meta
+      property="og:description"
+      content="PEcAn module for processing remote data"
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.data.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    PEcAn module for processing remote data
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.data.remote</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          PEcAn module for processing remote data
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/data.remote/docs/pkgdown.css b/modules/data.remote/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/data.remote/docs/pkgdown.css
+++ b/modules/data.remote/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
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-html, body {
+html,
+body {
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@@ -68,7 +69,7 @@ img {
 
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-  display:inline-block;
+  display: inline-block;
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@@ -89,10 +90,12 @@ a.anchor {
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 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
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 }
@@ -107,7 +110,6 @@ a.anchor {
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 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
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+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
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 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
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@@ -191,15 +217,35 @@ a.sourceLine:hover {
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 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
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diff --git a/modules/data.remote/docs/pkgdown.js b/modules/data.remote/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/data.remote/docs/pkgdown.js
+++ b/modules/data.remote/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
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-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
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@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/data.remote/docs/reference/call_MODIS.html b/modules/data.remote/docs/reference/call_MODIS.html
index c0e088a..7ba6a9d 100644
--- a/modules/data.remote/docs/reference/call_MODIS.html
+++ b/modules/data.remote/docs/reference/call_MODIS.html
@@ -2,198 +2,250 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>call_MODIS — call_MODIS • PEcAn.data.remote</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<!-- Font Awesome icons -->
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-<!-- clipboard.js -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="call_MODIS — call_MODIS" />
-
-<meta property="og:description" content="Get MODIS data by date and location" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>call_MODIS — call_MODIS • PEcAn.data.remote</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="call_MODIS — call_MODIS" />
+
+    <meta
+      property="og:description"
+      content="Get MODIS data by date and location"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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     <div class="container template-reference-topic">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.remote</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>call_MODIS</h1>
-    
-    <div class="hidden name"><code>call_MODIS.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>call_MODIS</h1>
 
-    <div class="ref-description">
-    
-    <p>Get MODIS data by date and location</p>
-    
-    </div>
+            <div class="hidden name"><code>call_MODIS.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>call_MODIS</span>(<span class='kw'>outfolder</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>fname</span> <span class='kw'>=</span> <span class='st'>"m_data.nc"</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
+          <div class="ref-description">
+            <p>Get MODIS data by date and location</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>call_MODIS</span>(<span class='kw'>outfolder</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>fname</span> <span class='kw'>=</span> <span class='st'>"m_data.nc"</span>, <span class='no'>start_date</span>, <span class='no'>end_date</span>,
   <span class='no'>lat</span>, <span class='no'>lon</span>, <span class='kw'>size</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>product</span> <span class='kw'>=</span> <span class='st'>"MOD15A2"</span>, <span class='kw'>band</span> <span class='kw'>=</span> <span class='st'>"Lai_1km"</span>,
   <span class='kw'>qc_band</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>sd_band</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outfolder</th>
-      <td><p>where the output file will be stored</p></td>
-    </tr>
-    <tr>
-      <th>fname</th>
-      <td><p>name of netcdf file to output</p></td>
-    </tr>
-    <tr>
-      <th>start_date</th>
-      <td><p>beginning of date range for LAI download in unambiguous date format</p></td>
-    </tr>
-    <tr>
-      <th>end_date</th>
-      <td><p>end of date range for LAI download in unambiguous date format</p></td>
-    </tr>
-    <tr>
-      <th>lat</th>
-      <td><p>Latitude of the pixel</p></td>
-    </tr>
-    <tr>
-      <th>lon</th>
-      <td><p>Longitude of the pixel</p></td>
-    </tr>
-    <tr>
-      <th>size</th>
-      <td><p>NS and WE distance in km to be included</p></td>
-    </tr>
-    <tr>
-      <th>product</th>
-      <td><p>MODIS product number</p></td>
-    </tr>
-    <tr>
-      <th>band</th>
-      <td><p>which measurement to extract</p></td>
-    </tr>
-    <tr>
-      <th>qc_band</th>
-      <td><p>which quality control band (optional)</p></td>
-    </tr>
-    <tr>
-      <th>sd_band</th>
-      <td><p>which standard deviation band (optional)</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>tell python whether or not to print debug statements (all or nothing)</p>
-<p>depends on a number of Python libraries. sudo -H pip install numpy suds netCDF4</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outfolder</th>
+              <td><p>where the output file will be stored</p></td>
+            </tr>
+            <tr>
+              <th>fname</th>
+              <td><p>name of netcdf file to output</p></td>
+            </tr>
+            <tr>
+              <th>start_date</th>
+              <td>
+                <p>
+                  beginning of date range for LAI download in unambiguous date
+                  format
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>end_date</th>
+              <td>
+                <p>
+                  end of date range for LAI download in unambiguous date format
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lat</th>
+              <td><p>Latitude of the pixel</p></td>
+            </tr>
+            <tr>
+              <th>lon</th>
+              <td><p>Longitude of the pixel</p></td>
+            </tr>
+            <tr>
+              <th>size</th>
+              <td><p>NS and WE distance in km to be included</p></td>
+            </tr>
+            <tr>
+              <th>product</th>
+              <td><p>MODIS product number</p></td>
+            </tr>
+            <tr>
+              <th>band</th>
+              <td><p>which measurement to extract</p></td>
+            </tr>
+            <tr>
+              <th>qc_band</th>
+              <td><p>which quality control band (optional)</p></td>
+            </tr>
+            <tr>
+              <th>sd_band</th>
+              <td><p>which standard deviation band (optional)</p></td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td>
+                <p>
+                  tell python whether or not to print debug statements (all or
+                  nothing)
+                </p>
+                <p>
+                  depends on a number of Python libraries. sudo -H pip install
+                  numpy suds netCDF4
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>test</span> <span class='kw'>&lt;-</span> <span class='fu'>call_MODIS</span>(<span class='kw'>start</span><span class='kw'>=</span><span class='st'>"2001001"</span>,<span class='kw'>end</span><span class='kw'>=</span><span class='st'>"2016366"</span>,<span class='kw'>lat</span><span class='kw'>=</span><span class='fl'>44.0646</span>,<span class='kw'>lon</span><span class='kw'>=</span>-<span class='fl'>71.28808</span>,<span class='kw'>size</span><span class='kw'>=</span><span class='fl'>3</span>,<span class='kw'>qc_band</span> <span class='kw'>=</span> <span class='st'>"FparLai_QC"</span>,<span class='kw'>sd_band</span> <span class='kw'>=</span> <span class='st'>"LaiStdDev_1km"</span>)
 <span class='co'># }</span># NOT RUN {
 # }
 </pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/data.remote/docs/reference/download.NLCD.html b/modules/data.remote/docs/reference/download.NLCD.html
index ebd5e86..1a5a839 100644
--- a/modules/data.remote/docs/reference/download.NLCD.html
+++ b/modules/data.remote/docs/reference/download.NLCD.html
@@ -2,155 +2,198 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>download.NLCD — download.NLCD • PEcAn.data.remote</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="download.NLCD — download.NLCD" />
-
-<meta property="og:description" content="Downloads and unzips the National Land Cover Database http://www.mrlc.gov/nlcd2011.php. Will automatically insert into PEcAn database if database connection provided." />
-<meta name="twitter:card" content="summary" />
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>download.NLCD — download.NLCD • PEcAn.data.remote</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="download.NLCD — download.NLCD" />
+
+    <meta
+      property="og:description"
+      content="Downloads and unzips the National Land Cover Database http://www.mrlc.gov/nlcd2011.php. Will automatically insert into PEcAn database if database connection provided."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <span class="icon-bar"></span>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.data.remote</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.data.remote</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>download.NLCD</h1>
-    
-    <div class="hidden name"><code>download.NLCD.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Downloads and unzips the National Land Cover Database http://www.mrlc.gov/nlcd2011.php. Will automatically insert into PEcAn database if database connection provided.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>download.NLCD</span>(<span class='no'>outdir</span>, <span class='kw'>year</span> <span class='kw'>=</span> <span class='fl'>2011</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>Directory to download NLCD to</p></td>
-    </tr>
-    <tr>
-      <th>year</th>
-      <td><p>which NLCD year to download</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>Optional database connection. If specified then the code will check to see if the file already exists in PEcAn before downloading, and will also create a database entry for new downloads</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>download.NLCD</h1>
+
+            <div class="hidden name"><code>download.NLCD.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Downloads and unzips the National Land Cover Database
+              http://www.mrlc.gov/nlcd2011.php. Will automatically insert into
+              PEcAn database if database connection provided.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>download.NLCD</span>(<span class='no'>outdir</span>, <span class='kw'>year</span> <span class='kw'>=</span> <span class='fl'>2011</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>Directory to download NLCD to</p></td>
+            </tr>
+            <tr>
+              <th>year</th>
+              <td><p>which NLCD year to download</p></td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td>
+                <p>
+                  Optional database connection. If specified then the code will
+                  check to see if the file already exists in PEcAn before
+                  downloading, and will also create a database entry for new
+                  downloads
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/data.remote/docs/reference/extract_NLCD.html b/modules/data.remote/docs/reference/extract_NLCD.html
index bddb2de..2c00a6d 100644
--- a/modules/data.remote/docs/reference/extract_NLCD.html
+++ b/modules/data.remote/docs/reference/extract_NLCD.html
@@ -2,166 +2,218 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>extract.NLCD — extract_NLCD • PEcAn.data.remote</title>
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-    <h1>extract.NLCD</h1>
-    
-    <div class="hidden name"><code>extract_NLCD.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>extract.NLCD</h1>
 
-    <div class="ref-description">
-    
-    <p>Based on codes from Christy Rollinson and from Max Joseph (http://mbjoseph.github.io/2014/11/08/nlcd.html)</p>
-    
-    </div>
+            <div class="hidden name"><code>extract_NLCD.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Based on codes from Christy Rollinson and from Max Joseph
+              (http://mbjoseph.github.io/2014/11/08/nlcd.html)
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>extract_NLCD</span>(<span class='no'>buffer</span>, <span class='no'>coords</span>, <span class='kw'>data_dir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>extract_NLCD</span>(<span class='no'>buffer</span>, <span class='no'>coords</span>, <span class='kw'>data_dir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>con</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>year</span> <span class='kw'>=</span> <span class='fl'>2011</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>buffer</th>
-      <td><p>search radius (meters)</p></td>
-    </tr>
-    <tr>
-      <th>coords</th>
-      <td><p>data frame containing elements 'long' and 'lat'. Currently just supports single point extraction.</p></td>
-    </tr>
-    <tr>
-      <th>data_dir</th>
-      <td><p>directory where input data is located. Can be NUL if con is specified</p></td>
-    </tr>
-    <tr>
-      <th>con</th>
-      <td><p>connection to PEcAn database. Can be NULL if data_dir is specified</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dataframe of fractional cover of different cover classes</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>buffer</th>
+              <td><p>search radius (meters)</p></td>
+            </tr>
+            <tr>
+              <th>coords</th>
+              <td>
+                <p>
+                  data frame containing elements 'long' and 'lat'. Currently
+                  just supports single point extraction.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>data_dir</th>
+              <td>
+                <p>
+                  directory where input data is located. Can be NUL if con is
+                  specified
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>con</th>
+              <td>
+                <p>
+                  connection to PEcAn database. Can be NULL if data_dir is
+                  specified
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>dataframe of fractional cover of different cover classes</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze
+        </div>
+      </div>
 
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-        
-        <td>
-          <p><code><a href="download.NLCD.html">download.NLCD()</a></code> </p>
-        </td>
-        <td><p>download.NLCD</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="extract_NLCD.html">extract_NLCD()</a></code> </p>
-        </td>
-        <td><p>extract.NLCD</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="call_MODIS.html">call_MODIS()</a></code>
+                  </p>
+                </td>
+                <td><p>call_MODIS</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="download.NLCD.html">download.NLCD()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>download.NLCD</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="extract_NLCD.html">extract_NLCD()</a></code>
+                  </p>
+                </td>
+                <td><p>extract.NLCD</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/LICENSE-text.html b/modules/emulator/docs/LICENSE-text.html
index b4e1d29..a4dc883 100644
--- a/modules/emulator/docs/LICENSE-text.html
+++ b/modules/emulator/docs/LICENSE-text.html
@@ -2,97 +2,126 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>License • PEcAn.emulator</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="License" />
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>License • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/authors.html b/modules/emulator/docs/authors.html
index 4a33bea..6d6afd3 100644
--- a/modules/emulator/docs/authors.html
+++ b/modules/emulator/docs/authors.html
@@ -2,122 +2,143 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Authors • PEcAn.emulator</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Authors" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Authors • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/docsearch.css b/modules/emulator/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/emulator/docs/docsearch.css
+++ b/modules/emulator/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/emulator/docs/docsearch.js b/modules/emulator/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/emulator/docs/docsearch.js
+++ b/modules/emulator/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/emulator/docs/index.html b/modules/emulator/docs/index.html
index 1856091..8da428b 100644
--- a/modules/emulator/docs/index.html
+++ b/modules/emulator/docs/index.html
@@ -1,107 +1,159 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Gausian Process emulator • PEcAn.emulator</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="Gausian Process emulator">
-<meta property="og:description" content="Implementation of a Gaussian Process model (both likelihood and
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Gausian Process emulator • PEcAn.emulator</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta property="og:title" content="Gausian Process emulator" />
+    <meta
+      property="og:description"
+      content="Implementation of a Gaussian Process model (both likelihood and
     bayesian approaches) for kriging and model emulation.  Includes functions
-    for sampling design and prediction.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    for sampling design and prediction."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    Implementation of a Gaussian Process model (both likelihood and
-    bayesian approaches) for kriging and model emulation.  Includes functions
-    for sampling design and prediction.
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          Implementation of a Gaussian Process model (both likelihood and
+          bayesian approaches) for kriging and model emulation. Includes
+          functions for sampling design and prediction.
+        </div>
 
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/emulator/docs/pkgdown.css b/modules/emulator/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/emulator/docs/pkgdown.css
+++ b/modules/emulator/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/emulator/docs/pkgdown.js b/modules/emulator/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/emulator/docs/pkgdown.js
+++ b/modules/emulator/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/emulator/docs/reference/GaussProcess.html b/modules/emulator/docs/reference/GaussProcess.html
index f14adec..49e197a 100644
--- a/modules/emulator/docs/reference/GaussProcess.html
+++ b/modules/emulator/docs/reference/GaussProcess.html
@@ -2,162 +2,199 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>GaussProcess — GaussProcess • PEcAn.emulator</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="GaussProcess — GaussProcess" />
-
-<meta property="og:description" content="GaussProcess" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>GaussProcess — GaussProcess • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="GaussProcess — GaussProcess" />
+
+    <meta property="og:description" content="GaussProcess" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <span class="icon-bar"></span>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>GaussProcess</h1>
-    
-    <div class="hidden name"><code>GaussProcess.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>GaussProcess</h1>
 
-    <div class="ref-description">
-    
-    <p>GaussProcess</p>
-    
-    </div>
+            <div class="hidden name"><code>GaussProcess.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>GaussProcess</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>GaussProcess</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>isotropic</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>nugget</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"bayes"</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>GaussProcess</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>isotropic</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>nugget</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"bayes"</span>,
   <span class='kw'>ngibbs</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>burnin</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>jump.ic</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1.1</span>, <span class='fl'>0.2</span>),
   <span class='kw'>prior</span> <span class='kw'>=</span> <span class='st'>"IG"</span>, <span class='kw'>mix</span> <span class='kw'>=</span> <span class='st'>"joint"</span>, <span class='kw'>psi</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>zeroMean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>exclude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>nugget</th>
-      <td><p>allows additional error in Y rather than fix interpolation to go through points</p></td>
-    </tr>
-    <tr>
-      <th>prior</th>
-      <td><p>'unif', 'IG'</p></td>
-    </tr>
-    <tr>
-      <th>mix</th>
-      <td><p>joint=mix over psi simultanously, each=mix over psi individually</p></td>
-    </tr>
-    <tr>
-      <th>exclude</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>nugget</th>
+              <td>
+                <p>
+                  allows additional error in Y rather than fix interpolation to
+                  go through points
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prior</th>
+              <td><p>'unif', 'IG'</p></td>
+            </tr>
+            <tr>
+              <th>mix</th>
+              <td>
+                <p>
+                  joint=mix over psi simultanously, each=mix over psi
+                  individually
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>exclude</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/arate.html b/modules/emulator/docs/reference/arate.html
index 91e1f47..7487047 100644
--- a/modules/emulator/docs/reference/arate.html
+++ b/modules/emulator/docs/reference/arate.html
@@ -2,137 +2,158 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
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-
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-
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-<script src="../pkgdown.js"></script>
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>arate — arate • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
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+    <![endif]-->
   </head>
 
   <body>
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>arate</h1>
-    
-    <div class="hidden name"><code>arate.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>arate</h1>
 
-    <div class="ref-description">
-    
-    <p>Acceptance rate</p>
-    
-    </div>
+            <div class="hidden name"><code>arate.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>arate</span>(<span class='no'>x</span>)</pre>
-        
+          <div class="ref-description">
+            <p>Acceptance rate</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>arate</span>(<span class='no'>x</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
-
diff --git a/modules/emulator/docs/reference/bounded.html b/modules/emulator/docs/reference/bounded.html
index a507b4c..b0859f1 100644
--- a/modules/emulator/docs/reference/bounded.html
+++ b/modules/emulator/docs/reference/bounded.html
@@ -2,133 +2,154 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
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-<meta property="og:title" content="bounded — bounded" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>bounded — bounded • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="bounded — bounded" />
+
+    <meta property="og:description" content="bounded" />
+    <meta name="twitter:card" content="summary" />
+
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+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
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-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>bounded</h1>
-    
-    <div class="hidden name"><code>bounded.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>bounded</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>bounded</h1>
 
-    <pre class="usage"><span class='fu'>bounded</span>(<span class='no'>xnew</span>, <span class='no'>rng</span>)</pre>
-        
+            <div class="hidden name"><code>bounded.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>bounded</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>bounded</span>(<span class='no'>xnew</span>, <span class='no'>rng</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/calcSpatialCov.html b/modules/emulator/docs/reference/calcSpatialCov.html
index 1d8bd2e..8016fb4 100644
--- a/modules/emulator/docs/reference/calcSpatialCov.html
+++ b/modules/emulator/docs/reference/calcSpatialCov.html
@@ -2,137 +2,158 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="calcSpatialCov — calcSpatialCov" />
-
-<meta property="og:description" content="calcSpatialCov" />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>calcSpatialCov — calcSpatialCov • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="calcSpatialCov — calcSpatialCov" />
+
+    <meta property="og:description" content="calcSpatialCov" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>calcSpatialCov</h1>
-    
-    <div class="hidden name"><code>calcSpatialCov.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>calcSpatialCov</h1>
 
-    <div class="ref-description">
-    
-    <p>calcSpatialCov</p>
-    
-    </div>
+            <div class="hidden name"><code>calcSpatialCov.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>calcSpatialCov</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-        
+          <div class="ref-description">
+            <p>calcSpatialCov</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>calcSpatialCov</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/emulator/docs/reference/calcSpatialCov.list.html b/modules/emulator/docs/reference/calcSpatialCov.list.html
index 368753d..9891493 100644
--- a/modules/emulator/docs/reference/calcSpatialCov.list.html
+++ b/modules/emulator/docs/reference/calcSpatialCov.list.html
@@ -2,162 +2,195 @@
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+
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+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
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+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>calcSpatialCov.list</h1>
-    
-    <div class="hidden name"><code>calcSpatialCov.list.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>calcSpatialCov.list</h1>
 
-    <div class="ref-description">
-    
-    <p>Currently assumes an exponential spatial dependency</p>
-    
-    </div>
+            <div class="hidden name"><code>calcSpatialCov.list.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Currently assumes an exponential spatial dependency</p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for list</span>
+          <pre class="usage"><span class='co'># S3 method for list</span>
 <span class='fu'><a href='calcSpatialCov.html'>calcSpatialCov</a></span>(<span class='no'>d</span>, <span class='no'>psi</span>, <span class='no'>tau</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>d</th>
-      <td><p>list of component spatial distance matrices</p></td>
-    </tr>
-    <tr>
-      <th>psi</th>
-      <td><p>spatial corr</p></td>
-    </tr>
-    <tr>
-      <th>tau</th>
-      <td><p>spatial var</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>can make gaussian by passing squared distance matrix</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>d</th>
+              <td><p>list of component spatial distance matrices</p></td>
+            </tr>
+            <tr>
+              <th>psi</th>
+              <td><p>spatial corr</p></td>
+            </tr>
+            <tr>
+              <th>tau</th>
+              <td><p>spatial var</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>can make gaussian by passing squared distance matrix</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
-
diff --git a/modules/emulator/docs/reference/calcSpatialCov.matrix.html b/modules/emulator/docs/reference/calcSpatialCov.matrix.html
index 439b433..dd775da 100644
--- a/modules/emulator/docs/reference/calcSpatialCov.matrix.html
+++ b/modules/emulator/docs/reference/calcSpatialCov.matrix.html
@@ -2,162 +2,197 @@
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+
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+    />
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+      content="Currently assumes an exponential spatial dependency"
+    />
+    <meta name="twitter:card" content="summary" />
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>calcSpatialCov.matrix</h1>
-    
-    <div class="hidden name"><code>calcSpatialCov.matrix.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>calcSpatialCov.matrix</h1>
 
-    <div class="ref-description">
-    
-    <p>Currently assumes an exponential spatial dependency</p>
-    
-    </div>
+            <div class="hidden name"><code>calcSpatialCov.matrix.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Currently assumes an exponential spatial dependency</p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for matrix</span>
+          <pre class="usage"><span class='co'># S3 method for matrix</span>
 <span class='fu'><a href='calcSpatialCov.html'>calcSpatialCov</a></span>(<span class='no'>d</span>, <span class='no'>psi</span>, <span class='no'>tau</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>d</th>
-      <td><p>spatial distance matrix</p></td>
-    </tr>
-    <tr>
-      <th>psi</th>
-      <td><p>spatial corr</p></td>
-    </tr>
-    <tr>
-      <th>tau</th>
-      <td><p>spatial var</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>can make gaussian by passing squared distance matrix</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>d</th>
+              <td><p>spatial distance matrix</p></td>
+            </tr>
+            <tr>
+              <th>psi</th>
+              <td><p>spatial corr</p></td>
+            </tr>
+            <tr>
+              <th>tau</th>
+              <td><p>spatial var</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>can make gaussian by passing squared distance matrix</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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   </body>
 </html>
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diff --git a/modules/emulator/docs/reference/calculate.prior.html b/modules/emulator/docs/reference/calculate.prior.html
index daf8638..ba80049 100644
--- a/modules/emulator/docs/reference/calculate.prior.html
+++ b/modules/emulator/docs/reference/calculate.prior.html
@@ -2,133 +2,154 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>calculate.prior</h1>
-    
-    <div class="hidden name"><code>calculate.prior.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>calculate.prior</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>calculate.prior</h1>
 
-    <pre class="usage"><span class='fu'>calculate.prior</span>(<span class='no'>samples</span>, <span class='no'>priors</span>)</pre>
-        
+            <div class="hidden name"><code>calculate.prior.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>calculate.prior</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>calculate.prior</span>(<span class='no'>samples</span>, <span class='no'>priors</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/ddist.html b/modules/emulator/docs/reference/ddist.html
index 00ab53d..6b1e2c9 100644
--- a/modules/emulator/docs/reference/ddist.html
+++ b/modules/emulator/docs/reference/ddist.html
@@ -2,133 +2,154 @@
 <!DOCTYPE html>
 <html>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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   </head>
 
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+                <span
+                  class="label label-default"
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+                  >1.6.0</span
+                >
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
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+                <li>
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+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>ddist</h1>
-    
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-    </div>
-
-    <div class="ref-description">
-    
-    <p>ddist</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>ddist</h1>
 
-    <pre class="usage"><span class='fu'>ddist</span>(<span class='no'>x</span>, <span class='no'>prior</span>)</pre>
-        
+            <div class="hidden name"><code>ddist.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>ddist</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>ddist</span>(<span class='no'>x</span>, <span class='no'>prior</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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+        </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/distance.html b/modules/emulator/docs/reference/distance.html
index 29cf64e..f78b1c4 100644
--- a/modules/emulator/docs/reference/distance.html
+++ b/modules/emulator/docs/reference/distance.html
@@ -2,153 +2,182 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
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-<!-- sticky kit -->
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-
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-<script src="../pkgdown.js"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>distance — distance • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="distance — distance" />
+
+    <meta property="og:description" content="distance" />
+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
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+              </button>
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+                <span
+                  class="label label-default"
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+                  >1.6.0</span
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>distance</h1>
-    
-    <div class="hidden name"><code>distance.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>distance</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>distance</span>(<span class='no'>x</span>, <span class='kw'>power</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>power</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dst</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>distance</h1>
+
+            <div class="hidden name"><code>distance.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>distance</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>distance</span>(<span class='no'>x</span>, <span class='kw'>power</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>power</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>dst</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/distance.martix.html b/modules/emulator/docs/reference/distance.martix.html
index 7b6cf1e..37edc40 100644
--- a/modules/emulator/docs/reference/distance.martix.html
+++ b/modules/emulator/docs/reference/distance.martix.html
@@ -2,153 +2,182 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>distance.matrix — distance.martix • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>distance.matrix</h1>
-    
-    <div class="hidden name"><code>distance.martix.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>distance.matrix</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>distance.matrix</span>(<span class='no'>x</span>, <span class='kw'>power</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>dim</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dim</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>d</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>distance.matrix</h1>
+
+            <div class="hidden name"><code>distance.martix.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>distance.matrix</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>distance.matrix</span>(<span class='no'>x</span>, <span class='kw'>power</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>dim</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dim</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>d</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
+        </div>
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diff --git a/modules/emulator/docs/reference/distance12.martix.html b/modules/emulator/docs/reference/distance12.martix.html
index 6105ccf..fe26137 100644
--- a/modules/emulator/docs/reference/distance12.martix.html
+++ b/modules/emulator/docs/reference/distance12.martix.html
@@ -2,153 +2,182 @@
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+
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>distance12.matrix</h1>
-    
-    <div class="hidden name"><code>distance12.martix.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>distance12.matrix</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>distance12.matrix</span>(<span class='no'>x</span>, <span class='no'>n1</span>, <span class='kw'>power</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>power</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>d</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>distance12.matrix</h1>
+
+            <div class="hidden name"><code>distance12.martix.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>distance12.matrix</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>distance12.matrix</span>(<span class='no'>x</span>, <span class='no'>n1</span>, <span class='kw'>power</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>power</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>d</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/emulator-package.html b/modules/emulator/docs/reference/emulator-package.html
index 86515d9..dcf2cda 100644
--- a/modules/emulator/docs/reference/emulator-package.html
+++ b/modules/emulator/docs/reference/emulator-package.html
@@ -2,169 +2,224 @@
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-
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+    />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Gausian Process emulator</h1>
-    
-    <div class="hidden name"><code>emulator-package.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Implementation of a Gaussian Process model (both likelihood and bayesian approaches) for kriging and model emulation.  Includes functions for sampling design and prediction.</p>
-    
-    </div>
-
-        
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <table class='table'>
-<tr><td>Package:</td><td>emulator</td></tr>
-<tr><td>Type:</td><td>Package</td></tr>
-<tr><td>Version:</td><td>1.0</td></tr>
-<tr><td>Date:</td><td>2007-10-11</td></tr>
-<tr><td>License:</td><td>GPL</td></tr>
-<tr><td></td><td>Package:</td></tr>
-</table>
-<p>~~ An overview of how to use the package, including the most important ~~
-~~ functions ~~</p>
-    
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
-    
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'></div>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#references">References</a></li>
-
-      <li><a href="#see-also">See also</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-Maintainer: Michael Dietze &lt;mdietze@fas.harvard.edu&gt;
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Gausian Process emulator</h1>
+
+            <div class="hidden name"><code>emulator-package.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Implementation of a Gaussian Process model (both likelihood and
+              bayesian approaches) for kriging and model emulation. Includes
+              functions for sampling design and prediction.
+            </p>
+          </div>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <table class="table">
+            <tr>
+              <td>Package:</td>
+              <td>emulator</td>
+            </tr>
+            <tr>
+              <td>Type:</td>
+              <td>Package</td>
+            </tr>
+            <tr>
+              <td>Version:</td>
+              <td>1.0</td>
+            </tr>
+            <tr>
+              <td>Date:</td>
+              <td>2007-10-11</td>
+            </tr>
+            <tr>
+              <td>License:</td>
+              <td>GPL</td>
+            </tr>
+            <tr>
+              <td></td>
+              <td>Package:</td>
+            </tr>
+          </table>
+
+          <p>
+            ~~ An overview of how to use the package, including the most
+            important ~~ ~~ functions ~~
+          </p>
+
+          <h2 class="hasAnchor" id="references">
+            <a class="anchor" href="#references"></a>References
+          </h2>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index"></div>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"></pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#references">References</a></li>
+
+            <li><a href="#see-also">See also</a></li>
+
+            <li><a href="#examples">Examples</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze Maintainer: Michael Dietze
+          &lt;mdietze@fas.harvard.edu&gt;
+        </div>
+      </div>
 
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diff --git a/modules/emulator/docs/reference/get_ss.html b/modules/emulator/docs/reference/get_ss.html
index 6c27953..aa668eb 100644
--- a/modules/emulator/docs/reference/get_ss.html
+++ b/modules/emulator/docs/reference/get_ss.html
@@ -2,133 +2,154 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
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+      crossorigin="anonymous"
+    />
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+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get_ss</h1>
-    
-    <div class="hidden name"><code>get_ss.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>get_ss</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get_ss</h1>
 
-    <pre class="usage"><span class='fu'>get_ss</span>(<span class='no'>gp</span>, <span class='no'>xnew</span>, <span class='no'>pos.check</span>)</pre>
-        
+            <div class="hidden name"><code>get_ss.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>get_ss</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>get_ss</span>(<span class='no'>gp</span>, <span class='no'>xnew</span>, <span class='no'>pos.check</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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+    </div>
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 </html>
-
diff --git a/modules/emulator/docs/reference/get_y.html b/modules/emulator/docs/reference/get_y.html
index 39bdbd4..ce343d1 100644
--- a/modules/emulator/docs/reference/get_y.html
+++ b/modules/emulator/docs/reference/get_y.html
@@ -2,133 +2,154 @@
 <!DOCTYPE html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>get_y</h1>
-    
-    <div class="hidden name"><code>get_y.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>get_y</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>get_y</h1>
 
-    <pre class="usage"><span class='fu'>get_y</span>(<span class='no'>SSnew</span>, <span class='no'>xnew</span>, <span class='no'>llik.fn</span>, <span class='no'>priors</span>, <span class='no'>llik.par</span>)</pre>
-        
+            <div class="hidden name"><code>get_y.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>get_y</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>get_y</span>(<span class='no'>SSnew</span>, <span class='no'>xnew</span>, <span class='no'>llik.fn</span>, <span class='no'>priors</span>, <span class='no'>llik.par</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/emulator/docs/reference/gp_mle.html b/modules/emulator/docs/reference/gp_mle.html
index ffb8f3b..70d42d9 100644
--- a/modules/emulator/docs/reference/gp_mle.html
+++ b/modules/emulator/docs/reference/gp_mle.html
@@ -2,153 +2,182 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>gp_mle — gp_mle • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <![endif]-->
   </head>
 
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+            <div class="navbar-header">
+              <button
+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>gp_mle</h1>
-    
-    <div class="hidden name"><code>gp_mle.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>gp_mle</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>gp_mle</span>(<span class='no'>theta</span>, <span class='no'>d</span>, <span class='no'>nugget</span>, <span class='no'>myY</span>, <span class='kw'>maxval</span> <span class='kw'>=</span> <span class='fl'>Inf</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>maxval</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>val</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>gp_mle</h1>
+
+            <div class="hidden name"><code>gp_mle.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>gp_mle</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>gp_mle</span>(<span class='no'>theta</span>, <span class='no'>d</span>, <span class='no'>nugget</span>, <span class='no'>myY</span>, <span class='kw'>maxval</span> <span class='kw'>=</span> <span class='fl'>Inf</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>maxval</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>val</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/gp_mle2.html b/modules/emulator/docs/reference/gp_mle2.html
index f0571a1..af0a978 100644
--- a/modules/emulator/docs/reference/gp_mle2.html
+++ b/modules/emulator/docs/reference/gp_mle2.html
@@ -2,133 +2,154 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>gp_mle2</h1>
-    
-    <div class="hidden name"><code>gp_mle2.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>zero mean version</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>gp_mle2</h1>
 
-    <pre class="usage"><span class='fu'>gp_mle2</span>(<span class='no'>theta</span>, <span class='no'>d</span>, <span class='no'>nugget</span>, <span class='no'>myY</span>, <span class='kw'>maxval</span> <span class='kw'>=</span> <span class='fl'>Inf</span>)</pre>
-        
+            <div class="hidden name"><code>gp_mle2.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>zero mean version</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>gp_mle2</span>(<span class='no'>theta</span>, <span class='no'>d</span>, <span class='no'>nugget</span>, <span class='no'>myY</span>, <span class='kw'>maxval</span> <span class='kw'>=</span> <span class='fl'>Inf</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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diff --git a/modules/emulator/docs/reference/gpeval.html b/modules/emulator/docs/reference/gpeval.html
index 421c331..118c8ac 100644
--- a/modules/emulator/docs/reference/gpeval.html
+++ b/modules/emulator/docs/reference/gpeval.html
@@ -2,151 +2,184 @@
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 <html>
   <head>
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+
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>gpeval</h1>
-    
-    <div class="hidden name"><code>gpeval.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculates the probability of a set of parameter values, given by xnew</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>gpeval</span>(<span class='no'>xnew</span>, <span class='no'>k</span>, <span class='no'>mu</span>, <span class='no'>tau</span>, <span class='no'>psi</span>, <span class='no'>x</span>, <span class='no'>rng</span>, <span class='no'>splinefcns</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>rng</th>
-      <td><p>range</p></td>
-    </tr>
-    <tr>
-      <th>splinefcns</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>gpeval</h1>
+
+            <div class="hidden name"><code>gpeval.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Calculates the probability of a set of parameter values, given by
+              xnew
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>gpeval</span>(<span class='no'>xnew</span>, <span class='no'>k</span>, <span class='no'>mu</span>, <span class='no'>tau</span>, <span class='no'>psi</span>, <span class='no'>x</span>, <span class='no'>rng</span>, <span class='no'>splinefcns</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>rng</th>
+              <td><p>range</p></td>
+            </tr>
+            <tr>
+              <th>splinefcns</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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-  
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+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/groupid.html b/modules/emulator/docs/reference/groupid.html
index 3bc6359..2493453 100644
--- a/modules/emulator/docs/reference/groupid.html
+++ b/modules/emulator/docs/reference/groupid.html
@@ -2,137 +2,158 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>groupid — groupid • PEcAn.emulator</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="groupid — groupid" />
-
-<meta property="og:description" content="groupid" />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>groupid — groupid • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="groupid — groupid" />
+
+    <meta property="og:description" content="groupid" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
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-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>groupid</h1>
-    
-    <div class="hidden name"><code>groupid.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>groupid</h1>
 
-    <div class="ref-description">
-    
-    <p>groupid</p>
-    
-    </div>
+            <div class="hidden name"><code>groupid.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>groupid</span>(<span class='no'>x</span>)</pre>
-        
+          <div class="ref-description">
+            <p>groupid</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>groupid</span>(<span class='no'>x</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/index.html b/modules/emulator/docs/reference/index.html
index 0edbc0b..46abbab 100644
--- a/modules/emulator/docs/reference/index.html
+++ b/modules/emulator/docs/reference/index.html
@@ -2,354 +2,507 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-<title>Function reference • PEcAn.emulator</title>
+    <title>Function reference • PEcAn.emulator</title>
 
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
 
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
 
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
 
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
 
+    <meta property="og:title" content="Function reference" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
-<meta property="og:title" content="Function reference" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
 
-      
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="GaussProcess.html">GaussProcess()</a></code> </p>
-        </td>
-        <td><p>GaussProcess</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="arate.html">arate()</a></code> </p>
-        </td>
-        <td><p>arate</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="bounded.html">bounded()</a></code> </p>
-        </td>
-        <td><p>bounded</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="calcSpatialCov.html">calcSpatialCov()</a></code> </p>
-        </td>
-        <td><p>calcSpatialCov</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="calcSpatialCov.list.html">calcSpatialCov(<i>&lt;list&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>calcSpatialCov.list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="calcSpatialCov.matrix.html">calcSpatialCov(<i>&lt;matrix&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>calcSpatialCov.matrix</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="calculate.prior.html">calculate.prior()</a></code> </p>
-        </td>
-        <td><p>calculate.prior</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ddist.html">ddist()</a></code> </p>
-        </td>
-        <td><p>ddist</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="distance.html">distance()</a></code> </p>
-        </td>
-        <td><p>distance</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="distance.martix.html">distance.matrix()</a></code> </p>
-        </td>
-        <td><p>distance.matrix</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="distance12.martix.html">distance12.matrix()</a></code> </p>
-        </td>
-        <td><p>distance12.matrix</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="emulator-package.html">emulator-package</a></code> </p>
-        </td>
-        <td><p>Gausian Process emulator</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_ss.html">get_ss()</a></code> </p>
-        </td>
-        <td><p>get_ss</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get_y.html">get_y()</a></code> </p>
-        </td>
-        <td><p>get_y</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="gp_mle.html">gp_mle()</a></code> </p>
-        </td>
-        <td><p>gp_mle</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="gp_mle2.html">gp_mle2()</a></code> </p>
-        </td>
-        <td><p>gp_mle2</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="gpeval.html">gpeval()</a></code> </p>
-        </td>
-        <td><p>gpeval</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="groupid.html">groupid()</a></code> </p>
-        </td>
-        <td><p>groupid</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="is.accepted.html">is.accepted()</a></code> </p>
-        </td>
-        <td><p>is.accepted</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="jump.html">jump()</a></code> </p>
-        </td>
-        <td><p>jump</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ldinvgamma.html">ldinvgamma()</a></code> </p>
-        </td>
-        <td><p>ldinvgamma</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="lhc.html">lhc()</a></code> </p>
-        </td>
-        <td><p>lhc</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="mcmc.GP.html">mcmc.GP()</a></code> </p>
-        </td>
-        <td><p>mcmc.GP</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="minimize.GP.html">minimize.GP()</a></code> </p>
-        </td>
-        <td><p>minimize.GP</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="mvjump.html">mvjump()</a></code> </p>
-        </td>
-        <td><p>mvjump</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="nderiv.html">nderiv()</a></code> </p>
-        </td>
-        <td><p>nderiv</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="p.html">p()</a></code> </p>
-        </td>
-        <td><p>p</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="p.jump.html">p(<i>&lt;jump&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>p.jump</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="p.mvjump.html">p(<i>&lt;mvjump&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>p.mvjump</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot.jump.html">plot(<i>&lt;jump&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>plot.jump</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot.mvjump.html">plot(<i>&lt;mvjump&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>plot.mvjump</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="predict.GP.html">predict(<i>&lt;GP&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>predict.GP</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="predict.density.html">predict(<i>&lt;density&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>predict.density</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="summarize.GP.html">summarize.GP()</a></code> </p>
-        </td>
-        <td><p>summarize.GP</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="update.jump.html">update(<i>&lt;jump&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>update.jump</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="update.mvjump.html">update(<i>&lt;mvjump&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>update.mvjump</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="GaussProcess.html">GaussProcess()</a></code>
+                  </p>
+                </td>
+                <td><p>GaussProcess</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="arate.html">arate()</a></code>
+                  </p>
+                </td>
+                <td><p>arate</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="bounded.html">bounded()</a></code>
+                  </p>
+                </td>
+                <td><p>bounded</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="calcSpatialCov.html">calcSpatialCov()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>calcSpatialCov</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="calcSpatialCov.list.html"
+                        >calcSpatialCov(<i>&lt;list&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>calcSpatialCov.list</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="calcSpatialCov.matrix.html"
+                        >calcSpatialCov(<i>&lt;matrix&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>calcSpatialCov.matrix</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="calculate.prior.html"
+                        >calculate.prior()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>calculate.prior</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ddist.html">ddist()</a></code>
+                  </p>
+                </td>
+                <td><p>ddist</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="distance.html">distance()</a></code>
+                  </p>
+                </td>
+                <td><p>distance</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="distance.martix.html"
+                        >distance.matrix()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>distance.matrix</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="distance12.martix.html"
+                        >distance12.matrix()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>distance12.matrix</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="emulator-package.html"
+                        >emulator-package</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Gausian Process emulator</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get_ss.html">get_ss()</a></code>
+                  </p>
+                </td>
+                <td><p>get_ss</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get_y.html">get_y()</a></code>
+                  </p>
+                </td>
+                <td><p>get_y</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="gp_mle.html">gp_mle()</a></code>
+                  </p>
+                </td>
+                <td><p>gp_mle</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="gp_mle2.html">gp_mle2()</a></code>
+                  </p>
+                </td>
+                <td><p>gp_mle2</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="gpeval.html">gpeval()</a></code>
+                  </p>
+                </td>
+                <td><p>gpeval</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="groupid.html">groupid()</a></code>
+                  </p>
+                </td>
+                <td><p>groupid</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="is.accepted.html">is.accepted()</a></code>
+                  </p>
+                </td>
+                <td><p>is.accepted</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="jump.html">jump()</a></code>
+                  </p>
+                </td>
+                <td><p>jump</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ldinvgamma.html">ldinvgamma()</a></code>
+                  </p>
+                </td>
+                <td><p>ldinvgamma</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="lhc.html">lhc()</a></code>
+                  </p>
+                </td>
+                <td><p>lhc</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="mcmc.GP.html">mcmc.GP()</a></code>
+                  </p>
+                </td>
+                <td><p>mcmc.GP</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="minimize.GP.html">minimize.GP()</a></code>
+                  </p>
+                </td>
+                <td><p>minimize.GP</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="mvjump.html">mvjump()</a></code>
+                  </p>
+                </td>
+                <td><p>mvjump</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="nderiv.html">nderiv()</a></code>
+                  </p>
+                </td>
+                <td><p>nderiv</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="p.html">p()</a></code>
+                  </p>
+                </td>
+                <td><p>p</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="p.jump.html">p(<i>&lt;jump&gt;</i>)</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>p.jump</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="p.mvjump.html"
+                        >p(<i>&lt;mvjump&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>p.mvjump</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot.jump.html"
+                        >plot(<i>&lt;jump&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>plot.jump</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot.mvjump.html"
+                        >plot(<i>&lt;mvjump&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>plot.mvjump</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="predict.GP.html"
+                        >predict(<i>&lt;GP&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>predict.GP</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="predict.density.html"
+                        >predict(<i>&lt;density&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>predict.density</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="summarize.GP.html">summarize.GP()</a></code>
+                  </p>
+                </td>
+                <td><p>summarize.GP</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="update.jump.html"
+                        >update(<i>&lt;jump&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>update.jump</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="update.mvjump.html"
+                        >update(<i>&lt;mvjump&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>update.mvjump</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/is.accepted.html b/modules/emulator/docs/reference/is.accepted.html
index 4a783e8..48c2484 100644
--- a/modules/emulator/docs/reference/is.accepted.html
+++ b/modules/emulator/docs/reference/is.accepted.html
@@ -2,133 +2,154 @@
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-      
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-        
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-      
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>is.accepted</h1>
-    
-    <div class="hidden name"><code>is.accepted.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>is.accepted</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>is.accepted</h1>
 
-    <pre class="usage"><span class='fu'>is.accepted</span>(<span class='no'>ycurr</span>, <span class='no'>ynew</span>, <span class='kw'>format</span> <span class='kw'>=</span> <span class='st'>"lin"</span>)</pre>
-        
+            <div class="hidden name"><code>is.accepted.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>is.accepted</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>is.accepted</span>(<span class='no'>ycurr</span>, <span class='no'>ynew</span>, <span class='kw'>format</span> <span class='kw'>=</span> <span class='st'>"lin"</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/jump.html b/modules/emulator/docs/reference/jump.html
index e7dc983..1915a94 100644
--- a/modules/emulator/docs/reference/jump.html
+++ b/modules/emulator/docs/reference/jump.html
@@ -2,151 +2,179 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-
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-<script src="../pkgdown.js"></script>
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-setClass jump" />
-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>jump — jump • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="jump — jump" />
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+      property="og:description"
+      content="jump
+setClass jump"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
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+                type="button"
+                class="navbar-toggle collapsed"
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+
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>jump</h1>
-    
-    <div class="hidden name"><code>jump.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>jump</p>
-<p>setClass jump</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>jump</span>(<span class='kw'>ic</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>rate</span> <span class='kw'>=</span> <span class='fl'>0.4</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>rate</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-Michael Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>jump</h1>
+
+            <div class="hidden name"><code>jump.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>jump</p>
+            <p>setClass jump</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>jump</span>(<span class='kw'>ic</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>rate</span> <span class='kw'>=</span> <span class='fl'>0.4</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>rate</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/modules/emulator/docs/reference/ldinvgamma.html b/modules/emulator/docs/reference/ldinvgamma.html
index 5449f91..596307d 100644
--- a/modules/emulator/docs/reference/ldinvgamma.html
+++ b/modules/emulator/docs/reference/ldinvgamma.html
@@ -2,153 +2,185 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<![endif]-->
-
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="ldinvgamma — ldinvgamma" />
+
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+      content="Log-dinvgamma, based on MCMCpack"
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+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>ldinvgamma</h1>
-    
-    <div class="hidden name"><code>ldinvgamma.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Log-dinvgamma, based on MCMCpack</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>ldinvgamma</span>(<span class='no'>x</span>, <span class='no'>shape</span>, <span class='kw'>scale</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>scale</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>log.density</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>ldinvgamma</h1>
+
+            <div class="hidden name"><code>ldinvgamma.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Log-dinvgamma, based on MCMCpack</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>ldinvgamma</span>(<span class='no'>x</span>, <span class='no'>shape</span>, <span class='kw'>scale</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>scale</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>log.density</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/lhc.html b/modules/emulator/docs/reference/lhc.html
index 3828637..022c8d9 100644
--- a/modules/emulator/docs/reference/lhc.html
+++ b/modules/emulator/docs/reference/lhc.html
@@ -2,157 +2,186 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- clipboard.js -->
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-
-<!-- sticky kit -->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="lhc — lhc" />
+
+    <meta property="og:description" content="Latin Hyper Cube" />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
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-  <a href="../reference/index.html">Reference</a>
-</li>
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-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>lhc</h1>
-    
-    <div class="hidden name"><code>lhc.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Latin Hyper Cube</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>lhc</span>(<span class='no'>x</span>, <span class='no'>n.samp</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>&lt;- list (n.dim x 2)</p></td>
-    </tr>
-    <tr>
-      <th>n.samp</th>
-      <td><p>number of samples</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Simple uniform sampling with LHC permutation</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>lhc</h1>
+
+            <div class="hidden name"><code>lhc.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Latin Hyper Cube</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>lhc</span>(<span class='no'>x</span>, <span class='no'>n.samp</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>&lt;- list (n.dim x 2)</p></td>
+            </tr>
+            <tr>
+              <th>n.samp</th>
+              <td><p>number of samples</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Simple uniform sampling with LHC permutation</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/mcmc.GP.html b/modules/emulator/docs/reference/mcmc.GP.html
index e3c79d8..3a086d0 100644
--- a/modules/emulator/docs/reference/mcmc.GP.html
+++ b/modules/emulator/docs/reference/mcmc.GP.html
@@ -2,166 +2,201 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<script src="../pkgdown.js"></script>
-
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-
-<meta property="og:title" content="mcmc.GP — mcmc.GP" />
-
-<meta property="og:description" content="Function to sample from a GP model
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>mcmc.GP — mcmc.GP • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="mcmc.GP — mcmc.GP" />
+
+    <meta
+      property="og:description"
+      content="Function to sample from a GP model
 that is assumed to be a -lnLikelihood surface
-with flat priors and bounded region" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
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+with flat priors and bounded region"
+    />
+    <meta name="twitter:card" content="summary" />
 
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>mcmc.GP</h1>
-    
-    <div class="hidden name"><code>mcmc.GP.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>mcmc.GP</h1>
 
-    <div class="ref-description">
-    
-    <p>Function to sample from a GP model
-that is assumed to be a -lnLikelihood surface
-with flat priors and bounded region</p>
-    
-    </div>
+            <div class="hidden name"><code>mcmc.GP.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function to sample from a GP model that is assumed to be a
+              -lnLikelihood surface with flat priors and bounded region
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>mcmc.GP</span>(<span class='no'>gp</span>, <span class='no'>x0</span>, <span class='no'>nmcmc</span>, <span class='no'>rng</span>, <span class='kw'>format</span> <span class='kw'>=</span> <span class='st'>"lin"</span>, <span class='kw'>mix</span> <span class='kw'>=</span> <span class='st'>"joint"</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>mcmc.GP</span>(<span class='no'>gp</span>, <span class='no'>x0</span>, <span class='no'>nmcmc</span>, <span class='no'>rng</span>, <span class='kw'>format</span> <span class='kw'>=</span> <span class='st'>"lin"</span>, <span class='kw'>mix</span> <span class='kw'>=</span> <span class='st'>"joint"</span>,
   <span class='kw'>splinefcns</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>jmp0</span> <span class='kw'>=</span> <span class='fl'>0.35</span> * (<span class='no'>rng</span>[, <span class='fl'>2</span>] - <span class='no'>rng</span>[, <span class='fl'>1</span>]),
   <span class='kw'>ar.target</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>priors</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='no'>settings</span>, <span class='kw'>run.block</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>n.of.obs</span>,
   <span class='no'>llik.fn</span>, <span class='no'>hyper.pars</span>, <span class='kw'>resume.list</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x0</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>format</th>
-      <td><p>lin = lnlike fcn, log = log(lnlike)</p></td>
-    </tr>
-    <tr>
-      <th>mix</th>
-      <td><p>each = jump each dim. independently, joint = jump all at once</p></td>
-    </tr>
-    <tr>
-      <th>priors</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x0</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>format</th>
+              <td><p>lin = lnlike fcn, log = log(lnlike)</p></td>
+            </tr>
+            <tr>
+              <th>mix</th>
+              <td>
+                <p>
+                  each = jump each dim. independently, joint = jump all at once
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>priors</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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 </html>
-
diff --git a/modules/emulator/docs/reference/minimize.GP.html b/modules/emulator/docs/reference/minimize.GP.html
index 4f79da3..cd241e0 100644
--- a/modules/emulator/docs/reference/minimize.GP.html
+++ b/modules/emulator/docs/reference/minimize.GP.html
@@ -2,151 +2,178 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+    <title>minimize.GP — minimize.GP • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+    />
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+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>minimize.GP</h1>
-    
-    <div class="hidden name"><code>minimize.GP.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>minimize.GP</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>minimize.GP</span>(<span class='no'>gp</span>, <span class='no'>rng</span>, <span class='no'>x0</span>, <span class='kw'>splinefuns</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x0</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>splinefuns</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>minimize.GP</h1>
+
+            <div class="hidden name"><code>minimize.GP.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>minimize.GP</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>minimize.GP</span>(<span class='no'>gp</span>, <span class='no'>rng</span>, <span class='no'>x0</span>, <span class='kw'>splinefuns</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x0</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>splinefuns</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/mvjump.html b/modules/emulator/docs/reference/mvjump.html
index a31707e..73ccd06 100644
--- a/modules/emulator/docs/reference/mvjump.html
+++ b/modules/emulator/docs/reference/mvjump.html
@@ -2,133 +2,154 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>mvjump — mvjump • PEcAn.emulator</title>
-
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-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<![endif]-->
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>mvjump — mvjump • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="mvjump — mvjump" />
+
+    <meta property="og:description" content="multivariate version" />
+    <meta name="twitter:card" content="summary" />
+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-  <a href="../index.html">
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-      <ul class="nav navbar-nav navbar-right">
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>mvjump</h1>
-    
-    <div class="hidden name"><code>mvjump.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>multivariate version</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>mvjump</h1>
 
-    <pre class="usage"><span class='fu'>mvjump</span>(<span class='kw'>ic</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>rate</span> <span class='kw'>=</span> <span class='fl'>0.4</span>, <span class='kw'>nc</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>mvjump.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>multivariate version</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>mvjump</span>(<span class='kw'>ic</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>rate</span> <span class='kw'>=</span> <span class='fl'>0.4</span>, <span class='kw'>nc</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/nderiv.html b/modules/emulator/docs/reference/nderiv.html
index 83259d2..8854567 100644
--- a/modules/emulator/docs/reference/nderiv.html
+++ b/modules/emulator/docs/reference/nderiv.html
@@ -2,143 +2,166 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="nderiv — nderiv" />
-
-<meta property="og:description" content="nderiv" />
-<meta name="twitter:card" content="summary" />
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-<!-- mathjax -->
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>nderiv — nderiv • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="nderiv — nderiv" />
+
+    <meta property="og:description" content="nderiv" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
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-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>nderiv</h1>
-    
-    <div class="hidden name"><code>nderiv.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>nderiv</h1>
 
-    <div class="ref-description">
-    
-    <p>nderiv</p>
-    
-    </div>
+            <div class="hidden name"><code>nderiv.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>nderiv</span>(<span class='no'>x</span>, <span class='no'>y</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <div class="ref-description">
+            <p>nderiv</p>
+          </div>
 
-    <p>der</p>
-    
+          <pre
+            class="usage"
+          ><span class='fu'>nderiv</span>(<span class='no'>x</span>, <span class='no'>y</span>)</pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>der</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/p.html b/modules/emulator/docs/reference/p.html
index 4432611..bcfbd13 100644
--- a/modules/emulator/docs/reference/p.html
+++ b/modules/emulator/docs/reference/p.html
@@ -2,133 +2,154 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>p — p • PEcAn.emulator</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-<!-- clipboard.js -->
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
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+    <link href="../pkgdown.css" rel="stylesheet" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="../reference/index.html">Reference</a>
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-      
-      <ul class="nav navbar-nav navbar-right">
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>p</h1>
-    
-    <div class="hidden name"><code>p.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>p</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>p</h1>
 
-    <pre class="usage"><span class='fu'>p</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>p.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>p</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>p</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/p.jump.html b/modules/emulator/docs/reference/p.jump.html
index 68468ab..9cfc11d 100644
--- a/modules/emulator/docs/reference/p.jump.html
+++ b/modules/emulator/docs/reference/p.jump.html
@@ -2,148 +2,173 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>p.jump — p.jump • PEcAn.emulator</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="p.jump — p.jump" />
-
-<meta property="og:description" content="p.jump" />
-<meta name="twitter:card" content="summary" />
-
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>p.jump — p.jump • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="p.jump — p.jump" />
+
+    <meta property="og:description" content="p.jump" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>p.jump</h1>
-    
-    <div class="hidden name"><code>p.jump.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>p.jump</h1>
 
-    <div class="ref-description">
-    
-    <p>p.jump</p>
-    
-    </div>
+            <div class="hidden name"><code>p.jump.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for jump</span>
-<span class='fu'><a href='p.html'>p</a></span>(<span class='no'>jmp</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>jmp</th>
-      <td><p>jump parameter</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>p.jump</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for jump</span>
+<span class='fu'><a href='p.html'>p</a></span>(<span class='no'>jmp</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>jmp</th>
+              <td><p>jump parameter</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/p.mvjump.html b/modules/emulator/docs/reference/p.mvjump.html
index 2cbcb6b..f494899 100644
--- a/modules/emulator/docs/reference/p.mvjump.html
+++ b/modules/emulator/docs/reference/p.mvjump.html
@@ -2,144 +2,169 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>p.mvjump — p.mvjump • PEcAn.emulator</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
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+                <span class="icon-bar"></span>
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>p.mvjump</h1>
-    
-    <div class="hidden name"><code>p.mvjump.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>p.mvjump</h1>
 
-    <div class="ref-description">
-    
-    <p>p.mvjump</p>
-    
-    </div>
+            <div class="hidden name"><code>p.mvjump.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for mvjump</span>
-<span class='fu'><a href='p.html'>p</a></span>(<span class='no'>jmp</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>jmp</th>
-      <td><p>jump parameter</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>p.mvjump</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for mvjump</span>
+<span class='fu'><a href='p.html'>p</a></span>(<span class='no'>jmp</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>jmp</th>
+              <td><p>jump parameter</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/plot.jump.html b/modules/emulator/docs/reference/plot.jump.html
index ed78d2c..e6dbb91 100644
--- a/modules/emulator/docs/reference/plot.jump.html
+++ b/modules/emulator/docs/reference/plot.jump.html
@@ -2,148 +2,173 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>plot.jump — plot.jump • PEcAn.emulator</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="plot.jump — plot.jump" />
-
-<meta property="og:description" content="plot.jump" />
-<meta name="twitter:card" content="summary" />
-
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-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>plot.jump — plot.jump • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="plot.jump — plot.jump" />
+
+    <meta property="og:description" content="plot.jump" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <span class="icon-bar"></span>
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
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-  <a href="../index.html">
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-  <a href="../reference/index.html">Reference</a>
-</li>
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-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>plot.jump</h1>
-    
-    <div class="hidden name"><code>plot.jump.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>plot.jump</h1>
 
-    <div class="ref-description">
-    
-    <p>plot.jump</p>
-    
-    </div>
+            <div class="hidden name"><code>plot.jump.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for jump</span>
-<span class='fu'>plot</span>(<span class='no'>jmp</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>jmp</th>
-      <td><p>jump parameter</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>plot.jump</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for jump</span>
+<span class='fu'>plot</span>(<span class='no'>jmp</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>jmp</th>
+              <td><p>jump parameter</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/plot.mvjump.html b/modules/emulator/docs/reference/plot.mvjump.html
index 1ab0fa6..f28f96c 100644
--- a/modules/emulator/docs/reference/plot.mvjump.html
+++ b/modules/emulator/docs/reference/plot.mvjump.html
@@ -2,148 +2,173 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+                <span
+                  class="label label-default"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+            </div>
+
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
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+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>plot.mvjump</h1>
-    
-    <div class="hidden name"><code>plot.mvjump.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>plot.mvjump</h1>
 
-    <div class="ref-description">
-    
-    <p>plot.mvjump</p>
-    
-    </div>
+            <div class="hidden name"><code>plot.mvjump.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for mvjump</span>
-<span class='fu'>plot</span>(<span class='no'>jmp</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>jmp</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>plot.mvjump</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for mvjump</span>
+<span class='fu'>plot</span>(<span class='no'>jmp</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>jmp</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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 </html>
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diff --git a/modules/emulator/docs/reference/predict.GP.html b/modules/emulator/docs/reference/predict.GP.html
index 8a6d88f..3555b70 100644
--- a/modules/emulator/docs/reference/predict.GP.html
+++ b/modules/emulator/docs/reference/predict.GP.html
@@ -2,153 +2,178 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>predict.GP — predict.GP • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+
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+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      
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-        
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-      
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-</div><!--/.navbar -->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>predict.GP</h1>
-    
-    <div class="hidden name"><code>predict.GP.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>predict.GP</h1>
 
-    <div class="ref-description">
-    
-    <p>predict.GP</p>
-    
-    </div>
+            <div class="hidden name"><code>predict.GP.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>predict.GP</p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for GP</span>
+          <pre class="usage"><span class='co'># S3 method for GP</span>
 <span class='fu'>predict</span>(<span class='no'>gp</span>, <span class='no'>xpred</span>, <span class='kw'>cI</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>pI</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>splinefcns</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>cI</th>
-      <td><p>credible interval</p></td>
-    </tr>
-    <tr>
-      <th>pI</th>
-      <td><p>prediction interval</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>cI</th>
+              <td><p>credible interval</p></td>
+            </tr>
+            <tr>
+              <th>pI</th>
+              <td><p>prediction interval</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/modules/emulator/docs/reference/predict.density.html b/modules/emulator/docs/reference/predict.density.html
index 91c5d88..8aa1c08 100644
--- a/modules/emulator/docs/reference/predict.density.html
+++ b/modules/emulator/docs/reference/predict.density.html
@@ -2,154 +2,184 @@
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 <html>
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>predict.density</h1>
-    
-    <div class="hidden name"><code>predict.density.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>predict.density</h1>
 
-    <div class="ref-description">
-    
-    <p>Simple interpolation of a density object to new points</p>
-    
-    </div>
+            <div class="hidden name"><code>predict.density.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Simple interpolation of a density object to new points</p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for density</span>
+          <pre class="usage"><span class='co'># S3 method for density</span>
 <span class='fu'>predict</span>(<span class='no'>den</span>, <span class='no'>xnew</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>xnew</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>ynew</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>xnew</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>ynew</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/emulator/docs/reference/summarize.GP.html b/modules/emulator/docs/reference/summarize.GP.html
index d9e0c7a..92e7b77 100644
--- a/modules/emulator/docs/reference/summarize.GP.html
+++ b/modules/emulator/docs/reference/summarize.GP.html
@@ -2,147 +2,174 @@
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 <html>
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>summarize.GP</h1>
-    
-    <div class="hidden name"><code>summarize.GP.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>summarize.GP</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>summarize.GP</span>(<span class='no'>gp</span>, <span class='kw'>pdf_file</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>txt_file</th>
-      <td></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Michael Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>summarize.GP</h1>
+
+            <div class="hidden name"><code>summarize.GP.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>summarize.GP</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>summarize.GP</span>(<span class='no'>gp</span>, <span class='kw'>pdf_file</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>txt_file</th>
+              <td></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/update.jump.html b/modules/emulator/docs/reference/update.jump.html
index 3cc13de..5c39dc2 100644
--- a/modules/emulator/docs/reference/update.jump.html
+++ b/modules/emulator/docs/reference/update.jump.html
@@ -2,158 +2,185 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="update.jump — update.jump" />
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-<meta property="og:description" content="update.jump" />
-<meta name="twitter:card" content="summary" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>update.jump — update.jump • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="update.jump — update.jump" />
+
+    <meta property="og:description" content="update.jump" />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
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-    <div id="navbar" class="navbar-collapse collapse">
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-  <a href="../index.html">
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-  <a href="../reference/index.html">Reference</a>
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-      
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-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.emulator</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>update.jump</h1>
-    
-    <div class="hidden name"><code>update.jump.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>update.jump</h1>
 
-    <div class="ref-description">
-    
-    <p>update.jump</p>
-    
-    </div>
+            <div class="hidden name"><code>update.jump.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>update.jump</p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for jump</span>
+          <pre class="usage"><span class='co'># S3 method for jump</span>
 <span class='fu'>update</span>(<span class='no'>jmp</span>, <span class='no'>chain</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>jmp</th>
-      <td><p>jump parameter</p></td>
-    </tr>
-    <tr>
-      <th>chain</th>
-      <td><p>mcmc chain</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>jmp updated jump parameter</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>jmp</th>
+              <td><p>jump parameter</p></td>
+            </tr>
+            <tr>
+              <th>chain</th>
+              <td><p>mcmc chain</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>jmp updated jump parameter</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/emulator/docs/reference/update.mvjump.html b/modules/emulator/docs/reference/update.mvjump.html
index 377ad90..8650e17 100644
--- a/modules/emulator/docs/reference/update.mvjump.html
+++ b/modules/emulator/docs/reference/update.mvjump.html
@@ -2,134 +2,153 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- jquery -->
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>update.mvjump — update.mvjump • PEcAn.emulator</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+                type="button"
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>update.mvjump</h1>
-    
-    <div class="hidden name"><code>update.mvjump.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>update.mvjump</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>update.mvjump</h1>
 
-    <pre class="usage"><span class='co'># S3 method for mvjump</span>
-<span class='fu'>update</span>(<span class='no'>jmp</span>, <span class='no'>chain</span>)</pre>
-        
+            <div class="hidden name"><code>update.mvjump.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>update.mvjump</p>
+          </div>
 
-  </div>
-</div>
+          <pre class="usage"><span class='co'># S3 method for mvjump</span>
+<span class='fu'>update</span>(<span class='no'>jmp</span>, <span class='no'>chain</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
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diff --git a/modules/meta.analysis/docs/LICENSE-text.html b/modules/meta.analysis/docs/LICENSE-text.html
index fef3982..5504587 100644
--- a/modules/meta.analysis/docs/LICENSE-text.html
+++ b/modules/meta.analysis/docs/LICENSE-text.html
@@ -2,109 +2,144 @@
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.MA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                <li>
+                  <a href="reference/index.html">Reference</a>
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+                <li class="dropdown">
+                  <a
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+                    class="dropdown-toggle"
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+                    role="button"
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="articles/single.MA_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
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+
+              <ul class="nav navbar-nav navbar-right"></ul>
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -133,27 +168,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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   </body>
 </html>
-
diff --git a/modules/meta.analysis/docs/articles/index.html b/modules/meta.analysis/docs/articles/index.html
index c1e3e00..af81610 100644
--- a/modules/meta.analysis/docs/articles/index.html
+++ b/modules/meta.analysis/docs/articles/index.html
@@ -2,133 +2,166 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+                  >1.6.0</span
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-    <div class="section ">
-      <h3>All vignettes</h3>
-      <p class="section-desc"></p>
+          <div class="section ">
+            <h3>All vignettes</h3>
+            <p class="section-desc"></p>
 
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index f2438ee..5f82d11 100644
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@@ -1,93 +1,178 @@
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+        <div class="col-md-9 contents">
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+            <h1></h1>
 
-    </div>
+            <div class="hidden name"><code>single.MA_demo.Rmd</code></div>
+          </div>
 
-    
-    
-<div id="meta-analysis-example-of-single-ma" class="section level1">
-<h1 class="hasAnchor">
-<a href="#meta-analysis-example-of-single-ma" class="anchor"></a>Meta-analysis: Example of Single.MA</h1>
-<p>Individual Meta-analysis</p>
-<p>Individual meta-analysis for a specific trait and PFT is run by the function single.MA. This will allow power analysis to run repeated MA outside of the full loop over traits and PFTs.</p>
-<p>The first step is to convert the R distribution to JAGS distribution. The prior transformed is then stored in jagsprior and the parameters are renamed as “distn”, “a”, “b” and “n”. The input used here is a simple example with 4 observations. r2bugs.distributions function is to convert R parameterizations to BUGS paramaterizations or to convert from BUGS to R. It can work on the distributions including normal, weibull, gamma, chsq, binormial, negative binormial. The input of this function are information of the prior distribution, including the name of the distribution and 2 parameters. It will convert the parameterization format from R to BUGS or from BUGS to R automaticaly.</p>
-<p>jagify is to convert queried data to format required by JAGS meta-analysis model.</p>
-<p>In the single.MA function, when input the trait data and prior, it will transfer the prior from R parameterization into BUGS parameterization by using the function r2bugs.distributions. Using the jags.model function, the Bayesian graphical model is generated based on the initials. The posterior samples in mcmc.list format are then created as the output of the function.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">require</span>(knitr)
+          <div id="meta-analysis-example-of-single-ma" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#meta-analysis-example-of-single-ma" class="anchor"></a
+              >Meta-analysis: Example of Single.MA
+            </h1>
+            <p>Individual Meta-analysis</p>
+            <p>
+              Individual meta-analysis for a specific trait and PFT is run by
+              the function single.MA. This will allow power analysis to run
+              repeated MA outside of the full loop over traits and PFTs.
+            </p>
+            <p>
+              The first step is to convert the R distribution to JAGS
+              distribution. The prior transformed is then stored in jagsprior
+              and the parameters are renamed as “distn”, “a”, “b” and “n”. The
+              input used here is a simple example with 4 observations.
+              r2bugs.distributions function is to convert R parameterizations to
+              BUGS paramaterizations or to convert from BUGS to R. It can work
+              on the distributions including normal, weibull, gamma, chsq,
+              binormial, negative binormial. The input of this function are
+              information of the prior distribution, including the name of the
+              distribution and 2 parameters. It will convert the
+              parameterization format from R to BUGS or from BUGS to R
+              automaticaly.
+            </p>
+            <p>
+              jagify is to convert queried data to format required by JAGS
+              meta-analysis model.
+            </p>
+            <p>
+              In the single.MA function, when input the trait data and prior, it
+              will transfer the prior from R parameterization into BUGS
+              parameterization by using the function r2bugs.distributions. Using
+              the jags.model function, the Bayesian graphical model is generated
+              based on the initials. The posterior samples in mcmc.list format
+              are then created as the output of the function.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">require</span>(knitr)
 opts_chunk<span class="op">$</span><span class="kw">set</span>(<span class="dt">echo =</span> <span class="ot">FALSE</span>, <span class="dt">message =</span> <span class="ot">FALSE</span>, <span class="dt">results=</span><span class="st">'hide'</span>, <span class="dt">cache=</span><span class="ot">TRUE</span>, 
                <span class="dt">eval =</span> <span class="ot">FALSE</span> ## just to allow .md to be compiled
                )
@@ -101,8 +186,9 @@ <h1 class="hasAnchor">
 tauB &lt;-<span class="st"> </span><span class="fl">0.001</span>
 prior &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">distn =</span> <span class="st">"norm"</span>, <span class="dt">parama =</span> <span class="dv">0</span>, <span class="dt">paramb =</span> <span class="dv">2</span>, <span class="dt">n =</span> <span class="ot">NA</span>)
 ##running single.MA
-output &lt;-<span class="st"> </span><span class="kw"><a href="../reference/single.MA.html">single.MA</a></span>(data, j.chains, j.iter, tauA, tauB, prior,jag.model.file, <span class="dt">overdispersed=</span><span class="ot">TRUE</span>)</code></pre></div>
-<pre><code>## Compiling model graph
+output &lt;-<span class="st"> </span><span class="kw"><a href="../reference/single.MA.html">single.MA</a></span>(data, j.chains, j.iter, tauA, tauB, prior,jag.model.file, <span class="dt">overdispersed=</span><span class="ot">TRUE</span>)</code></pre>
+            </div>
+            <pre><code>## Compiling model graph
 ##    Resolving undeclared variables
 ##    Allocating nodes
 ## Graph information:
@@ -111,35 +197,45 @@ <h1 class="hasAnchor">
 ##    Total graph size: 25
 ## 
 ## Initializing model</code></pre>
-<p>The meta-analysis outputs are summarized by the pecan.ma.summary function. It will create several log files for all the traits to record the R output of the convergency diagnosis, and several PDF file for all the traits to store the diagnosis plot of convergency. G-R diagnostics is used to test convergence. The diagnose result is output into the log file. If the JAGS model failed to converge, a warning will also be generated.</p>
-</div>
-  </div>
+            <p>
+              The meta-analysis outputs are summarized by the pecan.ma.summary
+              function. It will create several log files for all the traits to
+              record the R output of the convergency diagnosis, and several PDF
+              file for all the traits to store the diagnosis plot of
+              convergency. G-R diagnostics is used to test convergence. The
+              diagnose result is output into the log file. If the JAGS model
+              failed to converge, a warning will also be generated.
+            </p>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#meta-analysis-example-of-single-ma">Meta-analysis: Example of Single.MA</a></li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a href="#meta-analysis-example-of-single-ma"
+                  >Meta-analysis: Example of Single.MA</a
+                >
+              </li>
+            </ul>
+          </div>
+        </div>
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index f7c8871..67386c1 100644
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@@ -2,158 +2,179 @@
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+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.MA</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/single.MA_demo.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.MA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/single.MA_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/meta.analysis/docs/docsearch.css b/modules/meta.analysis/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/meta.analysis/docs/docsearch.css
+++ b/modules/meta.analysis/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/meta.analysis/docs/docsearch.js b/modules/meta.analysis/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/meta.analysis/docs/docsearch.js
+++ b/modules/meta.analysis/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/meta.analysis/docs/index.html b/modules/meta.analysis/docs/index.html
index 253f4b3..db280ed 100644
--- a/modules/meta.analysis/docs/index.html
+++ b/modules/meta.analysis/docs/index.html
@@ -1,125 +1,187 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for meta-analysis • PEcAn.MA</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
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-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for meta-analysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>PEcAn functions used for meta-analysis • PEcAn.MA</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for meta-analysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation. The PEcAn.MA package contains
-    the functions used in the Bayesian meta-analysis of trait data.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    the functions used in the Bayesian meta-analysis of trait data."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.MA</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/single.MA_demo.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.MA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation. The PEcAn.MA package contains
-    the functions used in the Bayesian meta-analysis of trait data.
-  </div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
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+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+                    Articles
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
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-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/single.MA_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation. The PEcAn.MA package
+          contains the functions used in the Bayesian meta-analysis of trait
+          data.
+        </div>
 
-  </div>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
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+            </ul>
+          </div>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
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-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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       </footer>
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   </body>
 </html>
diff --git a/modules/meta.analysis/docs/pkgdown.css b/modules/meta.analysis/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/meta.analysis/docs/pkgdown.css
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diff --git a/modules/meta.analysis/docs/pkgdown.js b/modules/meta.analysis/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/meta.analysis/docs/pkgdown.js
+++ b/modules/meta.analysis/docs/pkgdown.js
@@ -1,18 +1,21 @@
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+      var copyButton =
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diff --git a/modules/meta.analysis/docs/reference/approx.posterior.html b/modules/meta.analysis/docs/reference/approx.posterior.html
index 83616f4..9156b1d 100644
--- a/modules/meta.analysis/docs/reference/approx.posterior.html
+++ b/modules/meta.analysis/docs/reference/approx.posterior.html
@@ -2,198 +2,253 @@
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+
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+      content="Approximate posterior — approx.posterior"
+    />
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.MA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
+                  <a
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/single.MA_demo.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
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+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Approximate posterior</h1>
-    
-    <div class="hidden name"><code>approx.posterior.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Approximate posterior</h1>
 
-    <div class="ref-description">
-    
-    <p>Approximate the posterior MCMC with a closed form pdf</p>
-    
-    </div>
+            <div class="hidden name"><code>approx.posterior.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>approx.posterior</span>(<span class='no'>trait.mcmc</span>, <span class='no'>priors</span>, <span class='kw'>trait.data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>outdir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <div class="ref-description">
+            <p>Approximate the posterior MCMC with a closed form pdf</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>approx.posterior</span>(<span class='no'>trait.mcmc</span>, <span class='no'>priors</span>, <span class='kw'>trait.data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>outdir</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>filename.flag</span> <span class='kw'>=</span> <span class='st'>""</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.mcmc</th>
-      <td><p>meta analysis outputs</p></td>
-    </tr>
-    <tr>
-      <th>priors</th>
-      <td><p>dataframe of priors used in meta analysis</p></td>
-    </tr>
-    <tr>
-      <th>trait.data</th>
-      <td><p>data used in meta-analysis (used for plotting)</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>directory in which to plot results</p></td>
-    </tr>
-    <tr>
-      <th>filename.flag</th>
-      <td><p>text to be included in the posteriors.pdf filename to make unique</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>posteriors data frame, similar to priors,
-but with closed form pdfs fit to meta-analysis results</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>returns priors where posterior MCMC are missing</p>
-<p>NOTE: this function is similar to PEcAn.priors::fit.dist</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.mcmc</th>
+              <td><p>meta analysis outputs</p></td>
+            </tr>
+            <tr>
+              <th>priors</th>
+              <td><p>dataframe of priors used in meta analysis</p></td>
+            </tr>
+            <tr>
+              <th>trait.data</th>
+              <td><p>data used in meta-analysis (used for plotting)</p></td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>directory in which to plot results</p></td>
+            </tr>
+            <tr>
+              <th>filename.flag</th>
+              <td>
+                <p>
+                  text to be included in the posteriors.pdf filename to make
+                  unique
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            posteriors data frame, similar to priors, but with closed form pdfs
+            fit to meta-analysis results
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>returns priors where posterior MCMC are missing</p>
+          <p>NOTE: this function is similar to PEcAn.priors::fit.dist</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
   <span class='fu'>data</span>(<span class='st'>'trait.mcmc'</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>'PEcAn.utils'</span>)
   <span class='fu'>data</span>(<span class='st'>'prior.distns'</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>'PEcAn.utils'</span>)
   <span class='fu'>approx.posterior</span>(<span class='no'>trait.mcmc</span>, <span class='kw'>priors</span> <span class='kw'>=</span> <span class='no'>prior.distns</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson, Mike Dietze
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          David LeBauer, Carl Davidson, Mike Dietze
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
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index 31d9485..d7f2c66 100644
--- a/modules/meta.analysis/docs/reference/index.html
+++ b/modules/meta.analysis/docs/reference/index.html
@@ -2,209 +2,290 @@
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
 
-<!-- Font Awesome icons -->
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+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
 
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
 
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
 
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
 
+    <meta property="og:title" content="Function reference" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
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+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.MA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
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-      <ul class="nav navbar-nav navbar-right">
-        
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-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
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-      </header>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/single.MA_demo.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
 
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="approx.posterior.html">approx.posterior()</a></code> </p>
-        </td>
-        <td><p>Approximate posterior</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="jagify.html">jagify()</a></code> </p>
-        </td>
-        <td><p>Prepare trait data for JAGS meta-analysis</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="p.point.in.prior.html">p.point.in.prior()</a></code> </p>
-        </td>
-        <td><p>find quantile of point within prior distribution</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pecan.ma.html">pecan.ma()</a></code> </p>
-        </td>
-        <td><p>Trait Meta-analysis</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pecan.ma.summary.html">pecan.ma.summary()</a></code> </p>
-        </td>
-        <td><p>Generate summary statistics and diagnostics for PEcAn meta.analysis</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="run.meta.analysis.html">run.meta.analysis()</a></code> </p>
-        </td>
-        <td><p>Invoke PEcAn meta.analysis
-This will use the following items from setings:
-- settings$pfts
-- settings$database$bety
-- settings$database$dbfiles
-- settings$meta.analysis$update</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="single.MA.html">single.MA()</a></code> </p>
-        </td>
-        <td><p>Single MA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="transform.nas.html">transform(<i>&lt;nas&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Function to remove NA values from database queries</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.ma.model.html">write.ma.model()</a></code> </p>
-        </td>
-        <td><p>write.ma.model</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-      </footer>
-   </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="approx.posterior.html"
+                        >approx.posterior()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Approximate posterior</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="jagify.html">jagify()</a></code>
+                  </p>
+                </td>
+                <td><p>Prepare trait data for JAGS meta-analysis</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="p.point.in.prior.html"
+                        >p.point.in.prior()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>find quantile of point within prior distribution</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pecan.ma.html">pecan.ma()</a></code>
+                  </p>
+                </td>
+                <td><p>Trait Meta-analysis</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="pecan.ma.summary.html"
+                        >pecan.ma.summary()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Generate summary statistics and diagnostics for PEcAn
+                    meta.analysis
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="run.meta.analysis.html"
+                        >run.meta.analysis()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Invoke PEcAn meta.analysis This will use the following items
+                    from setings: - settings$pfts - settings$database$bety -
+                    settings$database$dbfiles - settings$meta.analysis$update
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="single.MA.html">single.MA()</a></code>
+                  </p>
+                </td>
+                <td><p>Single MA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="transform.nas.html"
+                        >transform(<i>&lt;nas&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Function to remove NA values from database queries</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.ma.model.html">write.ma.model()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>write.ma.model</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
-  
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/meta.analysis/docs/reference/jagify.html b/modules/meta.analysis/docs/reference/jagify.html
index a6b57fe..af326ce 100644
--- a/modules/meta.analysis/docs/reference/jagify.html
+++ b/modules/meta.analysis/docs/reference/jagify.html
@@ -2,165 +2,213 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Prepare trait data for JAGS meta-analysis</h1>
-    
-    <div class="hidden name"><code>jagify.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert queried data to format required by JAGS meta-analysis model</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>jagify</span>(<span class='no'>result</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>result</th>
-      <td><p>input trait data</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>result transformed to meet requirements of PEcAn meta-analysis model</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Prepare trait data for JAGS meta-analysis</h1>
+
+            <div class="hidden name"><code>jagify.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Convert queried data to format required by JAGS meta-analysis
+              model
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>jagify</span>(<span class='no'>result</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>result</th>
+              <td><p>input trait data</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            result transformed to meet requirements of PEcAn meta-analysis model
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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diff --git a/modules/meta.analysis/docs/reference/p.point.in.prior.html b/modules/meta.analysis/docs/reference/p.point.in.prior.html
index 58f2722..615d84c 100644
--- a/modules/meta.analysis/docs/reference/p.point.in.prior.html
+++ b/modules/meta.analysis/docs/reference/p.point.in.prior.html
@@ -2,175 +2,223 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>find quantile of point within prior distribution</h1>
-    
-    <div class="hidden name"><code>p.point.in.prior.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>compare point to prior distribution</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>p.point.in.prior</span>(<span class='no'>point</span>, <span class='no'>prior</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>point</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>prior</th>
-      <td><p>list of distn, parama, paramb</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>result of p&lt;distn&gt;(point, parama, paramb)</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>used to compare data to prior, meta analysis posterior to prior</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>find quantile of point within prior distribution</h1>
+
+            <div class="hidden name"><code>p.point.in.prior.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>compare point to prior distribution</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>p.point.in.prior</span>(<span class='no'>point</span>, <span class='no'>prior</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>point</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>prior</th>
+              <td><p>list of distn, parama, paramb</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>result of p&lt;distn&gt;(point, parama, paramb)</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>used to compare data to prior, meta analysis posterior to prior</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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 </html>
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diff --git a/modules/meta.analysis/docs/reference/pecan.ma.html b/modules/meta.analysis/docs/reference/pecan.ma.html
index 3c9930b..f49e246 100644
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+    />
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-    Articles
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+                  title="Released package"
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+                        >UNKNOWN TITLE</a
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Trait Meta-analysis</h1>
-    
-    <div class="hidden name"><code>pecan.ma.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Trait Meta-analysis</h1>
 
-    <div class="ref-description">
-    
-    <p>Runs heirarchical meta-analysis of plant trait data</p>
-    
-    </div>
+            <div class="hidden name"><code>pecan.ma.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>pecan.ma</span>(<span class='no'>trait.data</span>, <span class='no'>prior.distns</span>, <span class='no'>taupriors</span>, <span class='no'>j.iter</span>, <span class='no'>outdir</span>,
+          <div class="ref-description">
+            <p>Runs heirarchical meta-analysis of plant trait data</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pecan.ma</span>(<span class='no'>trait.data</span>, <span class='no'>prior.distns</span>, <span class='no'>taupriors</span>, <span class='no'>j.iter</span>, <span class='no'>outdir</span>,
   <span class='kw'>random</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>overdispersed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.data</th>
-      <td><p>list of dataframes, one per trait for which data is available, generated by call to query.traits()</p></td>
-    </tr>
-    <tr>
-      <th>prior.distns</th>
-      <td><p>dataframe of prior distributions generated by call to query.priors()</p></td>
-    </tr>
-    <tr>
-      <th>taupriors</th>
-      <td><p>priors on variance parameters, can be scaled as needed with data mean</p></td>
-    </tr>
-    <tr>
-      <th>j.iter</th>
-      <td><p>number of mcmc samples</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>output directory</p></td>
-    </tr>
-    <tr>
-      <th>random</th>
-      <td><p>use random effects, FALSE by default</p></td>
-    </tr>
-    <tr>
-      <th>overdispersed</th>
-      <td><p>TRUE by default, if set to FALSE, data mean will be used as starting point for MCMC chains (use with caution)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>four chains with 5000 total samples from posterior</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><code>pecan.ma</code> runs a heirarchical Bayes meta-analytical model.
-This model combines prior information with data from studies on the particular species or group of interest.
-Data that is incorporated into the meta-analysis include the mean (Y), sample size (n),
-and precision (obs.prec). 
-Where a set of data includes more than one level of treatment, comes from more than one site,
-or comes from both field and greenhouse studies, these variables are included as random (treatment, site)
-or fixed (greenhouse) effects. 
-The pecan.ma function writes a model for each specific data set and prior using the write.ma.model()
-function to modify the ma.model.template.bug generic model.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.data</th>
+              <td>
+                <p>
+                  list of dataframes, one per trait for which data is available,
+                  generated by call to query.traits()
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prior.distns</th>
+              <td>
+                <p>
+                  dataframe of prior distributions generated by call to
+                  query.priors()
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>taupriors</th>
+              <td>
+                <p>
+                  priors on variance parameters, can be scaled as needed with
+                  data mean
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>j.iter</th>
+              <td><p>number of mcmc samples</p></td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>output directory</p></td>
+            </tr>
+            <tr>
+              <th>random</th>
+              <td><p>use random effects, FALSE by default</p></td>
+            </tr>
+            <tr>
+              <th>overdispersed</th>
+              <td>
+                <p>
+                  TRUE by default, if set to FALSE, data mean will be used as
+                  starting point for MCMC chains (use with caution)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>four chains with 5000 total samples from posterior</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            <code>pecan.ma</code> runs a heirarchical Bayes meta-analytical
+            model. This model combines prior information with data from studies
+            on the particular species or group of interest. Data that is
+            incorporated into the meta-analysis include the mean (Y), sample
+            size (n), and precision (obs.prec). Where a set of data includes
+            more than one level of treatment, comes from more than one site, or
+            comes from both field and greenhouse studies, these variables are
+            included as random (treatment, site) or fixed (greenhouse) effects.
+            The pecan.ma function writes a model for each specific data set and
+            prior using the write.ma.model() function to modify the
+            ma.model.template.bug generic model.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>prior.distns</span> <span class='kw'>&lt;-</span> <span class='fu'>query.priors</span>(<span class='st'>'ebifarm.c4crop'</span>, <span class='fu'>c</span>(<span class='st'>'SLA'</span>, <span class='st'>'c2n_leaf'</span>))
 <span class='no'>trait.data</span> <span class='kw'>&lt;-</span> <span class='fu'>query.traits</span>(<span class='st'>'938'</span>, <span class='fu'>c</span>(<span class='st'>'SLA'</span>, <span class='st'>'c2n_leaf'</span>))
 <span class='fu'>pecan.ma</span>(<span class='no'>prior.distns</span>, <span class='no'>trait.data</span>, <span class='fl'>25000</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Michael C. Dietze
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          David LeBauer, Michael C. Dietze
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
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 </html>
-
diff --git a/modules/meta.analysis/docs/reference/pecan.ma.summary.html b/modules/meta.analysis/docs/reference/pecan.ma.summary.html
index 87f6438..358dd06 100644
--- a/modules/meta.analysis/docs/reference/pecan.ma.summary.html
+++ b/modules/meta.analysis/docs/reference/pecan.ma.summary.html
@@ -2,186 +2,253 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate summary statistics and diagnostics for PEcAn meta.analysis</h1>
-    
-    <div class="hidden name"><code>pecan.ma.summary.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generate summary statistics and diagnostics for PEcAn meta.analysis</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pecan.ma.summary</span>(<span class='no'>mcmc.object</span>, <span class='no'>pft</span>, <span class='no'>outdir</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.2</span>, <span class='kw'>gg</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mcmc.object</th>
-      <td><p>JAGS mcmc output from <code><a href='pecan.ma.html'>pecan.ma</a></code></p></td>
-    </tr>
-    <tr>
-      <th>pft</th>
-      <td><p>plant functional type</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>output directory</p></td>
-    </tr>
-    <tr>
-      <th>threshold</th>
-      <td><p>Gelman-Rubin convergence diagnostic (MGPRF)
-default = 1.2 following Bolker 2008 Ecological Models and Data in R</p></td>
-    </tr>
-    <tr>
-      <th>gg</th>
-      <td><p>produce extra diagnostic plots using the "ggmcmc" package? Caution: very slow!</p></td>
-    </tr>
-    </table>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Generate summary statistics and diagnostics for PEcAn
+              meta.analysis
+            </h1>
+
+            <div class="hidden name"><code>pecan.ma.summary.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Generate summary statistics and diagnostics for PEcAn
+              meta.analysis
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pecan.ma.summary</span>(<span class='no'>mcmc.object</span>, <span class='no'>pft</span>, <span class='no'>outdir</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.2</span>, <span class='kw'>gg</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mcmc.object</th>
+              <td>
+                <p>
+                  JAGS mcmc output from
+                  <code><a href="pecan.ma.html">pecan.ma</a></code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pft</th>
+              <td><p>plant functional type</p></td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>output directory</p></td>
+            </tr>
+            <tr>
+              <th>threshold</th>
+              <td>
+                <p>
+                  Gelman-Rubin convergence diagnostic (MGPRF) default = 1.2
+                  following Bolker 2008 Ecological Models and Data in R
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>gg</th>
+              <td>
+                <p>
+                  produce extra diagnostic plots using the "ggmcmc" package?
+                  Caution: very slow!
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>summary</span> <span class='kw'>&lt;-</span> <span class='fu'>pecan.ma.summary</span>(
  <span class='no'>trait.mcmc</span>,
  <span class='no'>settings</span>$<span class='no'>pfts</span>$<span class='no'>pft</span>,
  <span class='no'>settings</span>$<span class='no'>outdir</span>,
  <span class='no'>settings</span>$<span class='no'>meta.analysis</span>$<span class='no'>threshold</span>)
 <span class='co'># }</span></pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-            
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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+            <li><a href="#examples">Examples</a></li>
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+          <h2>Author</h2>
 
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diff --git a/modules/meta.analysis/docs/reference/run.meta.analysis.html b/modules/meta.analysis/docs/reference/run.meta.analysis.html
index d57f721..41403f8 100644
--- a/modules/meta.analysis/docs/reference/run.meta.analysis.html
+++ b/modules/meta.analysis/docs/reference/run.meta.analysis.html
@@ -2,205 +2,255 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Invoke PEcAn meta.analysis
-This will use the following items from setings:
-- settings$pfts
-- settings$database$bety
-- settings$database$dbfiles
-- settings$meta.analysis$update — run.meta.analysis • PEcAn.MA</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Invoke PEcAn meta.analysis This will use the following items from setings:
+      - settings$pfts - settings$database$bety - settings$database$dbfiles -
+      settings$meta.analysis$update — run.meta.analysis • PEcAn.MA
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      content="Invoke PEcAn meta.analysis
 This will use the following items from setings:
 - settings$pfts
 - settings$database$bety
 - settings$database$dbfiles
-- settings$meta.analysis$update — run.meta.analysis" />
-
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-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+- settings$meta.analysis$update — run.meta.analysis"
+    />
 
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-<![endif]-->
+    <meta property="og:description" content="Run meta analysis" />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
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-    Articles
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-        
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
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+                type="button"
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+                <a class="navbar-link" href="../index.html">PEcAn.MA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/single.MA_demo.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Invoke PEcAn meta.analysis
-This will use the following items from setings:
-- settings$pfts
-- settings$database$bety
-- settings$database$dbfiles
-- settings$meta.analysis$update</h1>
-    
-    <div class="hidden name"><code>run.meta.analysis.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Run meta analysis</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>run.meta.analysis</span>(<span class='no'>pfts</span>, <span class='no'>iterations</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.2</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Invoke PEcAn meta.analysis This will use the following items from
+              setings: - settings$pfts - settings$database$bety -
+              settings$database$dbfiles - settings$meta.analysis$update
+            </h1>
+
+            <div class="hidden name"><code>run.meta.analysis.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Run meta analysis</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>run.meta.analysis</span>(<span class='no'>pfts</span>, <span class='no'>iterations</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.2</span>,
   <span class='no'>dbfiles</span>, <span class='no'>database</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pfts</th>
-      <td><p>the list of pfts to get traits for</p></td>
-    </tr>
-    <tr>
-      <th>iterations</th>
-      <td><p>the number of iterations for the mcmc analysis</p></td>
-    </tr>
-    <tr>
-      <th>random</th>
-      <td><p>should random effects be used?</p></td>
-    </tr>
-    <tr>
-      <th>threshold</th>
-      <td><p>Gelman-Rubin convergence diagnostic, passed on to
-<code><a href='pecan.ma.summary.html'>pecan.ma.summary</a></code></p></td>
-    </tr>
-    <tr>
-      <th>dbfiles</th>
-      <td><p>location where previous results are found</p></td>
-    </tr>
-    <tr>
-      <th>database</th>
-      <td><p>database connection parameters</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing, as side effect saves <code>trait.mcmc</code> created by
-<code><a href='pecan.ma.html'>pecan.ma</a></code> and post.distns created by
-<code><a href='approx.posterior.html'>approx.posterior</a>(trait.mcmc, ...)</code>  to trait.mcmc.Rdata \
-and post.distns.Rdata, respectively</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pfts</th>
+              <td><p>the list of pfts to get traits for</p></td>
+            </tr>
+            <tr>
+              <th>iterations</th>
+              <td><p>the number of iterations for the mcmc analysis</p></td>
+            </tr>
+            <tr>
+              <th>random</th>
+              <td><p>should random effects be used?</p></td>
+            </tr>
+            <tr>
+              <th>threshold</th>
+              <td>
+                <p>
+                  Gelman-Rubin convergence diagnostic, passed on to
+                  <code
+                    ><a href="pecan.ma.summary.html">pecan.ma.summary</a></code
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>dbfiles</th>
+              <td><p>location where previous results are found</p></td>
+            </tr>
+            <tr>
+              <th>database</th>
+              <td><p>database connection parameters</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            nothing, as side effect saves <code>trait.mcmc</code> created by
+            <code><a href="pecan.ma.html">pecan.ma</a></code> and post.distns
+            created by
+            <code
+              ><a href="approx.posterior.html">approx.posterior</a>(trait.mcmc,
+              ...)</code
+            >
+            to trait.mcmc.Rdata \ and post.distns.Rdata, respectively
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin, David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Shawn Serbin, David LeBauer
+        </div>
+      </div>
 
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diff --git a/modules/meta.analysis/docs/reference/single.MA.html b/modules/meta.analysis/docs/reference/single.MA.html
index cb0571c..1de1e50 100644
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+++ b/modules/meta.analysis/docs/reference/single.MA.html
@@ -2,203 +2,256 @@
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+                  title="Released package"
+                  >1.6.0</span
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+                    role="button"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/single.MA_demo.html"
+                        >UNKNOWN TITLE</a
+                      >
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+              </ul>
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Single MA</h1>
-    
-    <div class="hidden name"><code>single.MA.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Single MA</h1>
 
-    <div class="ref-description">
-    
-    <p>Individual Meta-analysis</p>
-    
-    </div>
+            <div class="hidden name"><code>single.MA.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Individual Meta-analysis</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>single.MA</span>(<span class='no'>data</span>, <span class='no'>j.chains</span>, <span class='no'>j.iter</span>, <span class='no'>tauA</span>, <span class='no'>tauB</span>, <span class='no'>prior</span>, <span class='no'>jag.model.file</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>single.MA</span>(<span class='no'>data</span>, <span class='no'>j.chains</span>, <span class='no'>j.iter</span>, <span class='no'>tauA</span>, <span class='no'>tauB</span>, <span class='no'>prior</span>, <span class='no'>jag.model.file</span>,
   <span class='kw'>overdispersed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>j.chains</th>
-      <td><p>number of chains in meta-analysis</p></td>
-    </tr>
-    <tr>
-      <th>j.iter</th>
-      <td><p>number of mcmc samples</p></td>
-    </tr>
-    <tr>
-      <th>tauA</th>
-      <td><p>prior on variance parameters</p></td>
-    </tr>
-    <tr>
-      <th>tauB</th>
-      <td><p>prior on variance parameters</p></td>
-    </tr>
-    <tr>
-      <th>prior</th>
-      <td><p>data.frame with columns named 'distn', 'parama', 'paramb'
-e.g. <code>prior &lt;- data.frame(distn = 'weibull', parama = 0.5, paramb = 10, n = 1)</code></p></td>
-    </tr>
-    <tr>
-      <th>jag.model.file</th>
-      <td><p>file to which model will be written</p></td>
-    </tr>
-    <tr>
-      <th>overdispersed</th>
-      <td><p>if TRUE (default), chains start at overdispersed locations in parameter space (recommended)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>jags.out, an mcmc.object with results of meta-analysis</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Individual meta-analysis for a specific trait and PFT is run by the function
-single.MA. This will allow power analysis  to run repeated MA outside of the
-full loop over traits and PFTs.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>j.chains</th>
+              <td><p>number of chains in meta-analysis</p></td>
+            </tr>
+            <tr>
+              <th>j.iter</th>
+              <td><p>number of mcmc samples</p></td>
+            </tr>
+            <tr>
+              <th>tauA</th>
+              <td><p>prior on variance parameters</p></td>
+            </tr>
+            <tr>
+              <th>tauB</th>
+              <td><p>prior on variance parameters</p></td>
+            </tr>
+            <tr>
+              <th>prior</th>
+              <td>
+                <p>
+                  data.frame with columns named 'distn', 'parama', 'paramb' e.g.
+                  <code
+                    >prior &lt;- data.frame(distn = 'weibull', parama = 0.5,
+                    paramb = 10, n = 1)</code
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>jag.model.file</th>
+              <td><p>file to which model will be written</p></td>
+            </tr>
+            <tr>
+              <th>overdispersed</th>
+              <td>
+                <p>
+                  if TRUE (default), chains start at overdispersed locations in
+                  parameter space (recommended)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>jags.out, an mcmc.object with results of meta-analysis</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Individual meta-analysis for a specific trait and PFT is run by the
+            function single.MA. This will allow power analysis to run repeated
+            MA outside of the full loop over traits and PFTs.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Michael C. Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Michael C. Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/modules/meta.analysis/docs/reference/transform.nas.html b/modules/meta.analysis/docs/reference/transform.nas.html
index a291f99..1e9342c 100644
--- a/modules/meta.analysis/docs/reference/transform.nas.html
+++ b/modules/meta.analysis/docs/reference/transform.nas.html
@@ -2,162 +2,206 @@
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+      PEcAn.MA
+    </title>
+
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
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+                <span
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+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
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+                  <a href="../index.html">
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
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+
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+                  </a>
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+                    <li>
+                      <a href="../articles/single.MA_demo.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function to remove NA values from database queries</h1>
-    
-    <div class="hidden name"><code>transform.nas.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Function to remove NA values from database queries</h1>
 
-    <div class="ref-description">
-    
-    <p>Transform NA values in data exported from BETYdb</p>
-    
-    </div>
+            <div class="hidden name"><code>transform.nas.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for nas</span>
+          <div class="ref-description">
+            <p>Transform NA values in data exported from BETYdb</p>
+          </div>
+
+          <pre class="usage"><span class='co'># S3 method for nas</span>
 <span class='fu'>transform</span>(<span class='no'>data</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>data</th>
-      <td><p>input data</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>A data frame NAs sensibly replaced</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>data</th>
+              <td><p>input data</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>A data frame NAs sensibly replaced</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/meta.analysis/docs/reference/write.ma.model.html b/modules/meta.analysis/docs/reference/write.ma.model.html
index 55eb745..1b17d92 100644
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+++ b/modules/meta.analysis/docs/reference/write.ma.model.html
@@ -2,216 +2,277 @@
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.MA</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-      <a href="../articles/single.MA_demo.html">UNKNOWN TITLE</a>
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-        
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-      
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.MA</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/single.MA_demo.html"
+                        >UNKNOWN TITLE</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>write.ma.model</h1>
-    
-    <div class="hidden name"><code>write.ma.model.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>write.ma.model</h1>
 
-    <div class="ref-description">
-    
-    <p>Convert template ma.model.template.R to a JAGS model.</p>
-    
-    </div>
+            <div class="hidden name"><code>write.ma.model.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert template ma.model.template.R to a JAGS model.</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>write.ma.model</span>(<span class='no'>modelfile</span>, <span class='no'>outfile</span>, <span class='no'>reg.model</span>, <span class='no'>pr.dist</span>, <span class='no'>pr.param.a</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>write.ma.model</span>(<span class='no'>modelfile</span>, <span class='no'>outfile</span>, <span class='no'>reg.model</span>, <span class='no'>pr.dist</span>, <span class='no'>pr.param.a</span>,
   <span class='no'>pr.param.b</span>, <span class='no'>n</span>, <span class='no'>trt.n</span>, <span class='no'>site.n</span>, <span class='no'>ghs.n</span>, <span class='no'>tauA</span>, <span class='no'>tauB</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>modelfile</th>
-      <td><p>model template file (ma.model.template.R)</p></td>
-    </tr>
-    <tr>
-      <th>outfile</th>
-      <td><p>file name of model created</p></td>
-    </tr>
-    <tr>
-      <th>reg.model</th>
-      <td><p>structure of regression model</p></td>
-    </tr>
-    <tr>
-      <th>pr.dist</th>
-      <td><p>A string representing the root distribution name used by R, e.g. 'norm', 'lnorm', 'gamma', 'beta', etc.</p></td>
-    </tr>
-    <tr>
-      <th>pr.param.a</th>
-      <td><p>first parameter value accepted by <code>pr.dist</code></p></td>
-    </tr>
-    <tr>
-      <th>pr.param.b</th>
-      <td><p>second parameter value accepted by <code>pr.dist</code></p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>number of observations in data</p></td>
-    </tr>
-    <tr>
-      <th>trt.n</th>
-      <td><p>number of distinct treatments in data</p></td>
-    </tr>
-    <tr>
-      <th>site.n</th>
-      <td><p>number of distinct sites in data</p></td>
-    </tr>
-    <tr>
-      <th>ghs.n</th>
-      <td><p>= 1 if only non-greenhouse or greenhouse studies included, 2 if both</p></td>
-    </tr>
-    <tr>
-      <th>tauA</th>
-      <td><p>parameter a for gamma prior on precision</p></td>
-    </tr>
-    <tr>
-      <th>tauB</th>
-      <td><p>parameter b for gamma prior on precision</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Nothing, but as a side effect, the model is written</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Writes a meta-analysis model based on available data and prior specification. Adapted from <code>write.model</code></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>modelfile</th>
+              <td><p>model template file (ma.model.template.R)</p></td>
+            </tr>
+            <tr>
+              <th>outfile</th>
+              <td><p>file name of model created</p></td>
+            </tr>
+            <tr>
+              <th>reg.model</th>
+              <td><p>structure of regression model</p></td>
+            </tr>
+            <tr>
+              <th>pr.dist</th>
+              <td>
+                <p>
+                  A string representing the root distribution name used by R,
+                  e.g. 'norm', 'lnorm', 'gamma', 'beta', etc.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pr.param.a</th>
+              <td>
+                <p>first parameter value accepted by <code>pr.dist</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>pr.param.b</th>
+              <td>
+                <p>second parameter value accepted by <code>pr.dist</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td><p>number of observations in data</p></td>
+            </tr>
+            <tr>
+              <th>trt.n</th>
+              <td><p>number of distinct treatments in data</p></td>
+            </tr>
+            <tr>
+              <th>site.n</th>
+              <td><p>number of distinct sites in data</p></td>
+            </tr>
+            <tr>
+              <th>ghs.n</th>
+              <td>
+                <p>
+                  = 1 if only non-greenhouse or greenhouse studies included, 2
+                  if both
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>tauA</th>
+              <td><p>parameter a for gamma prior on precision</p></td>
+            </tr>
+            <tr>
+              <th>tauB</th>
+              <td><p>parameter b for gamma prior on precision</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Nothing, but as a side effect, the model is written</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Writes a meta-analysis model based on available data and prior
+            specification. Adapted from <code>write.model</code>
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer and Mike Dietze, based on original work on the <code>write.model</code> function in the <code>R2WinBUGS</code> package by Jouni Kerman and Uwe Ligges.
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer and Mike Dietze, based on original work on the
+          <code>write.model</code> function in the
+          <code>R2WinBUGS</code> package by Jouni Kerman and Uwe Ligges.
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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-
diff --git a/modules/photosynthesis/docs/LICENSE-text.html b/modules/photosynthesis/docs/LICENSE-text.html
index 1f0a201..4b03284 100644
--- a/modules/photosynthesis/docs/LICENSE-text.html
+++ b/modules/photosynthesis/docs/LICENSE-text.html
@@ -2,109 +2,149 @@
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.photosynthesis</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/ResponseCurves.html">Fitting Hierarchical Bayes photosynthetic response curves</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html"
+                  >PEcAn.photosynthesis</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/ResponseCurves.html"
+                        >Fitting Hierarchical Bayes photosynthetic response
+                        curves</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -136,27 +176,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/photosynthesis/docs/articles/ResponseCurves.html b/modules/photosynthesis/docs/articles/ResponseCurves.html
index db58041..0c3e8cf 100644
--- a/modules/photosynthesis/docs/articles/ResponseCurves.html
+++ b/modules/photosynthesis/docs/articles/ResponseCurves.html
@@ -1,191 +1,399 @@
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+            <h1>Fitting Hierarchical Bayes photosynthetic response curves</h1>
+            <h4 class="author">Mike Dietze</h4>
 
-      
-      </header><div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header toc-ignore">
-      <h1>Fitting Hierarchical Bayes photosynthetic response curves</h1>
-                        <h4 class="author">Mike Dietze</h4>
-            
             <h4 class="date">June 25, 2015</h4>
-      
-      
-      <div class="hidden name"><code>ResponseCurves.Rmd</code></div>
 
-    </div>
+            <div class="hidden name"><code>ResponseCurves.Rmd</code></div>
+          </div>
 
-    
-    
-<div id="introduction" class="section level2">
-<h2 class="hasAnchor">
-<a href="#introduction" class="anchor"></a>Introduction</h2>
-<p>This package is designed to fit the Farquhar, von Caemmerer, and Berry (1980) photosynthesis model [FvCB model] to leaf-level photosynthetic data. The statistical model generalizes the Hierarchial Bayesian approach described in Feng and Dietze (2013). The important advance that this approach provides is the ability to include covariates (e.g. leaf traits) in a mixed effects model describing key model parameters, <span class="math inline">\(\alpha\)</span> and <span class="math inline">\(V_\textrm{cmax}\)</span>. At the moment the only supported random effect is a leaf-level effect, however fixed effects can be specified using standard R linear model notation, including interaction terms.</p>
-<p>This package includes functions for: loading photosynthetic data in the common LI-COR text-based format, performing visual QA/QC on that data, fitting the model to data, and generating diagnostic response-curve plots with confidence and predictive intervals. The diagnostic and QA/QC functions assume that data was collected as CO2 and light response curves (A-Ci and A-Q respectively). This assumption is not required for model fitting, so alternative sampling designs are allowed, as described by Dietze (2014).</p>
-<p>The version of the FvCB model used is described below, and at the moment does not include the TPU limitation term or temperature corrections (i.e. all data are assumed to be collected at the same leaf temperature, all parameters are specific to that temperature). It also assumes that electron transport rate, J, is a saturating function of <span class="math inline">\(J_{\textrm{max}}\)</span>.</p>
-<p><span class="math display">\[A_j = \frac{\alpha Q}{\sqrt{1+(\alpha^2 Q^2)/(J_\textrm{max}^2)}} \frac{C_i- \Gamma}{4 C_i + 8 \Gamma}\]</span></p>
-<p><span class="math display">\[A_c = V_{\textrm{cmax}} \frac{C_i - \Gamma}{C_i+ K_C (1+[O]/K_O) }\]</span></p>
-<p><span class="math display">\[A^{(m)} = min(A_j,A_c) - r\]</span></p>
-<p><span class="math display">\[A^{(o)} \sim N(A^{(m)},\tau)\]</span></p>
-<table class="table">
-<thead><tr class="header">
-<th>Parameter</th>
-<th>Symbol</th>
-<th>Definition</th>
-</tr></thead>
-<tbody>
-<tr class="odd">
-<td>alpha0</td>
-<td><span class="math inline">\(\alpha\)</span></td>
-<td>quantum yield (mol electrons/mole photon)</td>
-</tr>
-<tr class="even">
-<td>Jmax</td>
-<td><span class="math inline">\(J_{\textrm{max}}\)</span></td>
-<td>maximum electron transport</td>
-</tr>
-<tr class="odd">
-<td>cp</td>
-<td><span class="math inline">\(\Gamma\)</span></td>
-<td>CO2 compensation point</td>
-</tr>
-<tr class="even">
-<td>vmax0</td>
-<td><span class="math inline">\(V_{\textrm{cmax}}\)</span></td>
-<td>maximum Rubisco capacity (a.k.a Vcmax)</td>
-</tr>
-<tr class="odd">
-<td>r</td>
-<td><span class="math inline">\(R_\textrm{d}\)</span></td>
-<td>leaf respiration</td>
-</tr>
-<tr class="even">
-<td>tau</td>
-<td><span class="math inline">\(\tau\)</span></td>
-<td>residual precision</td>
-</tr>
-<tr class="odd">
-<td>q</td>
-<td><span class="math inline">\(Q\)</span></td>
-<td>PAR</td>
-</tr>
-<tr class="even">
-<td>pi</td>
-<td><span class="math inline">\(C_\textrm{i}\)</span></td>
-<td>CO2 concentration</td>
-</tr>
-</tbody>
-</table>
-<p>The ‘Parameter’ above refers to how the variable is referenced in the code, and thus the name that will be returned by the statistical fit.</p>
-<p>The hierarchical version of this model is equivalent to the standard model except that <span class="math inline">\(\alpha\)</span> and <span class="math inline">\(V_\textrm{cmax}\)</span> are mixed effect linear models of any covariates specified. These linear models assume uninformative Normal priors, while the random effects and residual errors are assumed to have Gamma priors on their precisions. All other priors are as described below in the example code. The FvCB model is fit using JAGS via the <em>rjags</em> package so outputs are <em>coda</em> mcmc.list objects that can be assessed and manipulated using standard tools in the <em>coda</em> package.</p>
-</div>
-<div id="install-package-from-github" class="section level2">
-<h2 class="hasAnchor">
-<a href="#install-package-from-github" class="anchor"></a>Install package from Github</h2>
-<p>You should only have to do this once, and you only have to do this if you are downloading just this package separate from the rest of PEcAn</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="op">!</span><span class="kw">require</span>(<span class="st">"PEcAn.photosynthesis"</span>, <span class="dt">character.only =</span> <span class="ot">TRUE</span>)) {
+          <div id="introduction" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#introduction" class="anchor"></a>Introduction
+            </h2>
+            <p>
+              This package is designed to fit the Farquhar, von Caemmerer, and
+              Berry (1980) photosynthesis model [FvCB model] to leaf-level
+              photosynthetic data. The statistical model generalizes the
+              Hierarchial Bayesian approach described in Feng and Dietze (2013).
+              The important advance that this approach provides is the ability
+              to include covariates (e.g. leaf traits) in a mixed effects model
+              describing key model parameters,
+              <span class="math inline">\(\alpha\)</span> and
+              <span class="math inline">\(V_\textrm{cmax}\)</span>. At the
+              moment the only supported random effect is a leaf-level effect,
+              however fixed effects can be specified using standard R linear
+              model notation, including interaction terms.
+            </p>
+            <p>
+              This package includes functions for: loading photosynthetic data
+              in the common LI-COR text-based format, performing visual QA/QC on
+              that data, fitting the model to data, and generating diagnostic
+              response-curve plots with confidence and predictive intervals. The
+              diagnostic and QA/QC functions assume that data was collected as
+              CO2 and light response curves (A-Ci and A-Q respectively). This
+              assumption is not required for model fitting, so alternative
+              sampling designs are allowed, as described by Dietze (2014).
+            </p>
+            <p>
+              The version of the FvCB model used is described below, and at the
+              moment does not include the TPU limitation term or temperature
+              corrections (i.e. all data are assumed to be collected at the same
+              leaf temperature, all parameters are specific to that
+              temperature). It also assumes that electron transport rate, J, is
+              a saturating function of
+              <span class="math inline">\(J_{\textrm{max}}\)</span>.
+            </p>
+            <p>
+              <span class="math display"
+                >\[A_j = \frac{\alpha Q}{\sqrt{1+(\alpha^2
+                Q^2)/(J_\textrm{max}^2)}} \frac{C_i- \Gamma}{4 C_i + 8
+                \Gamma}\]</span
+              >
+            </p>
+            <p>
+              <span class="math display"
+                >\[A_c = V_{\textrm{cmax}} \frac{C_i - \Gamma}{C_i+ K_C
+                (1+[O]/K_O) }\]</span
+              >
+            </p>
+            <p>
+              <span class="math display">\[A^{(m)} = min(A_j,A_c) - r\]</span>
+            </p>
+            <p>
+              <span class="math display">\[A^{(o)} \sim N(A^{(m)},\tau)\]</span>
+            </p>
+            <table class="table">
+              <thead>
+                <tr class="header">
+                  <th>Parameter</th>
+                  <th>Symbol</th>
+                  <th>Definition</th>
+                </tr>
+              </thead>
+              <tbody>
+                <tr class="odd">
+                  <td>alpha0</td>
+                  <td><span class="math inline">\(\alpha\)</span></td>
+                  <td>quantum yield (mol electrons/mole photon)</td>
+                </tr>
+                <tr class="even">
+                  <td>Jmax</td>
+                  <td><span class="math inline">\(J_{\textrm{max}}\)</span></td>
+                  <td>maximum electron transport</td>
+                </tr>
+                <tr class="odd">
+                  <td>cp</td>
+                  <td><span class="math inline">\(\Gamma\)</span></td>
+                  <td>CO2 compensation point</td>
+                </tr>
+                <tr class="even">
+                  <td>vmax0</td>
+                  <td>
+                    <span class="math inline">\(V_{\textrm{cmax}}\)</span>
+                  </td>
+                  <td>maximum Rubisco capacity (a.k.a Vcmax)</td>
+                </tr>
+                <tr class="odd">
+                  <td>r</td>
+                  <td><span class="math inline">\(R_\textrm{d}\)</span></td>
+                  <td>leaf respiration</td>
+                </tr>
+                <tr class="even">
+                  <td>tau</td>
+                  <td><span class="math inline">\(\tau\)</span></td>
+                  <td>residual precision</td>
+                </tr>
+                <tr class="odd">
+                  <td>q</td>
+                  <td><span class="math inline">\(Q\)</span></td>
+                  <td>PAR</td>
+                </tr>
+                <tr class="even">
+                  <td>pi</td>
+                  <td><span class="math inline">\(C_\textrm{i}\)</span></td>
+                  <td>CO2 concentration</td>
+                </tr>
+              </tbody>
+            </table>
+            <p>
+              The ‘Parameter’ above refers to how the variable is referenced in
+              the code, and thus the name that will be returned by the
+              statistical fit.
+            </p>
+            <p>
+              The hierarchical version of this model is equivalent to the
+              standard model except that
+              <span class="math inline">\(\alpha\)</span> and
+              <span class="math inline">\(V_\textrm{cmax}\)</span> are mixed
+              effect linear models of any covariates specified. These linear
+              models assume uninformative Normal priors, while the random
+              effects and residual errors are assumed to have Gamma priors on
+              their precisions. All other priors are as described below in the
+              example code. The FvCB model is fit using JAGS via the
+              <em>rjags</em> package so outputs are <em>coda</em> mcmc.list
+              objects that can be assessed and manipulated using standard tools
+              in the <em>coda</em> package.
+            </p>
+          </div>
+          <div id="install-package-from-github" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#install-package-from-github" class="anchor"></a>Install
+              package from Github
+            </h2>
+            <p>
+              You should only have to do this once, and you only have to do this
+              if you are downloading just this package separate from the rest of
+              PEcAn
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="cf">if</span> (<span class="op">!</span><span class="kw">require</span>(<span class="st">"PEcAn.photosynthesis"</span>, <span class="dt">character.only =</span> <span class="ot">TRUE</span>)) {
   devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"PecanProject/pecan/modules/photosynthesis"</span>) 
 }
-knitr<span class="op">::</span>opts_chunk<span class="op">$</span><span class="kw">set</span>(<span class="dt">cache =</span> <span class="ot">TRUE</span>)</code></pre></div>
-</div>
-<div id="load-library-and-example-data" class="section level2">
-<h2 class="hasAnchor">
-<a href="#load-library-and-example-data" class="anchor"></a>Load library and example data</h2>
-<p>In this example we are using a set of files that are built into the package, but you could easily replace <em>filenames</em> with vector of your own filenames, for example using <em>list.files</em> to look up all the files in a directory</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAn.photosynthesis)
+knitr<span class="op">::</span>opts_chunk<span class="op">$</span><span class="kw">set</span>(<span class="dt">cache =</span> <span class="ot">TRUE</span>)</code></pre>
+            </div>
+          </div>
+          <div id="load-library-and-example-data" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#load-library-and-example-data" class="anchor"></a>Load
+              library and example data
+            </h2>
+            <p>
+              In this example we are using a set of files that are built into
+              the package, but you could easily replace <em>filenames</em> with
+              vector of your own filenames, for example using
+              <em>list.files</em> to look up all the files in a directory
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">library</span>(PEcAn.photosynthesis)
 
 ## Get list of LI-COR 6400 file names (ASCII not xls)
 filenames &lt;-<span class="st"> </span><span class="kw">system.file</span>(<span class="st">"extdata"</span>, <span class="kw">paste0</span>(<span class="st">"flux-course-"</span>,<span class="kw">rep</span>(<span class="dv">1</span><span class="op">:</span><span class="dv">6</span>,<span class="dt">each=</span><span class="dv">2</span>),<span class="kw">c</span>(<span class="st">"aci"</span>,<span class="st">"aq"</span>)), <span class="dt">package =</span> <span class="st">"PEcAn.photosynthesis"</span>)
 
 ## Load files to a list
-master =<span class="st"> </span><span class="kw">lapply</span>(filenames, read_Licor)</code></pre></div>
-</div>
-<div id="run-qaqc-checks" class="section level2">
-<h2 class="hasAnchor">
-<a href="#run-qaqc-checks" class="anchor"></a>run QA/QC checks</h2>
-<p>The code below performs a set of interactive QA/QC checks on the LI-COR data that’s been loaded. Because it’s interactive it isn’t run when this vignette is knit.</p>
-<p>If you want to get a feel for how the code works you’ll want to run it first on just one file, rather than looping over all the files</p>
-<pre><code>master[[1]] &lt;- Licor_QC(master[[1]])</code></pre>
-<p>On the first screen you will be shown an A-Ci curve. Click on points that are outliers that you want to remove. Be aware that these points will not change color in <strong>THIS SCREEN</strong>, but will be updated in the next. Also be aware that if your data set is not an A-Ci curve (or contains both A-Ci and A-Q curves) there are points that may look like outliers just because they are data from the other curve. When you are done selecting outliers, click <strong>[esc]</strong> to move to the next screen.</p>
-<p>The second screen then verifies the status of point selections from the first screen and gives you an opportunity to unselect points that had been flagged as ‘fail’.</p>
-<p>The third and fourth screens are the equivalent plots for the A-Q (light response) curves.</p>
-<p>Finally, this function returns a copy of the original data with a new column, “QC”, added. This column will flag all passed values with 1, all unchecked values with 0, and all failed values with -1.</p>
-<p>The function Licor_QC has an optional arguement, <em>curve</em>, which can be set to either “ACi” or “AQ” if you only want to perform one of these diagnostics rather than both (which is the default).</p>
-<p>Also, the QC code attempts to automatically separate which points are part of the ACi curve from which parts are part of the AQ curve, based on how close points are to the the variable which is supposed to be held constant. The optional variable “tol” controls the tolerance of this filter, and is expressed as a proportion of the fixed value. The default value, 0.05, corresponds to a 5% deviation. For example, in the ACi curve the light level should be held constant so the code filters the PARi variable to find the mode and then included any data that’s within 5% of the mode in the ACi curve.</p>
-<p>Once you have a feel for the QA/QC function, you’ll want to run it for all the data you’ve loaded.</p>
-<pre><code>for(i in 1:length(master)){
+master =<span class="st"> </span><span class="kw">lapply</span>(filenames, read_Licor)</code></pre>
+            </div>
+          </div>
+          <div id="run-qaqc-checks" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#run-qaqc-checks" class="anchor"></a>run QA/QC checks
+            </h2>
+            <p>
+              The code below performs a set of interactive QA/QC checks on the
+              LI-COR data that’s been loaded. Because it’s interactive it isn’t
+              run when this vignette is knit.
+            </p>
+            <p>
+              If you want to get a feel for how the code works you’ll want to
+              run it first on just one file, rather than looping over all the
+              files
+            </p>
+            <pre><code>master[[1]] &lt;- Licor_QC(master[[1]])</code></pre>
+            <p>
+              On the first screen you will be shown an A-Ci curve. Click on
+              points that are outliers that you want to remove. Be aware that
+              these points will not change color in
+              <strong>THIS SCREEN</strong>, but will be updated in the next.
+              Also be aware that if your data set is not an A-Ci curve (or
+              contains both A-Ci and A-Q curves) there are points that may look
+              like outliers just because they are data from the other curve.
+              When you are done selecting outliers, click
+              <strong>[esc]</strong> to move to the next screen.
+            </p>
+            <p>
+              The second screen then verifies the status of point selections
+              from the first screen and gives you an opportunity to unselect
+              points that had been flagged as ‘fail’.
+            </p>
+            <p>
+              The third and fourth screens are the equivalent plots for the A-Q
+              (light response) curves.
+            </p>
+            <p>
+              Finally, this function returns a copy of the original data with a
+              new column, “QC”, added. This column will flag all passed values
+              with 1, all unchecked values with 0, and all failed values with
+              -1.
+            </p>
+            <p>
+              The function Licor_QC has an optional arguement, <em>curve</em>,
+              which can be set to either “ACi” or “AQ” if you only want to
+              perform one of these diagnostics rather than both (which is the
+              default).
+            </p>
+            <p>
+              Also, the QC code attempts to automatically separate which points
+              are part of the ACi curve from which parts are part of the AQ
+              curve, based on how close points are to the the variable which is
+              supposed to be held constant. The optional variable “tol” controls
+              the tolerance of this filter, and is expressed as a proportion of
+              the fixed value. The default value, 0.05, corresponds to a 5%
+              deviation. For example, in the ACi curve the light level should be
+              held constant so the code filters the PARi variable to find the
+              mode and then included any data that’s within 5% of the mode in
+              the ACi curve.
+            </p>
+            <p>
+              Once you have a feel for the QA/QC function, you’ll want to run it
+              for all the data you’ve loaded.
+            </p>
+            <pre><code>for(i in 1:length(master)){
     master[[i]] = Licor_QC(master[[i]])
 }</code></pre>
-</div>
-<div id="merge-data-into-one-data-frame" class="section level2">
-<h2 class="hasAnchor">
-<a href="#merge-data-into-one-data-frame" class="anchor"></a>Merge data into one data frame</h2>
-<p>Once data been’s checked we’ll merge it into one large data frame</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">dat &lt;-<span class="st"> </span><span class="kw">do.call</span>(<span class="st">"rbind"</span>, master)
+          </div>
+          <div id="merge-data-into-one-data-frame" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#merge-data-into-one-data-frame" class="anchor"></a>Merge
+              data into one data frame
+            </h2>
+            <p>
+              Once data been’s checked we’ll merge it into one large data frame
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">dat &lt;-<span class="st"> </span><span class="kw">do.call</span>(<span class="st">"rbind"</span>, master)
 
 ## if QC was done, remove both unchecked points and those that fail QC
 <span class="cf">if</span>(<span class="st">"QC"</span> <span class="op">%in%</span><span class="st"> </span><span class="kw">colnames</span>(dat)){
@@ -193,32 +401,76 @@ <h2 class="hasAnchor">
 } <span class="cf">else</span> {
   QC &lt;-<span class="st"> </span><span class="kw">rep</span>(<span class="dv">1</span>, <span class="kw">nrow</span>(dat))
   dat &lt;-<span class="st"> </span><span class="kw">cbind</span>(dat, QC)
-}</code></pre></div>
-</div>
-<div id="fit-fvcb-model-to-composite-data" class="section level2">
-<h2 class="hasAnchor">
-<a href="#fit-fvcb-model-to-composite-data" class="anchor"></a>Fit FvCB model to composite data</h2>
-<p>If you only want to fit the model to the data from one leaf you could do this as</p>
-<pre><code>fit1 &lt;- fitA(master[[1]])</code></pre>
-<p>Where the one required argument is the data frame of photosynthetic data. However, this code also allows use to fit the FvCB model to all of the data at once.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span>(<span class="kw">file.exists</span>(<span class="st">"fit.RData"</span>)){
+}</code></pre>
+            </div>
+          </div>
+          <div id="fit-fvcb-model-to-composite-data" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#fit-fvcb-model-to-composite-data" class="anchor"></a>Fit
+              FvCB model to composite data
+            </h2>
+            <p>
+              If you only want to fit the model to the data from one leaf you
+              could do this as
+            </p>
+            <pre><code>fit1 &lt;- fitA(master[[1]])</code></pre>
+            <p>
+              Where the one required argument is the data frame of
+              photosynthetic data. However, this code also allows use to fit the
+              FvCB model to all of the data at once.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="cf">if</span>(<span class="kw">file.exists</span>(<span class="st">"fit.RData"</span>)){
   <span class="kw">load</span>(<span class="st">"fit.RData"</span>)
 } <span class="cf">else</span>{
   fit &lt;-<span class="st"> </span><span class="kw"><a href="../reference/fitA.html">fitA</a></span>(dat)
   <span class="kw">save</span>(fit, <span class="dt">file =</span> <span class="st">"fit.RData"</span>)
-}</code></pre></div>
-<p>Because the MCMC can take a bit of time to run, in this example the code is written to load the existing fit if it exists, which just makes knitting the vignette more efficient.</p>
-<p>The returned object is a list with two mcmc.lists, “params” and “predict”, and the text of the JAGS model that was fit. We can look at this model below:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">writeLines</span>(fit<span class="op">$</span>model)</code></pre></div>
-<p>Note that the lines beginning with # are comments. Some of these comments are followed by specific tags, such as RLEAF.V and RLEAF.A, which are bits of code that will get turned on when we specify leaf random effects (see below).</p>
-<p>The ‘params’ mcmc.list contains the parameter estimate MCMC chains, which we can do standard MCMC diagnositics on.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">par</span>(<span class="dt">mfrow =</span> <span class="kw">c</span>(<span class="dv">2</span>, <span class="dv">1</span>))
+}</code></pre>
+            </div>
+            <p>
+              Because the MCMC can take a bit of time to run, in this example
+              the code is written to load the existing fit if it exists, which
+              just makes knitting the vignette more efficient.
+            </p>
+            <p>
+              The returned object is a list with two mcmc.lists, “params” and
+              “predict”, and the text of the JAGS model that was fit. We can
+              look at this model below:
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">writeLines</span>(fit<span class="op">$</span>model)</code></pre>
+            </div>
+            <p>
+              Note that the lines beginning with # are comments. Some of these
+              comments are followed by specific tags, such as RLEAF.V and
+              RLEAF.A, which are bits of code that will get turned on when we
+              specify leaf random effects (see below).
+            </p>
+            <p>
+              The ‘params’ mcmc.list contains the parameter estimate MCMC
+              chains, which we can do standard MCMC diagnositics on.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">par</span>(<span class="dt">mfrow =</span> <span class="kw">c</span>(<span class="dv">2</span>, <span class="dv">1</span>))
 <span class="kw">plot</span>(fit<span class="op">$</span>params, <span class="dt">auto.layout =</span> <span class="ot">FALSE</span>)    ## MCMC diagnostic plots
 <span class="kw">summary</span>(fit<span class="op">$</span>params) ## parameter estimates  
 <span class="kw">gelman.plot</span>(fit<span class="op">$</span>params, <span class="dt">auto.layout =</span> <span class="ot">FALSE</span>)
-<span class="kw">gelman.diag</span>(fit<span class="op">$</span>params)</code></pre></div>
-<p>The ‘predict’ object can be used to perform standard predictive diagnostics and to construct CI around curves</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">## predicted vs observed plot
+<span class="kw">gelman.diag</span>(fit<span class="op">$</span>params)</code></pre>
+            </div>
+            <p>
+              The ‘predict’ object can be used to perform standard predictive
+              diagnostics and to construct CI around curves
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">## predicted vs observed plot
 <span class="kw">par</span>(<span class="dt">mfrow =</span> <span class="kw">c</span>(<span class="dv">1</span>, <span class="dv">1</span>))
 mstats &lt;-<span class="st"> </span><span class="kw">summary</span>(fit<span class="op">$</span>predict)
 pmean &lt;-<span class="st"> </span>mstats<span class="op">$</span>statistics[<span class="kw">grep</span>(<span class="st">"pmean"</span>, <span class="kw">rownames</span>(mstats<span class="op">$</span>statistics)), <span class="dv">1</span>]
@@ -226,18 +478,61 @@ <h2 class="hasAnchor">
 <span class="kw">abline</span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dt">col =</span> <span class="dv">2</span>, <span class="dt">lwd =</span> <span class="dv">2</span>)
   
 ##   
-<span class="kw"><a href="../reference/plot_photo.html">plot_photo</a></span>(dat, fit)</code></pre></div>
-</div>
-<div id="refit-with-leaf-level-random-effects" class="section level2">
-<h2 class="hasAnchor">
-<a href="#refit-with-leaf-level-random-effects" class="anchor"></a>Refit with leaf-level random effects</h2>
-<p>Next, let’s look at how to specify leaf-level random effects in the model. To do so we’re going to add an extra arguement to the function, which is a list of model specifications.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">A.model &lt;-<span class="st"> </span><span class="kw">list</span>(<span class="dt">a.fixed =</span> <span class="ot">NULL</span>, <span class="dt">a.random =</span> <span class="st">"leaf"</span>, 
+<span class="kw"><a href="../reference/plot_photo.html">plot_photo</a></span>(dat, fit)</code></pre>
+            </div>
+          </div>
+          <div id="refit-with-leaf-level-random-effects" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#refit-with-leaf-level-random-effects" class="anchor"></a
+              >Refit with leaf-level random effects
+            </h2>
+            <p>
+              Next, let’s look at how to specify leaf-level random effects in
+              the model. To do so we’re going to add an extra arguement to the
+              function, which is a list of model specifications.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">A.model &lt;-<span class="st"> </span><span class="kw">list</span>(<span class="dt">a.fixed =</span> <span class="ot">NULL</span>, <span class="dt">a.random =</span> <span class="st">"leaf"</span>, 
                 <span class="dt">V.fixed =</span> <span class="ot">NULL</span>, <span class="dt">V.random =</span> <span class="st">"leaf"</span>, 
-                <span class="dt">n.iter =</span> <span class="dv">5000</span>, <span class="dt">match =</span> <span class="st">"fname"</span>)</code></pre></div>
-<p>In this list a refers to <span class="math inline">\(\alpha\)</span> and V refers to <span class="math inline">\(V_\textrm{cmax}\)</span>. Fixed refers to the specification of the fixed effects, which we’re leaving unspecified at the moment (NULL). Random refers to the specification of random effects, which we’re setting to ‘leaf’ in order allow <span class="math inline">\(alpha\)</span> and <span class="math inline">\(V_\textrm{cmax}\)</span> to vary on a leaf-by-leaf basis. Note: at the moment ‘leaf’ is the only valid random effect, though in the future we hope to allow the specification of arbitrary random effects in a covariate file (see next section for how to specify covariates). Next, <em>n.iter</em> refers to the number of MCMC iterations run by the model. Here we’re setting that to 5000, which is the default. You can increase this if you find the model isn’t converging. For example, if you wanted to increase the iterations with the previous default model, you would set all the fixed and random effects to NULL but increase n.iter. Finally, match is the variable used both to group records into individual leaves and to match individual leaves to covariate data. If you look at our photosynthesis dataframe, <em>dat</em>, you’ll see that it has a column <em>fname</em> that corresponds to the filename the data was read from (here we’re assuming each file contains the data for one leaf, but it’s not hard to add columns to your data if you want to group things in other ways)</p>
-<p>Once the model is specified, the fitting and diagnostics are the same as before.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span>(<span class="kw">file.exists</span>(<span class="st">"fitI.RData"</span>)){
+                <span class="dt">n.iter =</span> <span class="dv">5000</span>, <span class="dt">match =</span> <span class="st">"fname"</span>)</code></pre>
+            </div>
+            <p>
+              In this list a refers to
+              <span class="math inline">\(\alpha\)</span> and V refers to
+              <span class="math inline">\(V_\textrm{cmax}\)</span>. Fixed refers
+              to the specification of the fixed effects, which we’re leaving
+              unspecified at the moment (NULL). Random refers to the
+              specification of random effects, which we’re setting to ‘leaf’ in
+              order allow <span class="math inline">\(alpha\)</span> and
+              <span class="math inline">\(V_\textrm{cmax}\)</span> to vary on a
+              leaf-by-leaf basis. Note: at the moment ‘leaf’ is the only valid
+              random effect, though in the future we hope to allow the
+              specification of arbitrary random effects in a covariate file (see
+              next section for how to specify covariates). Next,
+              <em>n.iter</em> refers to the number of MCMC iterations run by the
+              model. Here we’re setting that to 5000, which is the default. You
+              can increase this if you find the model isn’t converging. For
+              example, if you wanted to increase the iterations with the
+              previous default model, you would set all the fixed and random
+              effects to NULL but increase n.iter. Finally, match is the
+              variable used both to group records into individual leaves and to
+              match individual leaves to covariate data. If you look at our
+              photosynthesis dataframe, <em>dat</em>, you’ll see that it has a
+              column <em>fname</em> that corresponds to the filename the data
+              was read from (here we’re assuming each file contains the data for
+              one leaf, but it’s not hard to add columns to your data if you
+              want to group things in other ways)
+            </p>
+            <p>
+              Once the model is specified, the fitting and diagnostics are the
+              same as before.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="cf">if</span>(<span class="kw">file.exists</span>(<span class="st">"fitI.RData"</span>)){
   <span class="kw">load</span>(<span class="st">"fitI.RData"</span>)
 } <span class="cf">else</span>{
   fitI &lt;-<span class="st"> </span><span class="kw"><a href="../reference/fitA.html">fitA</a></span>(dat,<span class="dt">model =</span> A.model)
@@ -257,22 +552,68 @@ <h2 class="hasAnchor">
 <span class="kw">abline</span>(<span class="dv">0</span>,<span class="dv">1</span>,<span class="dt">col=</span><span class="dv">2</span>,<span class="dt">lwd=</span><span class="dv">2</span>)
   
 ##   
-<span class="kw"><a href="../reference/plot_photo.html">plot_photo</a></span>(dat,fitI)</code></pre></div>
-</div>
-<div id="fitting-the-model-with-covariates" class="section level2">
-<h2 class="hasAnchor">
-<a href="#fitting-the-model-with-covariates" class="anchor"></a>Fitting the model with covariates</h2>
-<p>Next, let’s look at how to fit a model that includes covariates. To begin with let’s load up some covariate data. In this specific case the covariate data, leaf % Nitrogen, is simulated because no covariates were actually measured for these leaves.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">cov.data =<span class="st"> </span><span class="kw">read.csv</span>(<span class="kw">system.file</span>(<span class="st">"extdata"</span>, <span class="st">"cov.csv"</span>, <span class="dt">package =</span> <span class="st">"PEcAn.photosynthesis"</span>))
-knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(cov.data)</code></pre></div>
-<p>To define this model we’ll again define a list of model specifications. Specifically we are going to set <span class="math inline">\(Vcmax\)</span> to be linear functions of leaf N. To do this we’ll set V.fixed “N” and we’ll set V.random to NULL to turn off the leaf random effect. For this example we’ll leave <span class="math inline">\(\alpha\)</span> as random.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">C.model &lt;-<span class="st"> </span><span class="kw">list</span>(<span class="dt">a.fixed =</span> <span class="ot">NULL</span>, <span class="dt">a.random =</span> <span class="st">"leaf"</span>, 
+<span class="kw"><a href="../reference/plot_photo.html">plot_photo</a></span>(dat,fitI)</code></pre>
+            </div>
+          </div>
+          <div id="fitting-the-model-with-covariates" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#fitting-the-model-with-covariates" class="anchor"></a
+              >Fitting the model with covariates
+            </h2>
+            <p>
+              Next, let’s look at how to fit a model that includes covariates.
+              To begin with let’s load up some covariate data. In this specific
+              case the covariate data, leaf % Nitrogen, is simulated because no
+              covariates were actually measured for these leaves.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">cov.data =<span class="st"> </span><span class="kw">read.csv</span>(<span class="kw">system.file</span>(<span class="st">"extdata"</span>, <span class="st">"cov.csv"</span>, <span class="dt">package =</span> <span class="st">"PEcAn.photosynthesis"</span>))
+knitr<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/knitr/topics/kable">kable</a></span>(cov.data)</code></pre>
+            </div>
+            <p>
+              To define this model we’ll again define a list of model
+              specifications. Specifically we are going to set
+              <span class="math inline">\(Vcmax\)</span> to be linear functions
+              of leaf N. To do this we’ll set V.fixed “N” and we’ll set V.random
+              to NULL to turn off the leaf random effect. For this example we’ll
+              leave <span class="math inline">\(\alpha\)</span> as random.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r">C.model &lt;-<span class="st"> </span><span class="kw">list</span>(<span class="dt">a.fixed =</span> <span class="ot">NULL</span>, <span class="dt">a.random =</span> <span class="st">"leaf"</span>, 
                 <span class="dt">V.fixed=</span> <span class="st">"N"</span>, <span class="dt">V.random =</span> <span class="ot">NULL</span>,
-                <span class="dt">n.iter =</span> <span class="dv">5000</span>, <span class="dt">match =</span> <span class="st">"fname"</span>)</code></pre></div>
-<p>If we had additional covariates, for example SLA and chl (leaf chlorophyll), we might write that model as “N + SLA + chl” if we just wanted the direct effects and “N + SLA + chl + N<em>SLA + N</em>chl + SLA*chl" if we also wanted the pairwise interactions. That said, in this case we don’t have a large enough sample size to justify so many covariates.</p>
-<p>Also note that the rows in the photosynthesis data are matched to rows in the covariate data using the column specified in the arguement ‘match’. The default for this, fname, is the filename for the photosynthetic data. Typically one file corresponds to one leaf so each set of traits match to each file. If you have your data organized differently you’ll want to specify a different column match.</p>
-<p>To call the <em>fitA</em> function we now have to pass not just the photosynthetic data and the model, but also the covariate data. Otherwise the fit and diagnostics are identical to before.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span>(<span class="kw">file.exists</span>(<span class="st">"fitC.RData"</span>)){
+                <span class="dt">n.iter =</span> <span class="dv">5000</span>, <span class="dt">match =</span> <span class="st">"fname"</span>)</code></pre>
+            </div>
+            <p>
+              If we had additional covariates, for example SLA and chl (leaf
+              chlorophyll), we might write that model as “N + SLA + chl” if we
+              just wanted the direct effects and “N + SLA + chl + N<em
+                >SLA + N</em
+              >chl + SLA*chl" if we also wanted the pairwise interactions. That
+              said, in this case we don’t have a large enough sample size to
+              justify so many covariates.
+            </p>
+            <p>
+              Also note that the rows in the photosynthesis data are matched to
+              rows in the covariate data using the column specified in the
+              arguement ‘match’. The default for this, fname, is the filename
+              for the photosynthetic data. Typically one file corresponds to one
+              leaf so each set of traits match to each file. If you have your
+              data organized differently you’ll want to specify a different
+              column match.
+            </p>
+            <p>
+              To call the <em>fitA</em> function we now have to pass not just
+              the photosynthetic data and the model, but also the covariate
+              data. Otherwise the fit and diagnostics are identical to before.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="cf">if</span>(<span class="kw">file.exists</span>(<span class="st">"fitC.RData"</span>)){
   <span class="kw">load</span>(<span class="st">"fitC.RData"</span>)
 } <span class="cf">else</span>{
   fitC &lt;-<span class="st"> </span><span class="kw"><a href="../reference/fitA.html">fitA</a></span>(dat,cov.data,<span class="dt">model =</span> C.model)
@@ -293,50 +634,87 @@ <h2 class="hasAnchor">
 <span class="kw">abline</span>(<span class="dv">0</span>,<span class="dv">1</span>,<span class="dt">col=</span><span class="dv">2</span>,<span class="dt">lwd=</span><span class="dv">2</span>)
   
 ##   
-<span class="kw"><a href="../reference/plot_photo.html">plot_photo</a></span>(dat, fitC)</code></pre></div>
-</div>
-<div id="citations" class="section level2">
-<h2 class="hasAnchor">
-<a href="#citations" class="anchor"></a>Citations</h2>
-<p>Dietze, M.C. (2014). Gaps in knowledge and data driving uncertainty in models of photosynthesis. Photosynth. Res., 19, 3–14.</p>
-<p>Farquhar, G., Caemmerer, S. &amp; Berry, J.A. (1980). A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta, 149, 78–90.</p>
-<p>Feng, X. &amp; Dietze, M.C. (2013). Scale dependence in the effects of leaf ecophysiological traits on photosynthesis: Bayesian parameterization of photosynthesis models. New Phytol., 200, 1132–1144.</p>
-</div>
-  </div>
+<span class="kw"><a href="../reference/plot_photo.html">plot_photo</a></span>(dat, fitC)</code></pre>
+            </div>
+          </div>
+          <div id="citations" class="section level2">
+            <h2 class="hasAnchor">
+              <a href="#citations" class="anchor"></a>Citations
+            </h2>
+            <p>
+              Dietze, M.C. (2014). Gaps in knowledge and data driving
+              uncertainty in models of photosynthesis. Photosynth. Res., 19,
+              3–14.
+            </p>
+            <p>
+              Farquhar, G., Caemmerer, S. &amp; Berry, J.A. (1980). A
+              biochemical model of photosynthetic CO2 assimilation in leaves of
+              C3 species. Planta, 149, 78–90.
+            </p>
+            <p>
+              Feng, X. &amp; Dietze, M.C. (2013). Scale dependence in the
+              effects of leaf ecophysiological traits on photosynthesis:
+              Bayesian parameterization of photosynthesis models. New Phytol.,
+              200, 1132–1144.
+            </p>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#introduction">Introduction</a></li>
-      <li><a href="#install-package-from-github">Install package from Github</a></li>
-      <li><a href="#load-library-and-example-data">Load library and example data</a></li>
-      <li><a href="#run-qaqc-checks">run QA/QC checks</a></li>
-      <li><a href="#merge-data-into-one-data-frame">Merge data into one data frame</a></li>
-      <li><a href="#fit-fvcb-model-to-composite-data">Fit FvCB model to composite data</a></li>
-      <li><a href="#refit-with-leaf-level-random-effects">Refit with leaf-level random effects</a></li>
-      <li><a href="#fitting-the-model-with-covariates">Fitting the model with covariates</a></li>
-      <li><a href="#citations">Citations</a></li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li><a href="#introduction">Introduction</a></li>
+              <li>
+                <a href="#install-package-from-github"
+                  >Install package from Github</a
+                >
+              </li>
+              <li>
+                <a href="#load-library-and-example-data"
+                  >Load library and example data</a
+                >
+              </li>
+              <li><a href="#run-qaqc-checks">run QA/QC checks</a></li>
+              <li>
+                <a href="#merge-data-into-one-data-frame"
+                  >Merge data into one data frame</a
+                >
+              </li>
+              <li>
+                <a href="#fit-fvcb-model-to-composite-data"
+                  >Fit FvCB model to composite data</a
+                >
+              </li>
+              <li>
+                <a href="#refit-with-leaf-level-random-effects"
+                  >Refit with leaf-level random effects</a
+                >
+              </li>
+              <li>
+                <a href="#fitting-the-model-with-covariates"
+                  >Fitting the model with covariates</a
+                >
+              </li>
+              <li><a href="#citations">Citations</a></li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.photosynthesis</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/ResponseCurves.html">Fitting Hierarchical Bayes photosynthetic response curves</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html"
+                  >PEcAn.photosynthesis</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/ResponseCurves.html"
+                        >Fitting Hierarchical Bayes photosynthetic response
+                        curves</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
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+    </div>
   </body>
 </html>
-
diff --git a/modules/photosynthesis/docs/docsearch.css b/modules/photosynthesis/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/photosynthesis/docs/docsearch.css
+++ b/modules/photosynthesis/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/photosynthesis/docs/docsearch.js b/modules/photosynthesis/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/photosynthesis/docs/docsearch.js
+++ b/modules/photosynthesis/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/photosynthesis/docs/index.html b/modules/photosynthesis/docs/index.html
index 9309f68..070994a 100644
--- a/modules/photosynthesis/docs/index.html
+++ b/modules/photosynthesis/docs/index.html
@@ -1,127 +1,196 @@
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-<title>PEcAn functions used for leaf-level photosynthesis calculations • PEcAn.photosynthesis</title>
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-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for leaf-level photosynthesis calculations">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for leaf-level photosynthesis calculations •
+      PEcAn.photosynthesis
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
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+    <script
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    <!-- sticky kit -->
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+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for leaf-level photosynthesis calculations"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     workflow management tool that is designed to simplify the management of
     model parameterization, execution, and analysis. The goal of PECAn is to
     streamline the interaction between data and models, and to improve the
     efficacy of scientific investigation. The PEcAn.photosynthesis package
     contains functions used in the Hierarchical Bayesian calibration of the
-    Farquhar et al 1980 model.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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-</head>
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+    Farquhar et al 1980 model."
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+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.photosynthesis</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
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-      <a href="articles/ResponseCurves.html">Fitting Hierarchical Bayes photosynthetic response curves</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
-    workflow management tool that is designed to simplify the management of
-    model parameterization, execution, and analysis. The goal of PECAn is to
-    streamline the interaction between data and models, and to improve the
-    efficacy of scientific investigation. The PEcAn.photosynthesis package
-    contains functions used in the Hierarchical Bayesian calibration of the
-    Farquhar et al 1980 model.
-  </div>
-
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-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
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-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
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-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
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+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html"
+                  >PEcAn.photosynthesis</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/ResponseCurves.html"
+                        >Fitting Hierarchical Bayes photosynthetic response
+                        curves</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation. The
+          PEcAn.photosynthesis package contains functions used in the
+          Hierarchical Bayesian calibration of the Farquhar et al 1980 model.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
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+    </div>
   </body>
 </html>
diff --git a/modules/photosynthesis/docs/pkgdown.css b/modules/photosynthesis/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/photosynthesis/docs/pkgdown.css
+++ b/modules/photosynthesis/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
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-  display:inline-block;
+  display: inline-block;
   width: 30px;
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@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
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@@ -107,7 +110,6 @@ a.anchor {
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-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
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+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
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+pre,
+code {
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   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/photosynthesis/docs/pkgdown.js b/modules/photosynthesis/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/photosynthesis/docs/pkgdown.js
+++ b/modules/photosynthesis/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/photosynthesis/docs/reference/Licor_QC.html b/modules/photosynthesis/docs/reference/Licor_QC.html
index 25251fa..9d2e995 100644
--- a/modules/photosynthesis/docs/reference/Licor_QC.html
+++ b/modules/photosynthesis/docs/reference/Licor_QC.html
@@ -2,167 +2,217 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Licor_QC — Licor_QC • PEcAn.photosynthesis</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
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-
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Licor_QC — Licor_QC" />
-
-<meta property="og:description" content="Licor_QC" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Licor_QC — Licor_QC • PEcAn.photosynthesis</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Licor_QC — Licor_QC" />
+
+    <meta property="og:description" content="Licor_QC" />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.photosynthesis</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/ResponseCurves.html">Fitting Hierarchical Bayes photosynthetic response curves</a>
-    </li>
-  </ul>
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-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
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-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.photosynthesis</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ResponseCurves.html"
+                        >Fitting Hierarchical Bayes photosynthetic response
+                        curves</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Licor_QC</h1>
-    
-    <div class="hidden name"><code>Licor_QC.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Licor_QC</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>Licor_QC</span>(<span class='no'>dat</span>, <span class='kw'>curve</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"ACi"</span>, <span class='st'>"AQ"</span>), <span class='kw'>tol</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>data frame</p></td>
-    </tr>
-    <tr>
-      <th>curve</th>
-      <td><p>Whether to do Quality Control by examining the 'ACi' curve, the 'AQ' curve, or both</p></td>
-    </tr>
-    <tr>
-      <th>tol</th>
-      <td><p>Code automatically tries to separate ACi and AQ curves in the same dataset by detecting the 'reference' condition for light and CO2 respectively. This is the relative error around the mode in that detection.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Licor_QC</h1>
+
+            <div class="hidden name"><code>Licor_QC.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Licor_QC</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>Licor_QC</span>(<span class='no'>dat</span>, <span class='kw'>curve</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"ACi"</span>, <span class='st'>"AQ"</span>), <span class='kw'>tol</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td><p>data frame</p></td>
+            </tr>
+            <tr>
+              <th>curve</th>
+              <td>
+                <p>
+                  Whether to do Quality Control by examining the 'ACi' curve,
+                  the 'AQ' curve, or both
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>tol</th>
+              <td>
+                <p>
+                  Code automatically tries to separate ACi and AQ curves in the
+                  same dataset by detecting the 'reference' condition for light
+                  and CO2 respectively. This is the relative error around the
+                  mode in that detection.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
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index 0c7f117..b5c092c 100644
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@@ -2,149 +2,186 @@
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+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/ResponseCurves.html"
+                        >Fitting Hierarchical Bayes photosynthetic response
+                        curves</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>shaded confidence interval</h1>
-    
-    <div class="hidden name"><code>ciEnvelope.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>shaded confidence interval</h1>
 
-    <div class="ref-description">
-    
-    <p>shaded confidence interval</p>
-    
-    </div>
+            <div class="hidden name"><code>ciEnvelope.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>ciEnvelope</span>(<span class='no'>x</span>, <span class='no'>ylo</span>, <span class='no'>yhi</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='st'>"lightgrey"</span>, <span class='no'>...</span>)</pre>
-        
+          <div class="ref-description">
+            <p>shaded confidence interval</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>ciEnvelope</span>(<span class='no'>x</span>, <span class='no'>ylo</span>, <span class='no'>yhi</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='st'>"lightgrey"</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
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-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/photosynthesis/docs/reference/estimate_mode.html b/modules/photosynthesis/docs/reference/estimate_mode.html
index eb6e2dc..e48a70f 100644
--- a/modules/photosynthesis/docs/reference/estimate_mode.html
+++ b/modules/photosynthesis/docs/reference/estimate_mode.html
@@ -2,151 +2,181 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/ResponseCurves.html"
+                        >Fitting Hierarchical Bayes photosynthetic response
+                        curves</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>estimate_mode</h1>
-    
-    <div class="hidden name"><code>estimate_mode.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>estimate_mode</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>estimate_mode</h1>
 
-    <pre class="usage"><span class='fu'>estimate_mode</span>(<span class='no'>x</span>, <span class='kw'>adjust</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)</pre>
-        
+            <div class="hidden name"><code>estimate_mode.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>estimate_mode</p>
+          </div>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <pre
+            class="usage"
+          ><span class='fu'>estimate_mode</span>(<span class='no'>x</span>, <span class='kw'>adjust</span> <span class='kw'>=</span> <span class='fl'>0.1</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-Xiaohui Feng
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze Xiaohui Feng
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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-
+        <div class="copyright">
+          <p>Developed by .</p>
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diff --git a/modules/photosynthesis/docs/reference/fitA.html b/modules/photosynthesis/docs/reference/fitA.html
index abc36e0..a9627e1 100644
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+++ b/modules/photosynthesis/docs/reference/fitA.html
@@ -2,170 +2,240 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-  </a>
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-      <a href="../articles/ResponseCurves.html">Fitting Hierarchical Bayes photosynthetic response curves</a>
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+                >
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+                  <a href="../index.html">
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+                    data-toggle="dropdown"
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+                      <a href="../articles/ResponseCurves.html"
+                        >Fitting Hierarchical Bayes photosynthetic response
+                        curves</a
+                      >
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+                  </ul>
+                </li>
+              </ul>
+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>fitA</h1>
-    
-    <div class="hidden name"><code>fitA.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>fitA</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>fitA</span>(<span class='no'>flux.data</span>, <span class='kw'>cov.data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>flux.data</th>
-      <td><p>data.frame of Licor data, concatenated by rows, and with a leading column 'fname' that is used to count the number of curves and match to covariates</p></td>
-    </tr>
-    <tr>
-      <th>cov.data</th>
-      <td><p>data.frame of covariate data. Column names used in formulas</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>list including at least 6 components: the fixed effects model for alpha (a.fixed) and Vcmax (V.fixed), the random effects for these (a.random, V.random), the variable used to match the gas-exchange and covariate data (match), and the number of MCMC interations (n.iter). Additional optional arguments: TPU = TRUE turns on TPU limitation; Temp == 'Bernacchi01' turns on the Bernacchi et al 2001 temperature correction. If this is turned on all parameters are estimated for 25C, otherwise no temperature correction is applied. Setting Temp = 'June2004' will turn on the June et al 2004 Funct Plant Biol temperature correction to Jmax. Note: these two corrections are not mutually exclusive, you can set Temp = c('June2004','Bernacchi2001')</p>
-<p>Right now the fixed effects are specified as a string using the standard R lm formula syntax, but without the LHS variable (e.g. '~ SLA + chl + SLA:chl'). The tilde is optional. For random effects, the two options right now are just 'leaf' for leaf-level random effects and NULL. 'model' has a default that sets all effects to NULL (fit one curve to all data) and n.iter=1000.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-Xiaohui Feng
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>fitA</h1>
+
+            <div class="hidden name"><code>fitA.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>fitA</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>fitA</span>(<span class='no'>flux.data</span>, <span class='kw'>cov.data</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>flux.data</th>
+              <td>
+                <p>
+                  data.frame of Licor data, concatenated by rows, and with a
+                  leading column 'fname' that is used to count the number of
+                  curves and match to covariates
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>cov.data</th>
+              <td>
+                <p>
+                  data.frame of covariate data. Column names used in formulas
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td>
+                <p>
+                  list including at least 6 components: the fixed effects model
+                  for alpha (a.fixed) and Vcmax (V.fixed), the random effects
+                  for these (a.random, V.random), the variable used to match the
+                  gas-exchange and covariate data (match), and the number of
+                  MCMC interations (n.iter). Additional optional arguments: TPU
+                  = TRUE turns on TPU limitation; Temp == 'Bernacchi01' turns on
+                  the Bernacchi et al 2001 temperature correction. If this is
+                  turned on all parameters are estimated for 25C, otherwise no
+                  temperature correction is applied. Setting Temp = 'June2004'
+                  will turn on the June et al 2004 Funct Plant Biol temperature
+                  correction to Jmax. Note: these two corrections are not
+                  mutually exclusive, you can set Temp =
+                  c('June2004','Bernacchi2001')
+                </p>
+                <p>
+                  Right now the fixed effects are specified as a string using
+                  the standard R lm formula syntax, but without the LHS variable
+                  (e.g. '~ SLA + chl + SLA:chl'). The tilde is optional. For
+                  random effects, the two options right now are just 'leaf' for
+                  leaf-level random effects and NULL. 'model' has a default that
+                  sets all effects to NULL (fit one curve to all data) and
+                  n.iter=1000.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze Xiaohui Feng
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/photosynthesis/docs/reference/index.html b/modules/photosynthesis/docs/reference/index.html
index a33a07f..7bae1f1 100644
--- a/modules/photosynthesis/docs/reference/index.html
+++ b/modules/photosynthesis/docs/reference/index.html
@@ -2,186 +2,236 @@
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 <html>
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+
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+    ></script>
+    <!-- Bootstrap -->
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-      <tr>
-        
-        <td>
-          <p><code><a href="Licor_QC.html">Licor_QC()</a></code> </p>
-        </td>
-        <td><p>Licor_QC</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="ciEnvelope.html">ciEnvelope()</a></code> </p>
-        </td>
-        <td><p>shaded confidence interval</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="estimate_mode.html">estimate_mode()</a></code> </p>
-        </td>
-        <td><p>estimate_mode</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="fitA.html">fitA()</a></code> </p>
-        </td>
-        <td><p>fitA</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot_photo.html">plot_photo()</a></code> </p>
-        </td>
-        <td><p>plot_photo</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read_Licor.html">read_Licor()</a></code> </p>
-        </td>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
+
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
+
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="Licor_QC.html">Licor_QC()</a></code>
+                  </p>
+                </td>
+                <td><p>Licor_QC</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ciEnvelope.html">ciEnvelope()</a></code>
+                  </p>
+                </td>
+                <td><p>shaded confidence interval</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="estimate_mode.html">estimate_mode()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>estimate_mode</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="fitA.html">fitA()</a></code>
+                  </p>
+                </td>
+                <td><p>fitA</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="plot_photo.html">plot_photo()</a></code>
+                  </p>
+                </td>
+                <td><p>plot_photo</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="read_Licor.html">read_Licor()</a></code>
+                  </p>
+                </td>
+                <td><p>read_Licor</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/photosynthesis/docs/reference/plot_photo.html b/modules/photosynthesis/docs/reference/plot_photo.html
index d82f6df..f4b8b56 100644
--- a/modules/photosynthesis/docs/reference/plot_photo.html
+++ b/modules/photosynthesis/docs/reference/plot_photo.html
@@ -2,150 +2,182 @@
 <!DOCTYPE html>
 <html>
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
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+                >
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+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/ResponseCurves.html"
+                        >Fitting Hierarchical Bayes photosynthetic response
+                        curves</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
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+            <!--/.nav-collapse -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>plot_photo</h1>
-    
-    <div class="hidden name"><code>plot_photo.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>plot_photo</h1>
 
-    <div class="ref-description">
-    
-    <p>plot_photo</p>
-    
-    </div>
+            <div class="hidden name"><code>plot_photo.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>plot_photo</span>(<span class='no'>data</span>, <span class='no'>out</span>, <span class='kw'>curve</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"ACi"</span>, <span class='st'>"AQ"</span>), <span class='kw'>tol</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
-  <span class='kw'>byLeaf</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-        
+          <div class="ref-description">
+            <p>plot_photo</p>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <pre
+            class="usage"
+          ><span class='fu'>plot_photo</span>(<span class='no'>data</span>, <span class='no'>out</span>, <span class='kw'>curve</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"ACi"</span>, <span class='st'>"AQ"</span>), <span class='kw'>tol</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
+  <span class='kw'>byLeaf</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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 </html>
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diff --git a/modules/photosynthesis/docs/reference/read_Licor.html b/modules/photosynthesis/docs/reference/read_Licor.html
index 199cb07..c45f550 100644
--- a/modules/photosynthesis/docs/reference/read_Licor.html
+++ b/modules/photosynthesis/docs/reference/read_Licor.html
@@ -2,167 +2,205 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
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+
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+    <script src="../pkgdown.js"></script>
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+    <meta name="twitter:card" content="summary" />
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.photosynthesis</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+                  >PEcAn.photosynthesis</a
+                >
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+                  class="label label-default"
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+                  >1.6.0</span
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+                  <ul class="dropdown-menu" role="menu">
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+                      <a href="../articles/ResponseCurves.html"
+                        >Fitting Hierarchical Bayes photosynthetic response
+                        curves</a
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+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>read_Licor</h1>
-    
-    <div class="hidden name"><code>read_Licor.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>read_Licor</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read_Licor</span>(<span class='no'>filename</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>filename</th>
-      <td><p>name of the file to read</p></td>
-    </tr>
-    <tr>
-      <th>sep</th>
-      <td><p>file delimiter. defaults to tab</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>optional arguements forwarded to read.table</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>read_Licor</h1>
+
+            <div class="hidden name"><code>read_Licor.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>read_Licor</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read_Licor</span>(<span class='no'>filename</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>filename</th>
+              <td><p>name of the file to read</p></td>
+            </tr>
+            <tr>
+              <th>sep</th>
+              <td><p>file delimiter. defaults to tab</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>optional arguements forwarded to read.table</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze
+        </div>
+      </div>
 
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diff --git a/modules/priors/docs/LICENSE-text.html b/modules/priors/docs/LICENSE-text.html
index 5839407..d46dd54 100644
--- a/modules/priors/docs/LICENSE-text.html
+++ b/modules/priors/docs/LICENSE-text.html
@@ -2,109 +2,144 @@
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+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -138,27 +173,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/priors/docs/articles/index.html b/modules/priors/docs/articles/index.html
index 6c51075..cb5afbf 100644
--- a/modules/priors/docs/articles/index.html
+++ b/modules/priors/docs/articles/index.html
@@ -2,133 +2,164 @@
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 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Font Awesome icons -->
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
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+    <link
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+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    <!-- pkgdown -->
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+    <script src="../pkgdown.js"></script>
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+    <meta property="og:title" content="Articles" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
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-</li>
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-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.priors</a>
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+                  class="label label-default"
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+                  data-placement="bottom"
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+                  >1.6.0</span
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+            </div>
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-      <h1>Articles</h1>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Articles</h1>
+          </div>
 
-    <div class="section ">
-      <h3>All vignettes</h3>
-      <p class="section-desc"></p>
+          <div class="section ">
+            <h3>All vignettes</h3>
+            <p class="section-desc"></p>
 
-      <ul>
-        <li><a href="priors_demo.html">UNKNOWN TITLE</a></li>
-      </ul>
-    </div>
-  </div>
-</div>
+            <ul>
+              <li><a href="priors_demo.html">UNKNOWN TITLE</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/priors/docs/articles/priors_demo.html b/modules/priors/docs/articles/priors_demo.html
index c77f620..047650a 100644
--- a/modules/priors/docs/articles/priors_demo.html
+++ b/modules/priors/docs/articles/priors_demo.html
@@ -1,133 +1,305 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
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-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
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+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+    <meta property="og:title" content="" />
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+    <meta name="twitter:card" content="summary" />
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     <div class="container template-article">
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+      <header>
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+                type="button"
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+                data-toggle="collapse"
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+              </button>
+              <span class="navbar-brand">
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+                <span
+                  class="label label-default"
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-      
-      </header><div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header toc-ignore">
-      <h1></h1>
-            
-      
-      
-      <div class="hidden name"><code>priors_demo.Rmd</code></div>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
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+              <ul class="nav navbar-nav navbar-right"></ul>
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+          <!--/.container -->
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+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header toc-ignore">
+            <h1></h1>
 
-    </div>
+            <div class="hidden name"><code>priors_demo.Rmd</code></div>
+          </div>
 
-    
-    
-<div id="generating-priors-based-on-data-and-or-expert-knowledge" class="section level1">
-<h1 class="hasAnchor">
-<a href="#generating-priors-based-on-data-and-or-expert-knowledge" class="anchor"></a>Generating Priors based on Data and / or Expert knowledge:</h1>
-<div id="fitting-priors-to-data-point-estimates-all-grass-species-in-glopnet-" class="section level2">
-<h2 class="hasAnchor">
-<a href="#fitting-priors-to-data-point-estimates-all-grass-species-in-glopnet-" class="anchor"></a>Fitting priors to data (point estimates, all grass species in GLOPNET).</h2>
-<div id="example-specific-leaf-area-based-on-all-grasses" class="section level3">
-<h3 class="hasAnchor">
-<a href="#example-specific-leaf-area-based-on-all-grasses" class="anchor"></a>Example: Specific Leaf Area based on all grasses</h3>
-</div>
-<div id="mle-fit-to-glopnet-specific-leaf-area-data" class="section level3">
-<h3 class="hasAnchor">
-<a href="#mle-fit-to-glopnet-specific-leaf-area-data" class="anchor"></a>MLE Fit to glopnet Specific Leaf Area data</h3>
-<p>fit.dist function is in <code><a href="../reference/fit.dist.html">PEcAn.priors::fit.dist</a></code> (See source code: <a href="https://github.com/PecanProject/pecan/blob/master/modules/priors/R/priors.R" class="uri">https://github.com/PecanProject/pecan/blob/master/modules/priors/R/priors.R</a>)</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan/modules/priors"</span>)</code></pre></div>
-<p>The <code>fit.dist</code> function takes a vector of point estimates (in this case 125 observations of Specific Leaf Area from GLOPNET database are stored in <code>sladata</code>.</p>
-<p>First, it prints out the fits of a subset of distributions (the ‘f’ distribution could not be fit). Second, it prints the</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">dists =<span class="st">  </span><span class="kw">c</span>(<span class="st">'gamma'</span>, <span class="st">'lognormal'</span>,<span class="st">'weibull'</span>, <span class="st">'f'</span>)
-<span class="kw"><a href="../reference/fit.dist.html">fit.dist</a></span>(sladata, dists )</code></pre></div>
-<p>The <code>priorfig</code> function visualizes the chosen prior (line), with its mean and 95%CI (dots) as well as the data used to generate the figure.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">## priorfig(priordata = sladata, 
+          <div
+            id="generating-priors-based-on-data-and-or-expert-knowledge"
+            class="section level1"
+          >
+            <h1 class="hasAnchor">
+              <a
+                href="#generating-priors-based-on-data-and-or-expert-knowledge"
+                class="anchor"
+              ></a
+              >Generating Priors based on Data and / or Expert knowledge:
+            </h1>
+            <div
+              id="fitting-priors-to-data-point-estimates-all-grass-species-in-glopnet-"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#fitting-priors-to-data-point-estimates-all-grass-species-in-glopnet-"
+                  class="anchor"
+                ></a
+                >Fitting priors to data (point estimates, all grass species in
+                GLOPNET).
+              </h2>
+              <div
+                id="example-specific-leaf-area-based-on-all-grasses"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#example-specific-leaf-area-based-on-all-grasses"
+                    class="anchor"
+                  ></a
+                  >Example: Specific Leaf Area based on all grasses
+                </h3>
+              </div>
+              <div
+                id="mle-fit-to-glopnet-specific-leaf-area-data"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#mle-fit-to-glopnet-specific-leaf-area-data"
+                    class="anchor"
+                  ></a
+                  >MLE Fit to glopnet Specific Leaf Area data
+                </h3>
+                <p>
+                  fit.dist function is in
+                  <code
+                    ><a href="../reference/fit.dist.html"
+                      >PEcAn.priors::fit.dist</a
+                    ></code
+                  >
+                  (See source code:
+                  <a
+                    href="https://github.com/PecanProject/pecan/blob/master/modules/priors/R/priors.R"
+                    class="uri"
+                    >https://github.com/PecanProject/pecan/blob/master/modules/priors/R/priors.R</a
+                  >)
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">devtools<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"pecanproject/pecan/modules/priors"</span>)</code></pre>
+                </div>
+                <p>
+                  The <code>fit.dist</code> function takes a vector of point
+                  estimates (in this case 125 observations of Specific Leaf Area
+                  from GLOPNET database are stored in <code>sladata</code>.
+                </p>
+                <p>
+                  First, it prints out the fits of a subset of distributions
+                  (the ‘f’ distribution could not be fit). Second, it prints the
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">dists =<span class="st">  </span><span class="kw">c</span>(<span class="st">'gamma'</span>, <span class="st">'lognormal'</span>,<span class="st">'weibull'</span>, <span class="st">'f'</span>)
+<span class="kw"><a href="../reference/fit.dist.html">fit.dist</a></span>(sladata, dists )</code></pre>
+                </div>
+                <p>
+                  The <code>priorfig</code> function visualizes the chosen prior
+                  (line), with its mean and 95%CI (dots) as well as the data
+                  used to generate the figure.
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">## priorfig(priordata = sladata, 
 ##                                                  priordensity = slaprior, 
 ##                                                  trait = 'SLA')
-<span class="kw">print</span>(prior.figures<span class="op">$</span>SLA)</code></pre></div>
-</div>
-</div>
-<div id="fitting-priors-to-data-with-uncertainty-estimates-generating-posterior-predictive-distribution-of-an-unobserved-c4-grass-species-based-on-values-collected-from-many-pfts-" class="section level2">
-<h2 class="hasAnchor">
-<a href="#fitting-priors-to-data-with-uncertainty-estimates-generating-posterior-predictive-distribution-of-an-unobserved-c4-grass-species-based-on-values-collected-from-many-pfts-" class="anchor"></a>Fitting priors to data with uncertainty estimates (generating posterior predictive distribution of an unobserved C4 grass species based on values collected from many PFTs.</h2>
-<div id="vcmax-data-from-wullschleger-1993" class="section level3">
-<h3 class="hasAnchor">
-<a href="#vcmax-data-from-wullschleger-1993" class="anchor"></a>Vcmax data from Wullschleger (1993)</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">wullschleger.data &lt;-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">'inst/extdata/wullschleger1993updated.csv'</span>)</code></pre></div>
-</div>
-<div id="classify-wullschleger-data-into-functional-types" class="section level3">
-<h3 class="hasAnchor">
-<a href="#classify-wullschleger-data-into-functional-types" class="anchor"></a>Classify Wullschleger Data into Functional Types</h3>
-<div id="query-functional-types-from-bety" class="section level4">
-<h4 class="hasAnchor">
-<a href="#query-functional-types-from-bety" class="anchor"></a>1. query functional types from BETY</h4>
-<p>This code is not run here - data are provided in .csv file below. This code requires connection to the BETYdb MySQL server.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">wullschleger.species &lt;-<span class="st"> </span><span class="kw">vecpaste</span>(<span class="kw">unique</span>(wullschleger.data<span class="op">$</span>AcceptedSymbol))
+<span class="kw">print</span>(prior.figures<span class="op">$</span>SLA)</code></pre>
+                </div>
+              </div>
+            </div>
+            <div
+              id="fitting-priors-to-data-with-uncertainty-estimates-generating-posterior-predictive-distribution-of-an-unobserved-c4-grass-species-based-on-values-collected-from-many-pfts-"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#fitting-priors-to-data-with-uncertainty-estimates-generating-posterior-predictive-distribution-of-an-unobserved-c4-grass-species-based-on-values-collected-from-many-pfts-"
+                  class="anchor"
+                ></a
+                >Fitting priors to data with uncertainty estimates (generating
+                posterior predictive distribution of an unobserved C4 grass
+                species based on values collected from many PFTs.
+              </h2>
+              <div
+                id="vcmax-data-from-wullschleger-1993"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#vcmax-data-from-wullschleger-1993"
+                    class="anchor"
+                  ></a
+                  >Vcmax data from Wullschleger (1993)
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">wullschleger.data &lt;-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">'inst/extdata/wullschleger1993updated.csv'</span>)</code></pre>
+                </div>
+              </div>
+              <div
+                id="classify-wullschleger-data-into-functional-types"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#classify-wullschleger-data-into-functional-types"
+                    class="anchor"
+                  ></a
+                  >Classify Wullschleger Data into Functional Types
+                </h3>
+                <div
+                  id="query-functional-types-from-bety"
+                  class="section level4"
+                >
+                  <h4 class="hasAnchor">
+                    <a
+                      href="#query-functional-types-from-bety"
+                      class="anchor"
+                    ></a
+                    >1. query functional types from BETY
+                  </h4>
+                  <p>
+                    This code is not run here - data are provided in .csv file
+                    below. This code requires connection to the BETYdb MySQL
+                    server.
+                  </p>
+                  <div class="sourceCode">
+                    <pre
+                      class="sourceCode r"
+                    ><code class="sourceCode r">wullschleger.species &lt;-<span class="st"> </span><span class="kw">vecpaste</span>(<span class="kw">unique</span>(wullschleger.data<span class="op">$</span>AcceptedSymbol))
 ## load functional type data from BETY
 con &lt;-<span class="st"> </span><span class="cf">function</span>() {<span class="kw">query.bety.con</span>(<span class="dt">username =</span> <span class="st">"bety"</span>, <span class="dt">password =</span> <span class="st">"bety"</span>, 
                                    <span class="dt">host =</span> <span class="st">"localhost"</span>, <span class="dt">dbname =</span> <span class="st">"bety"</span>)}
 functional.data &lt;-<span class="st"> </span><span class="kw">query.bety</span>(<span class="kw">paste</span>(<span class="st">"select distinct AcceptedSymbol, scientificname, GrowthHabit, Category from species where AcceptedSymbol in ("</span>, wullschleger.species, <span class="st">") and GrowthHabit is not NULL and Category is not NULL;"</span>), <span class="kw">con</span>())
-<span class="kw">write.csv</span>(functional.data, <span class="st">'inst/extdata/wullschleger_join_usdaplants.csv'</span>)</code></pre></div>
-<p>Picking up with the Wullschleger dataset joined to USDA Plants functional type classifications …</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">functional.data &lt;-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">'inst/extdata/wullschleger_join_usdaplants.csv'</span>)
+<span class="kw">write.csv</span>(functional.data, <span class="st">'inst/extdata/wullschleger_join_usdaplants.csv'</span>)</code></pre>
+                  </div>
+                  <p>
+                    Picking up with the Wullschleger dataset joined to USDA
+                    Plants functional type classifications …
+                  </p>
+                  <div class="sourceCode">
+                    <pre
+                      class="sourceCode r"
+                    ><code class="sourceCode r">functional.data &lt;-<span class="st"> </span><span class="kw">read.csv</span>(<span class="st">'inst/extdata/wullschleger_join_usdaplants.csv'</span>)
 
 subshrubs &lt;-<span class="st"> </span><span class="kw">rownames</span>(wullschleger.data) <span class="op">%in%</span><span class="st"> </span><span class="kw">c</span>(<span class="kw">grep</span>(<span class="st">'Shrub'</span>,wullschleger.data<span class="op">$</span>GrowthHabit), <span class="kw">grep</span>(<span class="st">'Subshrub'</span>, wullschleger.data<span class="op">$</span>GrowthHabit))
 ########## 2. Merge functional type information into Wullschleger data
@@ -185,30 +357,63 @@ <h4 class="hasAnchor">
                             <span class="dt">Y =</span> <span class="kw">mean</span>(Y), 
                             <span class="dt">obs.prec =</span> <span class="dv">1</span><span class="op">/</span><span class="kw">sqrt</span>(<span class="kw">sum</span>((<span class="dv">1</span><span class="op">/</span>obs.prec)<span class="op">^</span><span class="dv">2</span>)), 
                             <span class="dt">ft =</span> <span class="kw">mean</span>(ft), <span class="co"># identity</span>
-                            <span class="dt">n =</span>  <span class="kw">sum</span>(n)) [,<span class="op">-</span><span class="dv">1</span>]</code></pre></div>
-<div id="add-data-from-c4-species" class="section level5">
-<h5 class="hasAnchor">
-<a href="#add-data-from-c4-species" class="anchor"></a>Add data from C4 species</h5>
-<p>Few measurements of Vcmax for C4 species were available. ###### Miscanthus: Wang D, Maughan MW, Sun J, Feng X, Miguez FE, Lee DK, Dietze MC, 2011. Impact of canopy nitrogen allocation on growth and photosynthesis of miscanthus (Miscanthus x giganteus). Oecologia, in press</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">dwang.vcmax &lt;-<span class="st"> </span><span class="kw">c</span>(<span class="fl">19.73</span>, <span class="fl">40.35</span>, <span class="fl">33.02</span>, <span class="fl">21.28</span>, <span class="fl">31.45</span>, <span class="fl">27.83</span>, <span class="fl">9.69</span>, <span class="fl">15.99</span>, <span class="fl">18.88</span>, <span class="fl">11.45</span>, <span class="fl">15.81</span>, <span class="fl">27.61</span>, <span class="dv">13</span>, <span class="fl">21.25</span>, <span class="fl">22.01</span>, <span class="fl">10.37</span>, <span class="fl">12.37</span>, <span class="fl">22.8</span>, <span class="fl">12.24</span>, <span class="fl">15.85</span>, <span class="fl">21.93</span>, <span class="fl">23.48</span>, <span class="fl">31.51</span>, <span class="fl">23.16</span>, <span class="fl">18.55</span>, <span class="fl">17.06</span>, <span class="fl">20.27</span>, <span class="fl">30.41</span>)
+                            <span class="dt">n =</span>  <span class="kw">sum</span>(n)) [,<span class="op">-</span><span class="dv">1</span>]</code></pre>
+                  </div>
+                  <div id="add-data-from-c4-species" class="section level5">
+                    <h5 class="hasAnchor">
+                      <a href="#add-data-from-c4-species" class="anchor"></a>Add
+                      data from C4 species
+                    </h5>
+                    <p>
+                      Few measurements of Vcmax for C4 species were available.
+                      ###### Miscanthus: Wang D, Maughan MW, Sun J, Feng X,
+                      Miguez FE, Lee DK, Dietze MC, 2011. Impact of canopy
+                      nitrogen allocation on growth and photosynthesis of
+                      miscanthus (Miscanthus x giganteus). Oecologia, in press
+                    </p>
+                    <div class="sourceCode">
+                      <pre
+                        class="sourceCode r"
+                      ><code class="sourceCode r">dwang.vcmax &lt;-<span class="st"> </span><span class="kw">c</span>(<span class="fl">19.73</span>, <span class="fl">40.35</span>, <span class="fl">33.02</span>, <span class="fl">21.28</span>, <span class="fl">31.45</span>, <span class="fl">27.83</span>, <span class="fl">9.69</span>, <span class="fl">15.99</span>, <span class="fl">18.88</span>, <span class="fl">11.45</span>, <span class="fl">15.81</span>, <span class="fl">27.61</span>, <span class="dv">13</span>, <span class="fl">21.25</span>, <span class="fl">22.01</span>, <span class="fl">10.37</span>, <span class="fl">12.37</span>, <span class="fl">22.8</span>, <span class="fl">12.24</span>, <span class="fl">15.85</span>, <span class="fl">21.93</span>, <span class="fl">23.48</span>, <span class="fl">31.51</span>, <span class="fl">23.16</span>, <span class="fl">18.55</span>, <span class="fl">17.06</span>, <span class="fl">20.27</span>, <span class="fl">30.41</span>)
 dwang.vcmax &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">Y =</span> <span class="kw">mean</span>(dwang.vcmax), 
                           <span class="dt">obs.prec =</span> <span class="dv">1</span><span class="op">/</span><span class="kw">sd</span>(dwang.vcmax),
                           <span class="dt">ft =</span> <span class="dv">2</span>,         <span class="co">#C4 Grass</span>
-                          <span class="dt">n =</span> <span class="kw">length</span>(dwang.vcmax))</code></pre></div>
-<div id="muhlenbergia-glomerata" class="section level6">
-<h6>Muhlenbergia glomerata</h6>
-<p>Kubien and Sage 2004. Low-temperature photosynthetic performance of a C4 grass and a co-occurring C3 grass native to high latitudes. Plant, Cell &amp; Environment DOI: 10.1111/j.1365-3040.2004.01196.x</p>
-<p>Data from figure 5 in Kubien and Sage (2004), average across plants grown at 14/10 degrees and 26/22 degrees</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">kubien.vcmax &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">Y =</span> <span class="kw">mean</span>(<span class="fl">23.4</span>, <span class="fl">24.8</span>), 
+                          <span class="dt">n =</span> <span class="kw">length</span>(dwang.vcmax))</code></pre>
+                    </div>
+                    <div id="muhlenbergia-glomerata" class="section level6">
+                      <h6>Muhlenbergia glomerata</h6>
+                      <p>
+                        Kubien and Sage 2004. Low-temperature photosynthetic
+                        performance of a C4 grass and a co-occurring C3 grass
+                        native to high latitudes. Plant, Cell &amp; Environment
+                        DOI: 10.1111/j.1365-3040.2004.01196.x
+                      </p>
+                      <p>
+                        Data from figure 5 in Kubien and Sage (2004), average
+                        across plants grown at 14/10 degrees and 26/22 degrees
+                      </p>
+                      <div class="sourceCode">
+                        <pre
+                          class="sourceCode r"
+                        ><code class="sourceCode r">kubien.vcmax &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">Y =</span> <span class="kw">mean</span>(<span class="fl">23.4</span>, <span class="fl">24.8</span>), 
                            <span class="dt">obs.prec =</span> <span class="dv">1</span><span class="op">/</span><span class="kw">sqrt</span>(<span class="fl">2.6</span><span class="op">^</span><span class="dv">2</span> <span class="op">+</span><span class="st"> </span><span class="fl">2.5</span><span class="op">^</span><span class="dv">2</span>), 
                            <span class="dt">n =</span> <span class="dv">8</span>, 
-                           <span class="dt">ft =</span> <span class="dv">2</span>)                      </code></pre></div>
-</div>
-<div id="zea-mays-corn" class="section level6">
-<h6>Zea Mays (Corn)</h6>
-<p>Massad, Tuzet, Bethenod 2007. The effect of temperature on C4-type leaf photosynthesis parameters. Plant, Cell &amp; Environment 30(9) 1191-1204. DOI: 10.1111/j.1365-3040.2007.01691.x</p>
-<p>data from fig 6a</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">massad.vcmax.data &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">vcmax =</span> <span class="kw">c</span>(<span class="fl">17.1</span>, <span class="fl">17.2</span>, <span class="fl">17.6</span>, <span class="dv">18</span>, <span class="fl">18.3</span>, <span class="fl">18.5</span>, <span class="fl">20.4</span>, <span class="fl">22.9</span>, <span class="fl">22.9</span>, <span class="fl">21.9</span>, <span class="fl">21.8</span>, <span class="fl">22.7</span>, <span class="fl">22.3</span>, <span class="fl">25.3</span>, <span class="fl">24.4</span>, <span class="fl">25.5</span>, <span class="fl">25.5</span>, <span class="fl">24.9</span>, <span class="fl">31.2</span>, <span class="fl">30.8</span>, <span class="fl">31.6</span>, <span class="fl">31.7</span>, <span class="fl">32.5</span>, <span class="fl">34.1</span>, <span class="fl">34.2</span>, <span class="fl">33.9</span>, <span class="fl">35.4</span>, <span class="dv">36</span>, <span class="dv">36</span>, <span class="fl">37.5</span>, <span class="fl">38.2</span>, <span class="fl">38.1</span>, <span class="fl">37.4</span>, <span class="fl">37.7</span>, <span class="fl">25.2</span>, <span class="fl">25.5</span>), 
+                           <span class="dt">ft =</span> <span class="dv">2</span>)                      </code></pre>
+                      </div>
+                    </div>
+                    <div id="zea-mays-corn" class="section level6">
+                      <h6>Zea Mays (Corn)</h6>
+                      <p>
+                        Massad, Tuzet, Bethenod 2007. The effect of temperature
+                        on C4-type leaf photosynthesis parameters. Plant, Cell
+                        &amp; Environment 30(9) 1191-1204. DOI:
+                        10.1111/j.1365-3040.2007.01691.x
+                      </p>
+                      <p>data from fig 6a</p>
+                      <div class="sourceCode">
+                        <pre
+                          class="sourceCode r"
+                        ><code class="sourceCode r">massad.vcmax.data &lt;-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">vcmax =</span> <span class="kw">c</span>(<span class="fl">17.1</span>, <span class="fl">17.2</span>, <span class="fl">17.6</span>, <span class="dv">18</span>, <span class="fl">18.3</span>, <span class="fl">18.5</span>, <span class="fl">20.4</span>, <span class="fl">22.9</span>, <span class="fl">22.9</span>, <span class="fl">21.9</span>, <span class="fl">21.8</span>, <span class="fl">22.7</span>, <span class="fl">22.3</span>, <span class="fl">25.3</span>, <span class="fl">24.4</span>, <span class="fl">25.5</span>, <span class="fl">25.5</span>, <span class="fl">24.9</span>, <span class="fl">31.2</span>, <span class="fl">30.8</span>, <span class="fl">31.6</span>, <span class="fl">31.7</span>, <span class="fl">32.5</span>, <span class="fl">34.1</span>, <span class="fl">34.2</span>, <span class="fl">33.9</span>, <span class="fl">35.4</span>, <span class="dv">36</span>, <span class="dv">36</span>, <span class="fl">37.5</span>, <span class="fl">38.2</span>, <span class="fl">38.1</span>, <span class="fl">37.4</span>, <span class="fl">37.7</span>, <span class="fl">25.2</span>, <span class="fl">25.5</span>), 
                                 <span class="dt">temp =</span> <span class="kw">c</span>(<span class="fl">20.5</span>, <span class="fl">24.6</span>, <span class="dv">21</span>, <span class="dv">19</span>, <span class="fl">21.9</span>, <span class="dv">15</span>, <span class="fl">19.6</span>, <span class="fl">14.3</span>, <span class="fl">20.8</span>, <span class="fl">23.4</span>, <span class="fl">24.8</span>, <span class="fl">25.9</span>, <span class="fl">24.1</span>, <span class="fl">22.8</span>, <span class="fl">27.9</span>, <span class="fl">31.7</span>, <span class="fl">35.5</span>, <span class="fl">39.3</span>, <span class="fl">37.9</span>, <span class="fl">42.4</span>, <span class="fl">41.5</span>, <span class="fl">48.7</span>, <span class="fl">33.3</span>, <span class="fl">33.3</span>, <span class="fl">31.5</span>, <span class="fl">39.1</span>, <span class="fl">38.8</span>, <span class="fl">43.3</span>, <span class="dv">50</span>, <span class="fl">38.4</span>, <span class="fl">35.7</span>, <span class="fl">34.4</span>, <span class="fl">31.9</span>, <span class="fl">33.9</span>, <span class="fl">32.1</span>, <span class="fl">33.7</span>))
 massad.vcmax &lt;-<span class="st"> </span><span class="kw">with</span>(massad.vcmax.data, <span class="kw">arrhenius.scaling</span>(<span class="dt">old.temp =</span> temp, 
                                                           <span class="dt">new.temp =</span> <span class="dv">25</span>, 
@@ -224,24 +429,55 @@ <h6>Zea Mays (Corn)</h6>
                         dwang.vcmax, 
                         ## xfeng.vcmax, 
                         kubien.vcmax, 
-                        massad.vcmax)</code></pre></div>
-</div>
-</div>
-<div id="take-a-look-at-the-raw-data-by-functional-type" class="section level5">
-<h5 class="hasAnchor">
-<a href="#take-a-look-at-the-raw-data-by-functional-type" class="anchor"></a>take a look at the raw data by functional type:</h5>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">qplot</span>(<span class="dt">data =</span> all.vcmax.data, <span class="dt">x =</span> <span class="kw">factor</span>(ft), <span class="dt">y =</span> Y, <span class="dt">geom =</span> <span class="st">'boxplot'</span>)</code></pre></div>
-</div>
-<div id="add-unobserved-c4-species-so-jags-calculates-posterior-predictive-distribution" class="section level5">
-<h5 class="hasAnchor">
-<a href="#add-unobserved-c4-species-so-jags-calculates-posterior-predictive-distribution" class="anchor"></a>Add unobserved C4 species so JAGS calculates posterior predictive distribution</h5>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">vcmax.data &lt;-<span class="st"> </span><span class="kw">rbind</span>(all.vcmax.data, 
-                    <span class="kw">data.frame</span>(<span class="dt">Y =</span> <span class="ot">NA</span>, <span class="dt">obs.prec =</span> <span class="ot">NA</span>, <span class="dt">ft =</span> <span class="dv">2</span>, <span class="dt">n =</span> <span class="dv">1</span>))</code></pre></div>
-</div>
-<div id="write-and-run-meta-analysis" class="section level5">
-<h5 class="hasAnchor">
-<a href="#write-and-run-meta-analysis" class="anchor"></a>Write and Run Meta-analysis</h5>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">writeLines</span>(<span class="dt">con =</span> <span class="st">"vcmax.prior.bug"</span>, 
+                        massad.vcmax)</code></pre>
+                      </div>
+                    </div>
+                  </div>
+                  <div
+                    id="take-a-look-at-the-raw-data-by-functional-type"
+                    class="section level5"
+                  >
+                    <h5 class="hasAnchor">
+                      <a
+                        href="#take-a-look-at-the-raw-data-by-functional-type"
+                        class="anchor"
+                      ></a
+                      >take a look at the raw data by functional type:
+                    </h5>
+                    <div class="sourceCode">
+                      <pre
+                        class="sourceCode r"
+                      ><code class="sourceCode r"><span class="kw">qplot</span>(<span class="dt">data =</span> all.vcmax.data, <span class="dt">x =</span> <span class="kw">factor</span>(ft), <span class="dt">y =</span> Y, <span class="dt">geom =</span> <span class="st">'boxplot'</span>)</code></pre>
+                    </div>
+                  </div>
+                  <div
+                    id="add-unobserved-c4-species-so-jags-calculates-posterior-predictive-distribution"
+                    class="section level5"
+                  >
+                    <h5 class="hasAnchor">
+                      <a
+                        href="#add-unobserved-c4-species-so-jags-calculates-posterior-predictive-distribution"
+                        class="anchor"
+                      ></a
+                      >Add unobserved C4 species so JAGS calculates posterior
+                      predictive distribution
+                    </h5>
+                    <div class="sourceCode">
+                      <pre
+                        class="sourceCode r"
+                      ><code class="sourceCode r">vcmax.data &lt;-<span class="st"> </span><span class="kw">rbind</span>(all.vcmax.data, 
+                    <span class="kw">data.frame</span>(<span class="dt">Y =</span> <span class="ot">NA</span>, <span class="dt">obs.prec =</span> <span class="ot">NA</span>, <span class="dt">ft =</span> <span class="dv">2</span>, <span class="dt">n =</span> <span class="dv">1</span>))</code></pre>
+                    </div>
+                  </div>
+                  <div id="write-and-run-meta-analysis" class="section level5">
+                    <h5 class="hasAnchor">
+                      <a href="#write-and-run-meta-analysis" class="anchor"></a
+                      >Write and Run Meta-analysis
+                    </h5>
+                    <div class="sourceCode">
+                      <pre
+                        class="sourceCode r"
+                      ><code class="sourceCode r"><span class="kw">writeLines</span>(<span class="dt">con =</span> <span class="st">"vcmax.prior.bug"</span>, 
            <span class="dt">text =</span>  <span class="st">"model{  </span>
 <span class="st">             for (k in 1:length(Y)){</span>
 <span class="st">               Y[k]  ~ dnorm(beta.ft[ft[k]], tau.y[k])T(0,)</span>
@@ -302,82 +538,167 @@ <h5 class="hasAnchor">
                <span class="kw">aes</span>(<span class="dt">x =</span> mean <span class="op">-</span><span class="st"> </span>se, <span class="dt">xend =</span> mean <span class="op">+</span><span class="st"> </span>se, 
                    <span class="dt">y =</span> <span class="dv">1</span><span class="op">:</span><span class="kw">sum</span>(vcmax.c4)<span class="op">/</span><span class="dv">2000</span>, <span class="dt">yend =</span> <span class="dv">1</span><span class="op">:</span><span class="kw">sum</span>(vcmax.c4)<span class="op">/</span><span class="dv">2000</span>))
 
-<span class="kw">print</span>(prior.figures[[<span class="st">'Vcmax'</span>]])</code></pre></div>
-</div>
-</div>
-</div>
-</div>
-<div id="fitting-priors-to-expert-constraint--" class="section level2">
-<h2 class="hasAnchor">
-<a href="#fitting-priors-to-expert-constraint--" class="anchor"></a>Fitting priors to expert constraint ().</h2>
-<div id="example-minimum-temperature-of-photosynthesis" class="section level3">
-<h3 class="hasAnchor">
-<a href="#example-minimum-temperature-of-photosynthesis" class="anchor"></a>Example: Minimum temperature of Photosynthesis</h3>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">TBD</code></pre></div>
-</div>
-</div>
-<div id="other-examples-approaches" class="section level2">
-<h2 class="hasAnchor">
-<a href="#other-examples-approaches" class="anchor"></a>Other Examples / Approaches</h2>
-<div id="examples" class="section level3">
-<h3 class="hasAnchor">
-<a href="#examples" class="anchor"></a>Examples</h3>
-<ul>
-<li>Estimating priors for the DALEC model in [models/dalec/inst/DALEC_priors.R](<a href="https://github.com/PecanProject/pecan/blob/master/models/dalec/inst/DALEC_priors.R" class="uri">https://github.com/PecanProject/pecan/blob/master/models/dalec/inst/DALEC_priors.R</a>
-</li>
-</ul>
-</div>
-<div id="package-rriskdistributions" class="section level3">
-<h3 class="hasAnchor">
-<a href="#package-rriskdistributions" class="anchor"></a>Package <code>rriskDistributions</code>
-</h3>
-<p>The <a href="http://cran.r-project.org/web/packages/rriskDistributions/index.html">rriskDistributions</a> useful for estimating priors …</p>
-<p>as well as individual functions for each distribution such as <code>get.&lt;somedist&gt;.par</code> that provide nice diagnostic plots (e.g. compare chosen points to cdf) for example, to compute the parameters of a Gamma distribution that fits a median of 2.5 and has a 95%CI of [1, 10]:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(rriskDistributions)
-<span class="kw">get.gamma.par</span>(<span class="dt">p =</span> <span class="kw">c</span>(<span class="fl">0.025</span>, <span class="fl">0.50</span>, <span class="fl">0.975</span>), <span class="dt">q =</span> <span class="kw">c</span>(<span class="dv">1</span>, <span class="fl">2.5</span>, <span class="dv">10</span>), <span class="dt">tol =</span> <span class="fl">0.1</span>)</code></pre></div>
-<p>The function <code>fit.pecr</code> provides a GUI to explore the fits of a range of distributions, e.g.:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">fit.perc</span>(<span class="dt">p =</span> <span class="kw">c</span>(<span class="fl">0.1</span>, <span class="fl">0.5</span>, <span class="fl">0.9</span>), <span class="dt">q =</span> <span class="kw">c</span>(<span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">90</span>), <span class="dt">tolConv =</span> <span class="fl">0.1</span>)</code></pre></div>
-<p>produces this:</p>
-<div class="figure">
-<img src="https://dl.dropboxusercontent.com/u/18092793/fit.perc_example.PNG" alt="image of rriskDistributions example that uses GUI"><p class="caption">image of rriskDistributions example that uses GUI</p>
-</div>
-</div>
-</div>
-</div>
-  </div>
+<span class="kw">print</span>(prior.figures[[<span class="st">'Vcmax'</span>]])</code></pre>
+                    </div>
+                  </div>
+                </div>
+              </div>
+            </div>
+            <div
+              id="fitting-priors-to-expert-constraint--"
+              class="section level2"
+            >
+              <h2 class="hasAnchor">
+                <a
+                  href="#fitting-priors-to-expert-constraint--"
+                  class="anchor"
+                ></a
+                >Fitting priors to expert constraint ().
+              </h2>
+              <div
+                id="example-minimum-temperature-of-photosynthesis"
+                class="section level3"
+              >
+                <h3 class="hasAnchor">
+                  <a
+                    href="#example-minimum-temperature-of-photosynthesis"
+                    class="anchor"
+                  ></a
+                  >Example: Minimum temperature of Photosynthesis
+                </h3>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r">TBD</code></pre>
+                </div>
+              </div>
+            </div>
+            <div id="other-examples-approaches" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#other-examples-approaches" class="anchor"></a>Other
+                Examples / Approaches
+              </h2>
+              <div id="examples" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#examples" class="anchor"></a>Examples
+                </h3>
+                <ul>
+                  <li>
+                    Estimating priors for the DALEC model in
+                    [models/dalec/inst/DALEC_priors.R](<a
+                      href="https://github.com/PecanProject/pecan/blob/master/models/dalec/inst/DALEC_priors.R"
+                      class="uri"
+                      >https://github.com/PecanProject/pecan/blob/master/models/dalec/inst/DALEC_priors.R</a
+                    >
+                  </li>
+                </ul>
+              </div>
+              <div id="package-rriskdistributions" class="section level3">
+                <h3 class="hasAnchor">
+                  <a href="#package-rriskdistributions" class="anchor"></a
+                  >Package <code>rriskDistributions</code>
+                </h3>
+                <p>
+                  The
+                  <a
+                    href="http://cran.r-project.org/web/packages/rriskDistributions/index.html"
+                    >rriskDistributions</a
+                  >
+                  useful for estimating priors …
+                </p>
+                <p>
+                  as well as individual functions for each distribution such as
+                  <code>get.&lt;somedist&gt;.par</code> that provide nice
+                  diagnostic plots (e.g. compare chosen points to cdf) for
+                  example, to compute the parameters of a Gamma distribution
+                  that fits a median of 2.5 and has a 95%CI of [1, 10]:
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw">library</span>(rriskDistributions)
+<span class="kw">get.gamma.par</span>(<span class="dt">p =</span> <span class="kw">c</span>(<span class="fl">0.025</span>, <span class="fl">0.50</span>, <span class="fl">0.975</span>), <span class="dt">q =</span> <span class="kw">c</span>(<span class="dv">1</span>, <span class="fl">2.5</span>, <span class="dv">10</span>), <span class="dt">tol =</span> <span class="fl">0.1</span>)</code></pre>
+                </div>
+                <p>
+                  The function <code>fit.pecr</code> provides a GUI to explore
+                  the fits of a range of distributions, e.g.:
+                </p>
+                <div class="sourceCode">
+                  <pre
+                    class="sourceCode r"
+                  ><code class="sourceCode r"><span class="kw">fit.perc</span>(<span class="dt">p =</span> <span class="kw">c</span>(<span class="fl">0.1</span>, <span class="fl">0.5</span>, <span class="fl">0.9</span>), <span class="dt">q =</span> <span class="kw">c</span>(<span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">90</span>), <span class="dt">tolConv =</span> <span class="fl">0.1</span>)</code></pre>
+                </div>
+                <p>produces this:</p>
+                <div class="figure">
+                  <img
+                    src="https://dl.dropboxusercontent.com/u/18092793/fit.perc_example.PNG"
+                    alt="image of rriskDistributions example that uses GUI"
+                  />
+                  <p class="caption">
+                    image of rriskDistributions example that uses GUI
+                  </p>
+                </div>
+              </div>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li>
-<a href="#generating-priors-based-on-data-and-or-expert-knowledge">Generating Priors based on Data and / or Expert knowledge:</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#fitting-priors-to-data-point-estimates-all-grass-species-in-glopnet-">Fitting priors to data (point estimates, all grass species in GLOPNET).</a></li>
-      <li><a href="#fitting-priors-to-data-with-uncertainty-estimates-generating-posterior-predictive-distribution-of-an-unobserved-c4-grass-species-based-on-values-collected-from-many-pfts-">Fitting priors to data with uncertainty estimates (generating posterior predictive distribution of an unobserved C4 grass species based on values collected from many PFTs.</a></li>
-      <li><a href="#fitting-priors-to-expert-constraint--">Fitting priors to expert constraint ().</a></li>
-      <li><a href="#other-examples-approaches">Other Examples / Approaches</a></li>
-      </ul>
-</li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li>
+                <a
+                  href="#generating-priors-based-on-data-and-or-expert-knowledge"
+                  >Generating Priors based on Data and / or Expert knowledge:</a
+                >
+                <ul class="nav nav-pills nav-stacked">
+                  <li>
+                    <a
+                      href="#fitting-priors-to-data-point-estimates-all-grass-species-in-glopnet-"
+                      >Fitting priors to data (point estimates, all grass
+                      species in GLOPNET).</a
+                    >
+                  </li>
+                  <li>
+                    <a
+                      href="#fitting-priors-to-data-with-uncertainty-estimates-generating-posterior-predictive-distribution-of-an-unobserved-c4-grass-species-based-on-values-collected-from-many-pfts-"
+                      >Fitting priors to data with uncertainty estimates
+                      (generating posterior predictive distribution of an
+                      unobserved C4 grass species based on values collected from
+                      many PFTs.</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#fitting-priors-to-expert-constraint--"
+                      >Fitting priors to expert constraint ().</a
+                    >
+                  </li>
+                  <li>
+                    <a href="#other-examples-approaches"
+                      >Other Examples / Approaches</a
+                    >
+                  </li>
+                </ul>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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diff --git a/modules/priors/docs/authors.html b/modules/priors/docs/authors.html
index bca239e..d4a4c91 100644
--- a/modules/priors/docs/authors.html
+++ b/modules/priors/docs/authors.html
@@ -2,134 +2,161 @@
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.priors</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/priors_demo.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.priors</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
 
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/priors/docs/docsearch.css b/modules/priors/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/priors/docs/docsearch.css
+++ b/modules/priors/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/priors/docs/docsearch.js b/modules/priors/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/priors/docs/docsearch.js
+++ b/modules/priors/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/priors/docs/index.html b/modules/priors/docs/index.html
index 4d8fcbd..5fd96b9 100644
--- a/modules/priors/docs/index.html
+++ b/modules/priors/docs/index.html
@@ -1,115 +1,178 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used to estimate priors from data • PEcAn.priors</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used to estimate priors from data">
-<meta property="og:description" content="Functions to estimate priors from data.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used to estimate priors from data • PEcAn.priors
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used to estimate priors from data"
+    />
+    <meta
+      property="og:description"
+      content="Functions to estimate priors from data."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.priors</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
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-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/priors_demo.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    Functions to estimate priors from data.
-  </div>
-
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-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
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-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.priors</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          Functions to estimate priors from data.
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/priors/docs/pkgdown.css b/modules/priors/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/priors/docs/pkgdown.css
+++ b/modules/priors/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/priors/docs/pkgdown.js b/modules/priors/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/priors/docs/pkgdown.js
+++ b/modules/priors/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/priors/docs/reference/create.density.df.html b/modules/priors/docs/reference/create.density.df.html
index 49f3172..25054bb 100644
--- a/modules/priors/docs/reference/create.density.df.html
+++ b/modules/priors/docs/reference/create.density.df.html
@@ -2,184 +2,234 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Create Density Data Frame from Sample — create.density.df • PEcAn.priors</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Create Density Data Frame from Sample — create.density.df" />
-
-<meta property="og:description" content="Returns a data frame from stats::density function" />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      Create Density Data Frame from Sample — create.density.df • PEcAn.priors
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Create Density Data Frame from Sample — create.density.df"
+    />
+
+    <meta
+      property="og:description"
+      content="Returns a data frame from stats::density function"
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAn.priors</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.priors</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Create Density Data Frame from Sample</h1>
-    
-    <div class="hidden name"><code>create.density.df.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Create Density Data Frame from Sample</h1>
 
-    <div class="ref-description">
-    
-    <p>Returns a data frame from stats::density function</p>
-    
-    </div>
+            <div class="hidden name"><code>create.density.df.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Returns a data frame from stats::density function</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>create.density.df</span>(<span class='kw'>samps</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>zero.bounded</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>create.density.df</span>(<span class='kw'>samps</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>zero.bounded</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>distribution</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>samps</th>
-      <td><p>a vector of samples from a distribution</p></td>
-    </tr>
-    <tr>
-      <th>zero.bounded</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>distribution</th>
-      <td><p>list with elements distn, parama, paramb,
-e.g. <code>list('norm', 0, 1)</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>data frame with x and y = dens(x)</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>samps</th>
+              <td><p>a vector of samples from a distribution</p></td>
+            </tr>
+            <tr>
+              <th>zero.bounded</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>distribution</th>
+              <td>
+                <p>
+                  list with elements distn, parama, paramb, e.g.
+                  <code>list('norm', 0, 1)</code>
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>data frame with x and y = dens(x)</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>prior.df</span> <span class='kw'>&lt;-</span> <span class='fu'>create.density.df</span>(<span class='kw'>distribution</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='st'>'norm'</span>,<span class='fl'>0</span>,<span class='fl'>1</span>))
 <span class='fu'>plot</span>(<span class='no'>prior.df</span>)
 <span class='no'>samp.df</span> <span class='kw'>&lt;-</span> <span class='fu'>create.density.df</span>(<span class='kw'>samps</span> <span class='kw'>=</span> <span class='fu'>rnorm</span>(<span class='fl'>100</span>))
 <span class='fu'>lines</span>(<span class='no'>samp.df</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          David LeBauer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/priors/docs/reference/fit.dist.html b/modules/priors/docs/reference/fit.dist.html
index 3cd4296..534a930 100644
--- a/modules/priors/docs/reference/fit.dist.html
+++ b/modules/priors/docs/reference/fit.dist.html
@@ -2,170 +2,205 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+    <meta property="og:description" content="Fit a distribution to data" />
+    <meta name="twitter:card" content="summary" />
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAn.priors</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
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-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-  </a>
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
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-      
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
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+              </button>
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+                <span
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+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Fit distribution to data</h1>
-    
-    <div class="hidden name"><code>fit.dist.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Fit distribution to data</h1>
 
-    <div class="ref-description">
-    
-    <p>Fit a distribution to data</p>
-    
-    </div>
+            <div class="hidden name"><code>fit.dist.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Fit a distribution to data</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>fit.dist</span>(<span class='no'>trait.data</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='fu'>colnames</span>(<span class='no'>trait.data</span>), <span class='kw'>dists</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"weibull"</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>fit.dist</span>(<span class='no'>trait.data</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='fu'>colnames</span>(<span class='no'>trait.data</span>), <span class='kw'>dists</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"weibull"</span>,
   <span class='st'>"lognormal"</span>, <span class='st'>"gamma"</span>), <span class='kw'>n</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.data</th>
-      <td><p>data for distribution</p></td>
-    </tr>
-    <tr>
-      <th>dists</th>
-      <td><p>list of distribution names</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>best fit distribution</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.data</th>
+              <td><p>data for distribution</p></td>
+            </tr>
+            <tr>
+              <th>dists</th>
+              <td><p>list of distribution names</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>best fit distribution</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/priors/docs/reference/get.quantiles.from.density.html b/modules/priors/docs/reference/get.quantiles.from.density.html
index 1ff55a7..6dc74ed 100644
--- a/modules/priors/docs/reference/get.quantiles.from.density.html
+++ b/modules/priors/docs/reference/get.quantiles.from.density.html
@@ -2,152 +2,202 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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+      PEcAn.priors
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+
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+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get the quantiles from prior density</h1>
-    
-    <div class="hidden name"><code>get.quantiles.from.density.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-
-    </div>
-
-    <pre class="usage"><span class='fu'>get.quantiles.from.density</span>(<span class='no'>density.df</span>, <span class='kw'>quantiles</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.025</span>, <span class='fl'>0.5</span>, <span class='fl'>0.975</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>quantiles</th>
-      <td><p>default is the median and 95<!-- % CI;} --></p>
-<p>priordensitydensity dataframe generated by <code><a href='create.density.df.html'>create.density.df</a></code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get the quantiles from prior density</h1>
+
+            <div class="hidden name">
+              <code>get.quantiles.from.density.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description"></div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.quantiles.from.density</span>(<span class='no'>density.df</span>, <span class='kw'>quantiles</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.025</span>, <span class='fl'>0.5</span>, <span class='fl'>0.975</span>))</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>quantiles</th>
+              <td>
+                <p>default is the median and 95<!-- % CI;} --></p>
+                <p>
+                  priordensitydensity dataframe generated by
+                  <code
+                    ><a href="create.density.df.html"
+                      >create.density.df</a
+                    ></code
+                  >
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/priors/docs/reference/get.sample.html b/modules/priors/docs/reference/get.sample.html
index 5a45eb8..445cdd4 100644
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+++ b/modules/priors/docs/reference/get.sample.html
@@ -2,177 +2,221 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+                  >1.6.0</span
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+              </span>
+            </div>
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get Samples</h1>
-    
-    <div class="hidden name"><code>get.sample.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Take n random samples from prior</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.sample</span>(<span class='no'>prior</span>, <span class='no'>n</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>prior</th>
-      <td><p>data.frame with distn, parama, paramb</p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>number of samples to return</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>vector with n random samples from prior</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Like pr.samp, with prior as a single input</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p><a href='pr.samp.html'>pr.samp</a></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get Samples</h1>
+
+            <div class="hidden name"><code>get.sample.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Take n random samples from prior</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.sample</span>(<span class='no'>prior</span>, <span class='no'>n</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>prior</th>
+              <td><p>data.frame with distn, parama, paramb</p></td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td><p>number of samples to return</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>vector with n random samples from prior</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Like pr.samp, with prior as a single input</p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p><a href="pr.samp.html">pr.samp</a></p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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diff --git a/modules/priors/docs/reference/index.html b/modules/priors/docs/reference/index.html
index 23ee74a..dc02ce4 100644
--- a/modules/priors/docs/reference/index.html
+++ b/modules/priors/docs/reference/index.html
@@ -2,222 +2,301 @@
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 <html>
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+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
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+    <!-- Bootstrap -->
 
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
 
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+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
 
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+    <!-- clipboard.js -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
 
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+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
 
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+    <!-- pkgdown -->
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+    <meta property="og:title" content="Function reference" />
 
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
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+            <div class="navbar-header">
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+                type="button"
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+                <a class="navbar-link" href="../index.html">PEcAn.priors</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
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-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
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-      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
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+              <ul class="nav navbar-nav">
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
 
-    <table class="ref-index">
-
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
-
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="create.density.df.html">create.density.df()</a></code> </p>
-        </td>
-        <td><p>Create Density Data Frame from Sample</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="fit.dist.html">fit.dist()</a></code> </p>
-        </td>
-        <td><p>Fit distribution to data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.quantiles.from.density.html">get.quantiles.from.density()</a></code> </p>
-        </td>
-        <td><p>Get the quantiles from prior density</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.sample.html">get.sample()</a></code> </p>
-        </td>
-        <td><p>Get Samples</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot.densities.html">plot(<i>&lt;densities&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Plot Trait Probability Densities</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot.posterior.density.html">plot(<i>&lt;posterior.density&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Add posterior density.</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot.prior.density.html">plot(<i>&lt;prior.density&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Add Prior Density</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot.trait.html">plot(<i>&lt;trait&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Plot trait density</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pr.dens.html">pr.dens()</a></code> </p>
-        </td>
-        <td><p>Calculate densities</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pr.samp.html">pr.samp()</a></code> </p>
-        </td>
-        <td><p>Sample from prior</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="prior.fn.html">prior.fn()</a></code> </p>
-        </td>
-        <td><p>prior.fn</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="priorfig.html">priorfig()</a></code> </p>
-        </td>
-        <td><p>Prior Figure</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
-
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-      </footer>
-   </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="create.density.df.html"
+                        >create.density.df()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Create Density Data Frame from Sample</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="fit.dist.html">fit.dist()</a></code>
+                  </p>
+                </td>
+                <td><p>Fit distribution to data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.quantiles.from.density.html"
+                        >get.quantiles.from.density()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get the quantiles from prior density</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.sample.html">get.sample()</a></code>
+                  </p>
+                </td>
+                <td><p>Get Samples</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot.densities.html"
+                        >plot(<i>&lt;densities&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Plot Trait Probability Densities</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot.posterior.density.html"
+                        >plot(<i>&lt;posterior.density&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Add posterior density.</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot.prior.density.html"
+                        >plot(<i>&lt;prior.density&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Add Prior Density</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot.trait.html"
+                        >plot(<i>&lt;trait&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Plot trait density</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pr.dens.html">pr.dens()</a></code>
+                  </p>
+                </td>
+                <td><p>Calculate densities</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pr.samp.html">pr.samp()</a></code>
+                  </p>
+                </td>
+                <td><p>Sample from prior</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="prior.fn.html">prior.fn()</a></code>
+                  </p>
+                </td>
+                <td><p>prior.fn</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="priorfig.html">priorfig()</a></code>
+                  </p>
+                </td>
+                <td><p>Prior Figure</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
+
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
-  
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/priors/docs/reference/plot.densities.html b/modules/priors/docs/reference/plot.densities.html
index 041ccff..4b5cebf 100644
--- a/modules/priors/docs/reference/plot.densities.html
+++ b/modules/priors/docs/reference/plot.densities.html
@@ -2,170 +2,211 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
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-
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+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Plot Trait Probability Densities — plot.densities"
+    />
+
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+      property="og:description"
+      content="Plot probability density and data"
+    />
+    <meta name="twitter:card" content="summary" />
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Plot Trait Probability Densities</h1>
-    
-    <div class="hidden name"><code>plot.densities.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Plot Trait Probability Densities</h1>
 
-    <div class="ref-description">
-    
-    <p>Plot probability density and data</p>
-    
-    </div>
+            <div class="hidden name"><code>plot.densities.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Plot probability density and data</p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for densities</span>
+          <pre class="usage"><span class='co'># S3 method for densities</span>
 <span class='fu'>plot</span>(<span class='no'>density.plot.inputs</span>, <span class='no'>outdir</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>outdir</th>
-      <td><p>directory in which to generate figure as pdf</p></td>
-    </tr>
-    <tr>
-      <th>sensitivity.results</th>
-      <td><p>list containing sa.samples and sa.splines</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>outputs plots in outdir/sensitivity.analysis.pdf file</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>outdir</th>
+              <td><p>directory in which to generate figure as pdf</p></td>
+            </tr>
+            <tr>
+              <th>sensitivity.results</th>
+              <td><p>list containing sa.samples and sa.splines</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>outputs plots in outdir/sensitivity.analysis.pdf file</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
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diff --git a/modules/priors/docs/reference/plot.posterior.density.html b/modules/priors/docs/reference/plot.posterior.density.html
index de67dec..736d9b0 100644
--- a/modules/priors/docs/reference/plot.posterior.density.html
+++ b/modules/priors/docs/reference/plot.posterior.density.html
@@ -2,170 +2,217 @@
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+                  </a>
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Add posterior density.</h1>
-    
-    <div class="hidden name"><code>plot.posterior.density.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Add posterior density.</h1>
 
-    <div class="ref-description">
-    
-    <p>Add posterior density to a plot</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>plot.posterior.density.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Add posterior density to a plot</p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for posterior.density</span>
+          <pre
+            class="usage"
+          ><span class='co'># S3 method for posterior.density</span>
 <span class='fu'>plot</span>(<span class='no'>posterior.density</span>, <span class='kw'>base.plot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>posterior.density</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>base.plot</th>
-      <td><p>a ggplot object (grob), created by <code>create.base.plot</code> if none provided</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>plot with posterior density line added</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>posterior.density</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>base.plot</th>
+              <td>
+                <p>
+                  a ggplot object (grob), created by
+                  <code>create.base.plot</code> if none provided
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>plot with posterior density line added</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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-
+    </div>
   </body>
 </html>
-
diff --git a/modules/priors/docs/reference/plot.prior.density.html b/modules/priors/docs/reference/plot.prior.density.html
index 50b2bbe..d4ca76a 100644
--- a/modules/priors/docs/reference/plot.prior.density.html
+++ b/modules/priors/docs/reference/plot.prior.density.html
@@ -2,187 +2,245 @@
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 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Add Prior Density</h1>
-    
-    <div class="hidden name"><code>plot.prior.density.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Add Prior Density</h1>
 
-    <div class="ref-description">
-    
-    <p>Plots a prior density from a parameterized probability distribution</p>
-    
-    </div>
+            <div class="hidden name"><code>plot.prior.density.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for prior.density</span>
+          <div class="ref-description">
+            <p>
+              Plots a prior density from a parameterized probability
+              distribution
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='co'># S3 method for prior.density</span>
 <span class='fu'>plot</span>(<span class='no'>prior.density</span>, <span class='kw'>base.plot</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>prior.color</span> <span class='kw'>=</span> <span class='st'>"black"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>prior.density</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>base.plot</th>
-      <td><p>a ggplot object (grob), created by <code>create.base.plot</code> if none provided</p></td>
-    </tr>
-    <tr>
-      <th>prior.color</th>
-      <td><p>color of line to be plotted</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>plot with prior density added</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p><code><a href='pr.dens.html'>pr.dens</a></code></p></div>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>prior.density</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>base.plot</th>
+              <td>
+                <p>
+                  a ggplot object (grob), created by
+                  <code>create.base.plot</code> if none provided
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prior.color</th>
+              <td><p>color of line to be plotted</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>plot with prior density added</p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>
+              <code><a href="pr.dens.html">pr.dens</a></code>
+            </p>
+          </div>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>plot.prior.density</span>(<span class='fu'><a href='pr.dens.html'>pr.dens</a></span>(<span class='st'>'norm'</span>, <span class='fl'>0</span>, <span class='fl'>1</span>))
 <span class='co'># }</span></pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#see-also">See also</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
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-</div>
+            <li><a href="#value">Value</a></li>
 
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+            <li><a href="#see-also">See also</a></li>
 
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+            <li><a href="#examples">Examples</a></li>
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+          <h2>Author</h2>
 
+          David LeBauer
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index d63132d..c9a1452 100644
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+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Plot trait density</h1>
-    
-    <div class="hidden name"><code>plot.trait.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Plot trait density</h1>
 
-    <div class="ref-description">
-    
-    <p>Plot trait density and data</p>
-    
-    </div>
+            <div class="hidden name"><code>plot.trait.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Plot trait density and data</p>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for trait</span>
+          <pre class="usage"><span class='co'># S3 method for trait</span>
 <span class='fu'>plot</span>(<span class='no'>trait</span>, <span class='kw'>prior</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>posterior.sample</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>trait.df</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fontsize</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>18</span>, <span class='kw'>axis</span> <span class='kw'>=</span> <span class='fl'>14</span>),
   <span class='kw'>x.lim</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>y.lim</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>logx</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait</th>
-      <td><p>character, name of trait to be plotted</p></td>
-    </tr>
-    <tr>
-      <th>prior</th>
-      <td><p>named distribution with parameters</p></td>
-    </tr>
-    <tr>
-      <th>posterior.sample</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>fontsize</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>trait.data</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>plot (grob) object</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait</th>
+              <td><p>character, name of trait to be plotted</p></td>
+            </tr>
+            <tr>
+              <th>prior</th>
+              <td><p>named distribution with parameters</p></td>
+            </tr>
+            <tr>
+              <th>posterior.sample</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>fontsize</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>trait.data</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>plot (grob) object</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>prior1</span> <span class='kw'>&lt;-</span> <span class='fu'>data.frame</span>(<span class='kw'>distn</span> <span class='kw'>=</span> <span class='st'>'norm'</span>,
                      <span class='kw'>parama</span> <span class='kw'>=</span> <span class='fl'>20</span>,
                      <span class='kw'>paramb</span> <span class='kw'>=</span> <span class='fl'>5</span>)
@@ -160,38 +200,34 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
           <span class='kw'>prior</span> <span class='kw'>=</span> <span class='no'>prior1</span>,
           <span class='kw'>trait.df</span> <span class='kw'>=</span> <span class='no'>data1</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          David LeBauer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/priors/docs/reference/pr.dens.html b/modules/priors/docs/reference/pr.dens.html
index 3e0c1c8..a93e0cb 100644
--- a/modules/priors/docs/reference/pr.dens.html
+++ b/modules/priors/docs/reference/pr.dens.html
@@ -2,187 +2,240 @@
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    <![endif]-->
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+                  >1.6.0</span
+                >
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+            </div>
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li class="dropdown">
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+                    class="dropdown-toggle"
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+                      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
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+
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+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate densities</h1>
-    
-    <div class="hidden name"><code>pr.dens.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculates density at n points across the range of a parameter</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pr.dens</span>(<span class='no'>distn</span>, <span class='no'>parama</span>, <span class='no'>paramb</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.001</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>distn</th>
-      <td><p>distribution</p></td>
-    </tr>
-    <tr>
-      <th>parama</th>
-      <td><p>parameter</p></td>
-    </tr>
-    <tr>
-      <th>paramb</th>
-      <td><p>parameter</p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>length of vector to be returned</p></td>
-    </tr>
-    <tr>
-      <th>alpha</th>
-      <td><p>sets range at which the distribution will be evaluated (e.g. from alpha to 1-alpha)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>dataframe with equally spaced x values and the corresponding densities</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>For a distribution and parameters, return the density for values ranging from alpha to 1-alpha</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate densities</h1>
+
+            <div class="hidden name"><code>pr.dens.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Calculates density at n points across the range of a parameter
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pr.dens</span>(<span class='no'>distn</span>, <span class='no'>parama</span>, <span class='no'>paramb</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.001</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>distn</th>
+              <td><p>distribution</p></td>
+            </tr>
+            <tr>
+              <th>parama</th>
+              <td><p>parameter</p></td>
+            </tr>
+            <tr>
+              <th>paramb</th>
+              <td><p>parameter</p></td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td><p>length of vector to be returned</p></td>
+            </tr>
+            <tr>
+              <th>alpha</th>
+              <td>
+                <p>
+                  sets range at which the distribution will be evaluated (e.g.
+                  from alpha to 1-alpha)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            dataframe with equally spaced x values and the corresponding
+            densities
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            For a distribution and parameters, return the density for values
+            ranging from alpha to 1-alpha
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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 </html>
-
diff --git a/modules/priors/docs/reference/pr.samp.html b/modules/priors/docs/reference/pr.samp.html
index 526b9b7..63424c5 100644
--- a/modules/priors/docs/reference/pr.samp.html
+++ b/modules/priors/docs/reference/pr.samp.html
@@ -2,179 +2,221 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Sample from prior — pr.samp • PEcAn.priors</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-
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-<link href="../pkgdown.css" rel="stylesheet">
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    <title>Sample from prior — pr.samp • PEcAn.priors</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Sample from prior — pr.samp" />
+
+    <meta
+      property="og:description"
+      content="Take n random samples from prior"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+    <![endif]-->
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAn.priors</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/priors_demo.html">UNKNOWN TITLE</a>
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Sample from prior</h1>
-    
-    <div class="hidden name"><code>pr.samp.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Take n random samples from prior</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pr.samp</span>(<span class='no'>distn</span>, <span class='no'>parama</span>, <span class='no'>paramb</span>, <span class='no'>n</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>distn</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>parama</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>paramb</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>number of samples to return</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>vector with n random samples from prior</p>
-    
-    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
-    <div class='dont-index'><p>{code<a href='get.sample.html'>get.sample</a></p></div>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#see-also">See also</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Sample from prior</h1>
+
+            <div class="hidden name"><code>pr.samp.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Take n random samples from prior</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pr.samp</span>(<span class='no'>distn</span>, <span class='no'>parama</span>, <span class='no'>paramb</span>, <span class='no'>n</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>distn</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>parama</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>paramb</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td><p>number of samples to return</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>vector with n random samples from prior</p>
+
+          <h2 class="hasAnchor" id="see-also">
+            <a class="anchor" href="#see-also"></a>See also
+          </h2>
+
+          <div class="dont-index">
+            <p>{code<a href="get.sample.html">get.sample</a></p>
+          </div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#see-also">See also</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+          <p>Developed by .</p>
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diff --git a/modules/priors/docs/reference/prior.fn.html b/modules/priors/docs/reference/prior.fn.html
index b80d0b2..c5a2d37 100644
--- a/modules/priors/docs/reference/prior.fn.html
+++ b/modules/priors/docs/reference/prior.fn.html
@@ -2,162 +2,211 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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+    <meta name="twitter:card" content="summary" />
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+
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
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-        <a class="navbar-link" href="../index.html">PEcAn.priors</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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+                    <span class="fa fa-home fa-lg"></span>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>prior.fn</h1>
-    
-    <div class="hidden name"><code>prior.fn.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-
-    </div>
-
-    <pre class="usage"><span class='fu'>prior.fn</span>(<span class='no'>parms</span>, <span class='no'>x</span>, <span class='no'>alpha</span>, <span class='no'>distn</span>, <span class='kw'>central.tendency</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>parms</th>
-      <td><p>target for optimization</p></td>
-    </tr>
-    <tr>
-      <th>x</th>
-      <td><p>vector with c(lcl, ucl, ct) lcl / ucl = confidence limits, ct = entral tendency</p></td>
-    </tr>
-    <tr>
-      <th>alpha</th>
-      <td><p>quantile at which lcl/ucl are estimated (e.g. for a 95<!-- % CI, alpha = 0.5)} --></p>
-<p>distnnamed distribution, one of 'lnorm', 'gamma', 'weibull', 'beta'; support for other distributions not currently implemented</p>
-<p>central.tendencyone of 'mode', 'median', and 'mean'</p>
-<p>traitname of trait, can be used for exceptions (currently used for trait == 'q')</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>prior.fn</h1>
+
+            <div class="hidden name"><code>prior.fn.Rd</code></div>
+          </div>
+
+          <div class="ref-description"></div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>prior.fn</span>(<span class='no'>parms</span>, <span class='no'>x</span>, <span class='no'>alpha</span>, <span class='no'>distn</span>, <span class='kw'>central.tendency</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>parms</th>
+              <td><p>target for optimization</p></td>
+            </tr>
+            <tr>
+              <th>x</th>
+              <td>
+                <p>
+                  vector with c(lcl, ucl, ct) lcl / ucl = confidence limits, ct
+                  = entral tendency
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>alpha</th>
+              <td>
+                <p>
+                  quantile at which lcl/ucl are estimated (e.g. for a 95<!-- % CI, alpha = 0.5)} -->
+                </p>
+                <p>
+                  distnnamed distribution, one of 'lnorm', 'gamma', 'weibull',
+                  'beta'; support for other distributions not currently
+                  implemented
+                </p>
+                <p>central.tendencyone of 'mode', 'median', and 'mean'</p>
+                <p>
+                  traitname of trait, can be used for exceptions (currently used
+                  for trait == 'q')
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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index 0c53c0a..01bc2b6 100644
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Prior Figure</h1>
-    
-    <div class="hidden name"><code>priorfig.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Prior Figure</h1>
 
-    <div class="ref-description">
-    
-    <p>Plot prior density and data</p>
-    
-    </div>
+            <div class="hidden name"><code>priorfig.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Plot prior density and data</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>priorfig</span>(<span class='kw'>priordata</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>priordensity</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='st'>""</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>priorfig</span>(<span class='kw'>priordata</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>priordensity</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>trait</span> <span class='kw'>=</span> <span class='st'>""</span>,
   <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>fontsize</span> <span class='kw'>=</span> <span class='fl'>18</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>priordata</th>
-      <td><p>observations to be plotted as points</p></td>
-    </tr>
-    <tr>
-      <th>priordensity</th>
-      <td><p>density of prior distribution, calculated by <code>prior.density</code></p></td>
-    </tr>
-    <tr>
-      <th>trait</th>
-      <td><p>name of trait</p></td>
-    </tr>
-    <tr>
-      <th>xlim</th>
-      <td><p>limits for x axis</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>plot / grob of prior distribution with data used to inform the distribution</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>priordata</th>
+              <td><p>observations to be plotted as points</p></td>
+            </tr>
+            <tr>
+              <th>priordensity</th>
+              <td>
+                <p>
+                  density of prior distribution, calculated by
+                  <code>prior.density</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>trait</th>
+              <td><p>name of trait</p></td>
+            </tr>
+            <tr>
+              <th>xlim</th>
+              <td><p>limits for x axis</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            plot / grob of prior distribution with data used to inform the
+            distribution
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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index 5ad4643..3e3b4d4 100644
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-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
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+    <title>License • PEcAnRTM</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="License" />
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+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-title-body">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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-        <a class="navbar-link" href="index.html">PEcAnRTM</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
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-<li>
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-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="articles/pecanrtm.vignette.html">The PEcAn RTM package</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAnRTM</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>License</h1>
-    </div>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>University of Illinois/NCSA Open Source License
+          <pre>
+University of Illinois/NCSA Open Source License
 
 Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
 
@@ -133,27 +170,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
-</pre>
-
-  </div>
-
-</div>
-
+</pre
+          >
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/rtm/docs/articles/index.html b/modules/rtm/docs/articles/index.html
index 08e4d9b..0cdf6ad 100644
--- a/modules/rtm/docs/articles/index.html
+++ b/modules/rtm/docs/articles/index.html
@@ -2,133 +2,168 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<!-- jquery -->
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-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="Articles" />
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Articles • PEcAnRTM</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta property="og:title" content="Articles" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-article-index">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
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-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAnRTM</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
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-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/pecanrtm.vignette.html">The PEcAn RTM package</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAnRTM</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-      <h1>Articles</h1>
-    </div>
-
-    <div class="section ">
-      <h3>All vignettes</h3>
-      <p class="section-desc"></p>
-
-      <ul>
-        <li><a href="pecanrtm.vignette.html">The PEcAn RTM package</a></li>
-      </ul>
-    </div>
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Articles</h1>
+          </div>
+
+          <div class="section ">
+            <h3>All vignettes</h3>
+            <p class="section-desc"></p>
+
+            <ul>
+              <li>
+                <a href="pecanrtm.vignette.html">The PEcAn RTM package</a>
+              </li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/rtm/docs/articles/pecanrtm.vignette.html b/modules/rtm/docs/articles/pecanrtm.vignette.html
index 9362486..2e633e6 100644
--- a/modules/rtm/docs/articles/pecanrtm.vignette.html
+++ b/modules/rtm/docs/articles/pecanrtm.vignette.html
@@ -1,111 +1,206 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>The PEcAn RTM package • PEcAnRTM</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script><meta property="og:title" content="The PEcAn RTM package">
-<meta property="og:description" content="">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>The PEcAn RTM package • PEcAnRTM</title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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-      <h1>The PEcAn RTM package</h1>
-                        <h4 class="author">Alexey Shiklomanov</h4>
-            
-      
-      
-      <div class="hidden name"><code>pecanrtm.vignette.Rmd</code></div>
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+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
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+          <div class="page-header toc-ignore">
+            <h1>The PEcAn RTM package</h1>
+            <h4 class="author">Alexey Shiklomanov</h4>
 
-    </div>
+            <div class="hidden name"><code>pecanrtm.vignette.Rmd</code></div>
+          </div>
 
-    
-    
-<div id="introduction" class="section level1">
-<h1 class="hasAnchor">
-<a href="#introduction" class="anchor"></a>Introduction</h1>
-<p>The PEcAnRTM package provides tools for analyses involving common radiative transfer models. The highlights of this package are its ability to efficiently run a suite of related leaf and canopy radiative transfer models, as well as to perform maximum likelihood and, particularly, Bayesian inversions of these models.</p>
-</div>
-<div id="installation" class="section level1">
-<h1 class="hasAnchor">
-<a href="#installation" class="anchor"></a>Installation</h1>
-<p>The easiest way to install this package is via <code>install_github</code> from the <code>devtools</code> package.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">install.packages</span>(<span class="st">"devtools"</span>)
+          <div id="introduction" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#introduction" class="anchor"></a>Introduction
+            </h1>
+            <p>
+              The PEcAnRTM package provides tools for analyses involving common
+              radiative transfer models. The highlights of this package are its
+              ability to efficiently run a suite of related leaf and canopy
+              radiative transfer models, as well as to perform maximum
+              likelihood and, particularly, Bayesian inversions of these models.
+            </p>
+          </div>
+          <div id="installation" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#installation" class="anchor"></a>Installation
+            </h1>
+            <p>
+              The easiest way to install this package is via
+              <code>install_github</code> from the
+              <code>devtools</code> package.
+            </p>
+            <div class="sourceCode">
+              <pre
+                class="sourceCode r"
+              ><code class="sourceCode r"><span class="kw">install.packages</span>(<span class="st">"devtools"</span>)
 <span class="kw">library</span>(devtools)
 <span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"ashiklom/pecan"</span>, <span class="dt">subdir =</span> <span class="st">"modules/rtm"</span>)
 <span class="co"># Defaults to branch 'master'. </span>
-<span class="co"># For custom branches, add `ref = "branchname"`</span></code></pre></div>
-<p>This package relies on a modern (&gt;= 2003) Fortran compiler, as determined by your R installation. On most Unix systems, this is standard, but R may specify a particular compiler version that you don’t have, resulting in an installation error. To fix this, simply add the following to your system <code>~/R/Makevars</code> file.</p>
-<pre><code>FC = gfortran</code></pre>
-</div>
-<div id="overview-of-features" class="section level1">
-<h1 class="hasAnchor">
-<a href="#overview-of-features" class="anchor"></a>Overview of features</h1>
-<div id="simulating-reflectance" class="section level2">
-<h2 class="hasAnchor">
-<a href="#simulating-reflectance" class="anchor"></a>Simulating reflectance</h2>
-<p>Available radiative transfer models are called by passing a vector of their parameters. Similar models with different versions (e.g. PROSPECT 4, 5, 5B) also have a “version” argument. These models return a matrix of reflectance, transmittance, and/or absorption spectra (depending on the model) at 1 nm resolution over the wavelength range 400 to 2500 nm.</p>
-<p>The PROSPECT family of models returns the reflectance (column 1) and transmittance (column 2) for an individual leaf as a function of 4 to 6 parameters (depending on the version).</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(PEcAnRTM)
+<span class="co"># For custom branches, add `ref = "branchname"`</span></code></pre>
+            </div>
+            <p>
+              This package relies on a modern (&gt;= 2003) Fortran compiler, as
+              determined by your R installation. On most Unix systems, this is
+              standard, but R may specify a particular compiler version that you
+              don’t have, resulting in an installation error. To fix this,
+              simply add the following to your system
+              <code>~/R/Makevars</code> file.
+            </p>
+            <pre><code>FC = gfortran</code></pre>
+          </div>
+          <div id="overview-of-features" class="section level1">
+            <h1 class="hasAnchor">
+              <a href="#overview-of-features" class="anchor"></a>Overview of
+              features
+            </h1>
+            <div id="simulating-reflectance" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#simulating-reflectance" class="anchor"></a>Simulating
+                reflectance
+              </h2>
+              <p>
+                Available radiative transfer models are called by passing a
+                vector of their parameters. Similar models with different
+                versions (e.g. PROSPECT 4, 5, 5B) also have a “version”
+                argument. These models return a matrix of reflectance,
+                transmittance, and/or absorption spectra (depending on the
+                model) at 1 nm resolution over the wavelength range 400 to 2500
+                nm.
+              </p>
+              <p>
+                The PROSPECT family of models returns the reflectance (column 1)
+                and transmittance (column 2) for an individual leaf as a
+                function of 4 to 6 parameters (depending on the version).
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">library</span>(PEcAnRTM)
 wl &lt;-<span class="st"> </span><span class="dv">400</span><span class="op">:</span><span class="dv">2500</span>
 params &lt;-<span class="st"> </span><span class="kw">c</span>(
   <span class="st">"N"</span> =<span class="st"> </span><span class="fl">1.4</span>, <span class="st">"Cab"</span> =<span class="st"> </span><span class="dv">40</span>, <span class="st">"Car"</span> =<span class="st"> </span><span class="dv">15</span>,
@@ -113,59 +208,186 @@ <h2 class="hasAnchor">
 )
 
 p4 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/prospect.html">prospect</a></span>(params[<span class="kw">c</span>(<span class="op">-</span><span class="dv">3</span>, <span class="op">-</span><span class="dv">4</span>)], <span class="dt">version =</span> <span class="dv">4</span>)
-p4</code></pre></div>
-<p>Notice only the first and last few lines of the spectra are printed, and the wavelength is annotated on the side. This is is because all RTM simulations in this package are of a special matrix class <code>spectra</code>.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">class</span>(p4)</code></pre></div>
-<p>This class allows traditional subsetting via index with single brackets (<code>[]</code>), as well as subsetting by wavelength with double brackets.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">p4[<span class="dv">1</span><span class="op">:</span><span class="dv">50</span>, <span class="dv">1</span>]
-p4[[<span class="dv">500</span><span class="op">:</span><span class="dv">520</span>, <span class="dv">2</span>]]</code></pre></div>
-<p>The package also provides special plotting (<code>plot</code>, <code>matplot</code>) and combining (<code>cbind</code>) methods. Note that the <code>cbind</code> method automatically matches wavelengths, which facilitates working with spectra with different wavelengths.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">p5 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/prospect.html">prospect</a></span>(params[<span class="op">-</span><span class="dv">4</span>], <span class="dt">version =</span> <span class="dv">5</span>)
+p4</code></pre>
+              </div>
+              <p>
+                Notice only the first and last few lines of the spectra are
+                printed, and the wavelength is annotated on the side. This is is
+                because all RTM simulations in this package are of a special
+                matrix class <code>spectra</code>.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">class</span>(p4)</code></pre>
+              </div>
+              <p>
+                This class allows traditional subsetting via index with single
+                brackets (<code>[]</code>), as well as subsetting by wavelength
+                with double brackets.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">p4[<span class="dv">1</span><span class="op">:</span><span class="dv">50</span>, <span class="dv">1</span>]
+p4[[<span class="dv">500</span><span class="op">:</span><span class="dv">520</span>, <span class="dv">2</span>]]</code></pre>
+              </div>
+              <p>
+                The package also provides special plotting (<code>plot</code>,
+                <code>matplot</code>) and combining (<code>cbind</code>)
+                methods. Note that the <code>cbind</code> method automatically
+                matches wavelengths, which facilitates working with spectra with
+                different wavelengths.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">p5 &lt;-<span class="st"> </span><span class="kw"><a href="../reference/prospect.html">prospect</a></span>(params[<span class="op">-</span><span class="dv">4</span>], <span class="dt">version =</span> <span class="dv">5</span>)
 p5b &lt;-<span class="st"> </span><span class="kw"><a href="../reference/prospect.html">prospect</a></span>(params, <span class="dt">version =</span> <span class="st">"5B"</span>)
 p_multi &lt;-<span class="st"> </span><span class="kw">cbind</span>(p4, p5, p5b)
 <span class="kw"><a href="../reference/matplot.html">matplot</a></span>(p_multi[, <span class="kw">c</span>(<span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">5</span>)], <span class="dt">lty =</span> <span class="dv">1</span><span class="op">:</span><span class="dv">3</span>, <span class="dt">col =</span> <span class="dv">2</span>, <span class="dt">ylim =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">1</span>))
 <span class="kw"><a href="../reference/matplot.html">matplot</a></span>(<span class="dv">1</span> <span class="op">-</span><span class="st"> </span>p_multi[, <span class="kw">c</span>(<span class="dv">2</span>, <span class="dv">4</span>, <span class="dv">6</span>)], <span class="dt">lty =</span> <span class="dv">1</span><span class="op">:</span><span class="dv">3</span>, <span class="dt">col =</span> <span class="dv">3</span>,  <span class="dt">add =</span> <span class="ot">TRUE</span>)
 <span class="kw">legend</span>(<span class="st">"topright"</span>, <span class="kw">c</span>(<span class="st">"Reflectance"</span>, <span class="st">"Transmittance"</span>), <span class="dt">col=</span><span class="kw">c</span>(<span class="dv">2</span>, <span class="dv">3</span>), <span class="dt">lty =</span> <span class="dv">1</span>)
-<span class="kw">legend</span>(<span class="st">"top"</span>, <span class="kw">c</span>(<span class="st">"4"</span>, <span class="st">"5"</span>, <span class="st">"5B"</span>), <span class="dt">lty =</span> <span class="dv">1</span><span class="op">:</span><span class="dv">3</span>)</code></pre></div>
-<p>The SAIL family of models returns the bidirectional (1), hemispherical directional (2), directional hemispherical (3), and bidirectional hemispherical (4) reflectance factors for a canopy with a given set of approximately 20 parameters. It is often coupled to the PROSPECT model as PRO4SAIL. (Again, note that the return type is a <code>spectra</code>, which leads <code>matplot</code> to automatically put wavelengths on the x axis.)</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">sail.params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/defparam.html">defparam</a></span>(<span class="st">"pro4sail"</span>)
+<span class="kw">legend</span>(<span class="st">"top"</span>, <span class="kw">c</span>(<span class="st">"4"</span>, <span class="st">"5"</span>, <span class="st">"5B"</span>), <span class="dt">lty =</span> <span class="dv">1</span><span class="op">:</span><span class="dv">3</span>)</code></pre>
+              </div>
+              <p>
+                The SAIL family of models returns the bidirectional (1),
+                hemispherical directional (2), directional hemispherical (3),
+                and bidirectional hemispherical (4) reflectance factors for a
+                canopy with a given set of approximately 20 parameters. It is
+                often coupled to the PROSPECT model as PRO4SAIL. (Again, note
+                that the return type is a <code>spectra</code>, which leads
+                <code>matplot</code> to automatically put wavelengths on the x
+                axis.)
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">sail.params &lt;-<span class="st"> </span><span class="kw"><a href="../reference/defparam.html">defparam</a></span>(<span class="st">"pro4sail"</span>)
 <span class="kw">print</span>(sail.params)
 p4s &lt;-<span class="st"> </span><span class="kw"><a href="../reference/pro4sail.html">pro4sail</a></span>(sail.params)
 <span class="kw"><a href="../reference/matplot.html">matplot</a></span>(p4s, <span class="dt">xlab=</span><span class="st">"Wavelength (nm)"</span>, <span class="dt">ylab=</span><span class="st">"Reflectance"</span>)
-<span class="kw">legend</span>(<span class="st">"topright"</span>, <span class="kw">as.character</span>(<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>), <span class="dt">col=</span><span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, <span class="dt">lty=</span><span class="dv">1</span><span class="op">:</span><span class="dv">4</span>)</code></pre></div>
-<p>The above example illustrates the use of <code>defparam</code> to get the default parameters for a particular model. Similarly, <code>model.list</code> is a <code>data.frame</code> containing all currently available models.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">print</span>(model.list)</code></pre></div>
-</div>
-<div id="inversion" class="section level2">
-<h2 class="hasAnchor">
-<a href="#inversion" class="anchor"></a>Inversion</h2>
-<p>A novel feature of this package is the ability to perform a Bayesian inversion of a Radiative Transfer Model. Here are several advantages of the Bayesian approach:</p>
-<ul>
-<li>
-<strong>Parameter uncertainty:</strong> The output of a Bayesian analysis is a full joint probability distribution of the model parameters, which includes a robust estimate of their uncertainy and covariance between parameters.</li>
-<li>
-<strong>Prior knowledge:</strong> If previous, independent estimates of parameters are available, these can be used to inform the model.</li>
-<li>
-<strong>Partitioning variability:</strong> Random effects models provide a powerful framework for understanding the sources of variability and uncertainty in a data set.</li>
-</ul>
-<p>An inversion can be performed using the <code>invert.auto</code> function, which uses the Metropolis Hastings MCMC algorithm to invert an arbitrary model. There are a lot of configuration options to <code>invert.auto</code>, so the recommended way to perform an inversion is to start with a default settings list, provided by the package itself. In the following sample, we demonstrate the default inversion of the PROSPECT model.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">invert.options &lt;-<span class="st"> </span>default.settings.prospect</code></pre></div>
-<p>The model to be inverted is, in this case, just a one-line call to the PROSPECT 5 model with the params vector. It returns a vector of reflectance values. The requirement is that the “model” output be as long as the length (or number of rows) of the observation vector (or matrix). In this case, the PROSPECT model returns 2101 reflectance values, so our observation also has to have this many points.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">invert.options<span class="op">$</span>model</code></pre></div>
-<p>The recommended way to set settings is to start with a default object and modify it. For example, in the following block, we reduce the length of the run to make it go a little faster.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">invert.options<span class="op">$</span>n.tries &lt;-<span class="st"> </span><span class="dv">1</span>      <span class="co"># Number of attempts</span>
+<span class="kw">legend</span>(<span class="st">"topright"</span>, <span class="kw">as.character</span>(<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>), <span class="dt">col=</span><span class="dv">1</span><span class="op">:</span><span class="dv">4</span>, <span class="dt">lty=</span><span class="dv">1</span><span class="op">:</span><span class="dv">4</span>)</code></pre>
+              </div>
+              <p>
+                The above example illustrates the use of
+                <code>defparam</code> to get the default parameters for a
+                particular model. Similarly, <code>model.list</code> is a
+                <code>data.frame</code> containing all currently available
+                models.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">print</span>(model.list)</code></pre>
+              </div>
+            </div>
+            <div id="inversion" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#inversion" class="anchor"></a>Inversion
+              </h2>
+              <p>
+                A novel feature of this package is the ability to perform a
+                Bayesian inversion of a Radiative Transfer Model. Here are
+                several advantages of the Bayesian approach:
+              </p>
+              <ul>
+                <li>
+                  <strong>Parameter uncertainty:</strong> The output of a
+                  Bayesian analysis is a full joint probability distribution of
+                  the model parameters, which includes a robust estimate of
+                  their uncertainy and covariance between parameters.
+                </li>
+                <li>
+                  <strong>Prior knowledge:</strong> If previous, independent
+                  estimates of parameters are available, these can be used to
+                  inform the model.
+                </li>
+                <li>
+                  <strong>Partitioning variability:</strong> Random effects
+                  models provide a powerful framework for understanding the
+                  sources of variability and uncertainty in a data set.
+                </li>
+              </ul>
+              <p>
+                An inversion can be performed using the
+                <code>invert.auto</code> function, which uses the Metropolis
+                Hastings MCMC algorithm to invert an arbitrary model. There are
+                a lot of configuration options to <code>invert.auto</code>, so
+                the recommended way to perform an inversion is to start with a
+                default settings list, provided by the package itself. In the
+                following sample, we demonstrate the default inversion of the
+                PROSPECT model.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">invert.options &lt;-<span class="st"> </span>default.settings.prospect</code></pre>
+              </div>
+              <p>
+                The model to be inverted is, in this case, just a one-line call
+                to the PROSPECT 5 model with the params vector. It returns a
+                vector of reflectance values. The requirement is that the
+                “model” output be as long as the length (or number of rows) of
+                the observation vector (or matrix). In this case, the PROSPECT
+                model returns 2101 reflectance values, so our observation also
+                has to have this many points.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">invert.options<span class="op">$</span>model</code></pre>
+              </div>
+              <p>
+                The recommended way to set settings is to start with a default
+                object and modify it. For example, in the following block, we
+                reduce the length of the run to make it go a little faster.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r">invert.options<span class="op">$</span>n.tries &lt;-<span class="st"> </span><span class="dv">1</span>      <span class="co"># Number of attempts</span>
 invert.options<span class="op">$</span>nchains &lt;-<span class="st"> </span><span class="dv">2</span>      <span class="co"># Number of MCMC chains</span>
 invert.options<span class="op">$</span>ngibbs &lt;-<span class="st"> </span><span class="dv">5000</span>    <span class="co"># Number of iterations per chain</span>
 invert.options<span class="op">$</span>burnin &lt;-<span class="st"> </span><span class="dv">1000</span>    <span class="co"># Length of burnin period</span>
-invert.options<span class="op">$</span>do.lsq.first &lt;-<span class="st"> </span><span class="ot">TRUE</span> <span class="co"># Initialize with results from a fast least-squares optimization algorithm</span></code></pre></div>
-<p>The full list of inversion options is below. See the documentation for <code>invert.auto</code> for a full description of each of these.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">names</span>(invert.options)</code></pre></div>
-<p>Now, we load some test data (for <em>Acer rubrum</em> leaves (<code>testspec_ACRU</code>, accessible through <code>data(testspec)</code>).</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">data</span>(testspec)
+invert.options<span class="op">$</span>do.lsq.first &lt;-<span class="st"> </span><span class="ot">TRUE</span> <span class="co"># Initialize with results from a fast least-squares optimization algorithm</span></code></pre>
+              </div>
+              <p>
+                The full list of inversion options is below. See the
+                documentation for <code>invert.auto</code> for a full
+                description of each of these.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">names</span>(invert.options)</code></pre>
+              </div>
+              <p>
+                Now, we load some test data (for <em>Acer rubrum</em> leaves
+                (<code>testspec_ACRU</code>, accessible through
+                <code>data(testspec)</code>).
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">data</span>(testspec)
 observed &lt;-<span class="st"> </span>testspec_ACRU[,<span class="dv">1</span>]
-<span class="kw">plot</span>(wl, observed, <span class="dt">xlab=</span><span class="st">"Wavelength"</span>, <span class="dt">ylab=</span><span class="st">"Reflectance"</span>, <span class="dt">type=</span><span class="st">'l'</span>)</code></pre></div>
-<p>To perform an inversion, just pass the observation matrix and the inversion settings into <code>invert.auto</code> (NOTE: <code>quiet = TRUE</code> suppresses the progress bar, which is done here to clean up the knitted document. <code>threshold = ...</code> sets the maximum value of the multivariate Gelman Diagnostic used to assess convergence – it defaults to 1.1, but we set it higher here for demosntrative purposes).</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span>(<span class="kw">file.exists</span>(<span class="st">"inversion.output.rds"</span>)){
+<span class="kw">plot</span>(wl, observed, <span class="dt">xlab=</span><span class="st">"Wavelength"</span>, <span class="dt">ylab=</span><span class="st">"Reflectance"</span>, <span class="dt">type=</span><span class="st">'l'</span>)</code></pre>
+              </div>
+              <p>
+                To perform an inversion, just pass the observation matrix and
+                the inversion settings into <code>invert.auto</code> (NOTE:
+                <code>quiet = TRUE</code> suppresses the progress bar, which is
+                done here to clean up the knitted document.
+                <code>threshold = ...</code> sets the maximum value of the
+                multivariate Gelman Diagnostic used to assess convergence – it
+                defaults to 1.1, but we set it higher here for demosntrative
+                purposes).
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="cf">if</span>(<span class="kw">file.exists</span>(<span class="st">"inversion.output.rds"</span>)){
     inversion.output &lt;-<span class="st"> </span><span class="kw">readRDS</span>(<span class="st">"inversion.output.rds"</span>)
 } <span class="cf">else</span> {
     inversion.output &lt;-<span class="st"> </span><span class="kw"><a href="../reference/invert.auto.html">invert.auto</a></span>(<span class="dt">observed =</span> observed,
@@ -173,9 +395,18 @@ <h2 class="hasAnchor">
                                     <span class="dt">quiet =</span> <span class="ot">TRUE</span>,
                                     <span class="dt">threshold =</span> <span class="fl">1.3</span>)
     <span class="kw">saveRDS</span>(inversion.output, <span class="st">"inversion.output.rds"</span>)
-}</code></pre></div>
-<p>The output of <code>invert.auto</code> is a list of two objects: A list of summary statistics for each parameter and an <code>mcmc.list</code> object of the samples for diagnostic purposes or calculation of other summary statistics.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">par</span>(<span class="dt">mfrow=</span><span class="kw">c</span>(<span class="dv">2</span>,<span class="dv">1</span>))
+}</code></pre>
+              </div>
+              <p>
+                The output of <code>invert.auto</code> is a list of two objects:
+                A list of summary statistics for each parameter and an
+                <code>mcmc.list</code> object of the samples for diagnostic
+                purposes or calculation of other summary statistics.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">par</span>(<span class="dt">mfrow=</span><span class="kw">c</span>(<span class="dv">2</span>,<span class="dv">1</span>))
 <span class="kw">plot</span>(inversion.output<span class="op">$</span>samples, <span class="dt">auto.layout=</span><span class="ot">FALSE</span>)
 
 <span class="kw">par</span>(<span class="dt">mfrow=</span><span class="kw">c</span>(<span class="dv">1</span>,<span class="dv">1</span>))
@@ -188,43 +419,45 @@ <h2 class="hasAnchor">
 
 <span class="kw">plot</span>(wl, observed, <span class="dt">type=</span><span class="st">'l'</span>, <span class="dt">col=</span><span class="dv">1</span>, <span class="dt">xlab=</span><span class="st">"wavelength (nm)"</span>, <span class="dt">ylab=</span><span class="st">"reflectance"</span>)
 <span class="kw">lines</span>(wl, prospect.sim, <span class="dt">type=</span><span class="st">'l'</span>, <span class="dt">col=</span><span class="dv">2</span>)
-<span class="kw">legend</span>(<span class="st">"topright"</span>, <span class="kw">c</span>(<span class="st">"observed"</span>, <span class="st">"predicted"</span>), <span class="dt">lty=</span><span class="dv">1</span>, <span class="dt">col=</span><span class="dv">1</span><span class="op">:</span><span class="dv">2</span>)</code></pre></div>
-</div>
-</div>
-  </div>
+<span class="kw">legend</span>(<span class="st">"topright"</span>, <span class="kw">c</span>(<span class="st">"observed"</span>, <span class="st">"predicted"</span>), <span class="dt">lty=</span><span class="dv">1</span>, <span class="dt">col=</span><span class="dv">1</span><span class="op">:</span><span class="dv">2</span>)</code></pre>
+              </div>
+            </div>
+          </div>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-        <div id="tocnav">
-      <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
-      <ul class="nav nav-pills nav-stacked">
-<li><a href="#introduction">Introduction</a></li>
-      <li><a href="#installation">Installation</a></li>
-      <li>
-<a href="#overview-of-features">Overview of features</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#simulating-reflectance">Simulating reflectance</a></li>
-      <li><a href="#inversion">Inversion</a></li>
-      </ul>
-</li>
-      </ul>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <div id="tocnav">
+            <h2 class="hasAnchor">
+              <a href="#tocnav" class="anchor"></a>Contents
+            </h2>
+            <ul class="nav nav-pills nav-stacked">
+              <li><a href="#introduction">Introduction</a></li>
+              <li><a href="#installation">Installation</a></li>
+              <li>
+                <a href="#overview-of-features">Overview of features</a>
+                <ul class="nav nav-pills nav-stacked">
+                  <li>
+                    <a href="#simulating-reflectance">Simulating reflectance</a>
+                  </li>
+                  <li><a href="#inversion">Inversion</a></li>
+                </ul>
+              </li>
+            </ul>
+          </div>
+        </div>
       </div>
 
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-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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index 5acbb17..d008bf7 100644
--- a/modules/rtm/docs/authors.html
+++ b/modules/rtm/docs/authors.html
@@ -2,142 +2,169 @@
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
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+    ></script>
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-<div class="row">
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-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Alexey Shiklomanov</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Alexey Shiklomanov</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/docsearch.css b/modules/rtm/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/rtm/docs/docsearch.css
+++ b/modules/rtm/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/rtm/docs/docsearch.js b/modules/rtm/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/rtm/docs/docsearch.js
+++ b/modules/rtm/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/rtm/docs/index.html b/modules/rtm/docs/index.html
index 26c90f0..54a3fa8 100644
--- a/modules/rtm/docs/index.html
+++ b/modules/rtm/docs/index.html
@@ -1,137 +1,245 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for radiative transfer modeling • PEcAnRTM</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for radiative transfer modeling">
-<meta property="og:description" content="This package contains functions for performing forward runs and
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for radiative transfer modeling • PEcAnRTM
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for radiative transfer modeling"
+    />
+    <meta
+      property="og:description"
+      content="This package contains functions for performing forward runs and
     inversions of radiative transfer models (RTMs). Inversions can be performed
     using maximum likelihood, or more complex hierarchical Bayesian methods.
-    Underlying numerical analyses are optimized for speed using Fortran code.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    Underlying numerical analyses are optimized for speed using Fortran code."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAnRTM</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-<li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-<li>
-      <a href="articles/pecanrtm.vignette.html">The PEcAn RTM package</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
-</div>
-<!--/.nav-collapse -->
-  </div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
-
-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    <div id="pecan-radiative-transfer-modeling-module" class="section level1">
-<div class="page-header"><h1 class="hasAnchor">
-<a href="#pecan-radiative-transfer-modeling-module" class="anchor"></a>PEcAn Radiative Transfer Modeling module</h1></div>
-<p><strong>Corresponding author</strong><br>
-Alexey Shiklomanov<br>
-Dept. of Earth and Environment<br>
-Boston University<br><a href="mailto:ashiklom@bu.edu">ashiklom@bu.edu</a></p>
-<div id="installation" class="section level2">
-<h2 class="hasAnchor">
-<a href="#installation" class="anchor"></a>Installation</h2>
-<p>Easiest way to install is via <code>install_github</code> from the <code>devtools</code> package.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools)
-<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"ashiklom/pecan"</span>, <span class="dt">subdir=</span><span class="st">"modules/rtm"</span>)</code></pre></div>
-<p>If you want a specific branch, do <code><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github(..., ref="&lt;branch&gt;")</a></code>.</p>
-<p>From there, you should be able to load the package in your typical R session.</p>
-<p><em>NOTE: On some OS X systems, the automatic specification of <code>gfortran</code> will fail, causing the installation to abort. To fix this issue, you will need to add something like the following the <code>~/.R/Makevars</code> file.</em></p>
-<pre><code>FC = gfortran</code></pre>
-<p>For more information, see the vignette (<code>vignettes/pecanrtm.vignettes.Rmd</code>).</p>
-</div>
-</div>
-  </div>
-
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
-<ul class="list-unstyled">
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
-</ul>
-</div>
-<div class="license">
-<h2>License</h2>
-<ul class="list-unstyled">
-<li>
-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
-</li>
-</ul>
-</div>
-<div class="developers">
-<h2>Developers</h2>
-<ul class="list-unstyled">
-<li><a href="authors.html">All authors...</a></li>
-</ul>
-</div>
+      <header>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAnRTM</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-  </div>
-</div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          <div
+            id="pecan-radiative-transfer-modeling-module"
+            class="section level1"
+          >
+            <div class="page-header">
+              <h1 class="hasAnchor">
+                <a
+                  href="#pecan-radiative-transfer-modeling-module"
+                  class="anchor"
+                ></a
+                >PEcAn Radiative Transfer Modeling module
+              </h1>
+            </div>
+            <p>
+              <strong>Corresponding author</strong><br />
+              Alexey Shiklomanov<br />
+              Dept. of Earth and Environment<br />
+              Boston University<br /><a href="mailto:ashiklom@bu.edu"
+                >ashiklom@bu.edu</a
+              >
+            </p>
+            <div id="installation" class="section level2">
+              <h2 class="hasAnchor">
+                <a href="#installation" class="anchor"></a>Installation
+              </h2>
+              <p>
+                Easiest way to install is via <code>install_github</code> from
+                the <code>devtools</code> package.
+              </p>
+              <div class="sourceCode">
+                <pre
+                  class="sourceCode r"
+                ><code class="sourceCode r"><span class="kw">library</span>(devtools)
+<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"ashiklom/pecan"</span>, <span class="dt">subdir=</span><span class="st">"modules/rtm"</span>)</code></pre>
+              </div>
+              <p>
+                If you want a specific branch, do
+                <code
+                  ><a
+                    href="http://www.rdocumentation.org/packages/devtools/topics/install_github"
+                    >install_github(..., ref="&lt;branch&gt;")</a
+                  ></code
+                >.
+              </p>
+              <p>
+                From there, you should be able to load the package in your
+                typical R session.
+              </p>
+              <p>
+                <em
+                  >NOTE: On some OS X systems, the automatic specification of
+                  <code>gfortran</code> will fail, causing the installation to
+                  abort. To fix this issue, you will need to add something like
+                  the following the <code>~/.R/Makevars</code> file.</em
+                >
+              </p>
+              <pre><code>FC = gfortran</code></pre>
+              <p>
+                For more information, see the vignette
+                (<code>vignettes/pecanrtm.vignettes.Rmd</code>).
+              </p>
+            </div>
+          </div>
+        </div>
 
-      <footer><div class="copyright">
-  <p>Developed by .</p>
-</div>
+        <div class="col-md-3" id="sidebar">
+          <div class="links">
+            <h2>Links</h2>
+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
+            </ul>
+          </div>
+          <div class="license">
+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
+            </ul>
+          </div>
+        </div>
+      </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-</div>
-
-  
-
+    </div>
   </body>
 </html>
diff --git a/modules/rtm/docs/pkgdown.css b/modules/rtm/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
--- a/modules/rtm/docs/pkgdown.css
+++ b/modules/rtm/docs/pkgdown.css
@@ -13,7 +13,8 @@
  *
  */
 
-html, body {
+html,
+body {
   height: 100%;
 }
 
@@ -68,7 +69,7 @@ img {
 
 a.anchor {
   margin-left: -30px;
-  display:inline-block;
+  display: inline-block;
   width: 30px;
   height: 30px;
   visibility: hidden;
@@ -89,10 +90,12 @@ a.anchor {
   }
 }
 
-
 /* Fixes for fixed navbar --------------------------*/
 
-.contents h1, .contents h2, .contents h3, .contents h4 {
+.contents h1,
+.contents h2,
+.contents h3,
+.contents h4 {
   padding-top: 60px;
   margin-top: -40px;
 }
@@ -107,7 +110,6 @@ a.anchor {
   }
 }
 
-
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -133,19 +135,41 @@ a.anchor {
 
 /* Reference index & topics ----------------------------------------------- */
 
-.ref-index th {font-weight: normal;}
+.ref-index th {
+  font-weight: normal;
+}
 
-.ref-index td {vertical-align: top;}
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index td {
+  vertical-align: top;
+}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
+.ref-index .alias {
+  width: 40%;
+}
+.ref-index .title {
+  width: 60%;
+}
 
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top;}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
+.ref-arguments th {
+  text-align: right;
+  padding-right: 10px;
+}
+.ref-arguments th,
+.ref-arguments td {
+  vertical-align: top;
+}
+.ref-arguments .name {
+  width: 20%;
+}
+.ref-arguments .desc {
+  width: 80%;
+}
 
 /* Nice scrolling for wide elements --------------------------------------- */
 
@@ -162,7 +186,8 @@ pre {
   border: 1px solid #eee;
 }
 
-pre, code {
+pre,
+code {
   background-color: #f8f8f8;
   color: #333;
 }
@@ -183,7 +208,8 @@ pre .img img {
   height: auto;
 }
 
-code a, pre a {
+code a,
+pre a {
   color: #375f84;
 }
 
@@ -191,15 +217,35 @@ a.sourceLine:hover {
   text-decoration: none;
 }
 
-.fl      {color: #1514b5;}
-.fu      {color: #000000;} /* function */
-.ch,.st  {color: #036a07;} /* string */
-.kw      {color: #264D66;} /* keyword */
-.co      {color: #888888;} /* comment */
+.fl {
+  color: #1514b5;
+}
+.fu {
+  color: #000000;
+} /* function */
+.ch,
+.st {
+  color: #036a07;
+} /* string */
+.kw {
+  color: #264d66;
+} /* keyword */
+.co {
+  color: #888888;
+} /* comment */
 
-.message { color: black;   font-weight: bolder;}
-.error   { color: orange;  font-weight: bolder;}
-.warning { color: #6A0366; font-weight: bolder;}
+.message {
+  color: black;
+  font-weight: bolder;
+}
+.error {
+  color: orange;
+  font-weight: bolder;
+}
+.warning {
+  color: #6a0366;
+  font-weight: bolder;
+}
 
 /* Clipboard --------------------------*/
 
diff --git a/modules/rtm/docs/pkgdown.js b/modules/rtm/docs/pkgdown.js
index de9bd72..ddf7401 100644
--- a/modules/rtm/docs/pkgdown.js
+++ b/modules/rtm/docs/pkgdown.js
@@ -1,18 +1,21 @@
 /* http://gregfranko.com/blog/jquery-best-practices/ */
 (function($) {
   $(function() {
-
     $("#sidebar")
-      .stick_in_parent({offset_top: 40})
-      .on('sticky_kit:bottom', function(e) {
-        $(this).parent().css('position', 'static');
+      .stick_in_parent({ offset_top: 40 })
+      .on("sticky_kit:bottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "static");
       })
-      .on('sticky_kit:unbottom', function(e) {
-        $(this).parent().css('position', 'relative');
+      .on("sticky_kit:unbottom", function(e) {
+        $(this)
+          .parent()
+          .css("position", "relative");
       });
 
-    $('body').scrollspy({
-      target: '#sidebar',
+    $("body").scrollspy({
+      target: "#sidebar",
       offset: 60
     });
 
@@ -23,8 +26,7 @@
     var max_length = -1;
     var pos = -1;
     for (var i = 0; i < links.length; i++) {
-      if (links[i].getAttribute("href") === "#")
-        continue;
+      if (links[i].getAttribute("href") === "#") continue;
       var path = paths(links[i].pathname);
 
       var length = prefix_length(cur_path, path);
@@ -47,40 +49,38 @@
     pieces.shift(); // always starts with /
 
     var end = pieces[pieces.length - 1];
-    if (end === "index.html" || end === "")
-      pieces.pop();
-    return(pieces);
+    if (end === "index.html" || end === "") pieces.pop();
+    return pieces;
   }
 
   function prefix_length(needle, haystack) {
-    if (needle.length > haystack.length)
-      return(0);
+    if (needle.length > haystack.length) return 0;
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return needle.length === 0 ? 1 : 0;
     }
 
     for (var i = 0; i < haystack.length; i++) {
-      if (needle[i] != haystack[i])
-        return(i);
+      if (needle[i] != haystack[i]) return i;
     }
 
-    return(haystack.length);
+    return haystack.length;
   }
 
   /* Clipboard --------------------------*/
 
   function changeTooltipMessage(element, msg) {
-    var tooltipOriginalTitle=element.getAttribute('data-original-title');
-    element.setAttribute('data-original-title', msg);
-    $(element).tooltip('show');
-    element.setAttribute('data-original-title', tooltipOriginalTitle);
+    var tooltipOriginalTitle = element.getAttribute("data-original-title");
+    element.setAttribute("data-original-title", msg);
+    $(element).tooltip("show");
+    element.setAttribute("data-original-title", tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if (Clipboard.isSupported()) {
     $(document).ready(function() {
-      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+      var copyButton =
+        "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -88,23 +88,23 @@
       $(copyButton).prependTo(".hasCopyButton");
 
       // Initialize tooltips:
-      $('.btn-copy-ex').tooltip({container: 'body'});
+      $(".btn-copy-ex").tooltip({ container: "body" });
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new Clipboard("[data-clipboard-copy]", {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
       });
 
-      clipboardBtnCopies.on('success', function(e) {
-        changeTooltipMessage(e.trigger, 'Copied!');
+      clipboardBtnCopies.on("success", function(e) {
+        changeTooltipMessage(e.trigger, "Copied!");
         e.clearSelection();
       });
 
-      clipboardBtnCopies.on('error', function() {
-        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on("error", function() {
+        changeTooltipMessage(e.trigger, "Press Ctrl+C or Command+C to copy");
       });
     });
   }
-})(window.jQuery || window.$)
+})(window.jQuery || window.$);
diff --git a/modules/rtm/docs/reference/EDR.html b/modules/rtm/docs/reference/EDR.html
index 32acf43..75db0b6 100644
--- a/modules/rtm/docs/reference/EDR.html
+++ b/modules/rtm/docs/reference/EDR.html
@@ -2,124 +2,170 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>ED radiative transfer module (EDR) wrapper function — EDR • PEcAnRTM</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-<meta property="og:title" content="ED radiative transfer module (EDR) wrapper function — EDR" />
-
-<meta property="og:description" content="This function provides a convenient way to call the ED
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>
+      ED radiative transfer module (EDR) wrapper function — EDR • PEcAnRTM
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="ED radiative transfer module (EDR) wrapper function — EDR"
+    />
+
+    <meta
+      property="og:description"
+      content="This function provides a convenient way to call the ED
 radiative transfer module (EDR, which simulates full spectral return of an
-ED patch for a given point in time) directly from R." />
-<meta name="twitter:card" content="summary" />
-
-
-
-<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
-
-<!--[if lt IE 9]>
-<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
+ED patch for a given point in time) directly from R."
+    />
+    <meta name="twitter:card" content="summary" />
 
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="../index.html">PEcAnRTM</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/pecanrtm.vignette.html">The PEcAn RTM package</a>
-    </li>
-  </ul>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAnRTM</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>ED radiative transfer module (EDR) wrapper function</h1>
-    
-    <div class="hidden name"><code>EDR.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This function provides a convenient way to call the ED
-radiative transfer module (EDR, which simulates full spectral return of an
-ED patch for a given point in time) directly from R.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>EDR</span>(<span class='no'>img_path</span>, <span class='no'>ed2in_path</span>, <span class='no'>spectra_list</span>, <span class='no'>trait.values</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>ED radiative transfer module (EDR) wrapper function</h1>
+
+            <div class="hidden name"><code>EDR.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This function provides a convenient way to call the ED radiative
+              transfer module (EDR, which simulates full spectral return of an
+              ED patch for a given point in time) directly from R.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>EDR</span>(<span class='no'>img_path</span>, <span class='no'>ed2in_path</span>, <span class='no'>spectra_list</span>, <span class='no'>trait.values</span>,
   <span class='kw'>soil_reflect_path</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"extdata"</span>, <span class='st'>"soil_reflect_par.dat"</span>,
   <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"PEcAnRTM"</span>), <span class='kw'>wood_reflect_path</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"extdata"</span>,
   <span class='st'>"wood_reflect_par.dat"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"PEcAnRTM"</span>), <span class='kw'>par.wl</span> <span class='kw'>=</span> <span class='fl'>400</span>:<span class='fl'>2499</span>,
@@ -128,121 +174,180 @@ <h1>ED radiative transfer module (EDR) wrapper function</h1>
   <span class='kw'>settings</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>model</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>revision</span> <span class='kw'>=</span> <span class='st'>"git"</span>, <span class='kw'>config.header</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)),
   <span class='kw'>singularity_args</span> <span class='kw'>=</span> <span class='fu'>list</span>(), <span class='kw'>clean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>stderr</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>verbose_error</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>img_path</th>
-      <td><p>Path to Singularity container (usually a <code>.simg</code> file)</p></td>
-    </tr>
-    <tr>
-      <th>ed2in_path</th>
-      <td><p>Path to ED2IN file.</p></td>
-    </tr>
-    <tr>
-      <th>spectra_list</th>
-      <td><p>List of spectral data matrices. Names must exactly match
-the PFTs given in <code>trait.values</code>. Each item must be a matrix of
-reflectance (labeled 'R' or 'reflectance') and transmittance (labeled 'T' or
-'transmittance') values. If the matrix is not of class <code>spectra</code> (see
-<code><a href='spectra.html'>spectra()</a></code>), it must also have a column of wavelength values (labeled
-'wl'). Such a matrix is returned by default by all versions of PROSPECT in
-this package.</p></td>
-    </tr>
-    <tr>
-      <th>trait.values</th>
-      <td><p>Named, hierarchical list of trait values for generating
-config.xml file. Names must be PFTs, and must exactly match names of
-<code>spectra_list</code>.</p></td>
-    </tr>
-    <tr>
-      <th>soil_reflect_path</th>
-      <td><p>Path to soil reflectance file (defaults to spectra
-in package <code>extdata</code>)</p></td>
-    </tr>
-    <tr>
-      <th>wood_reflect_path</th>
-      <td><p>Path to wood reflectance file (defaults to spectra
-in package <code>extdata</code>)</p></td>
-    </tr>
-    <tr>
-      <th>par.wl</th>
-      <td><p>Vector of wavelengths defining PAR region</p></td>
-    </tr>
-    <tr>
-      <th>nir.wl</th>
-      <td><p>Vector of wavelengths defining NIR region</p></td>
-    </tr>
-    <tr>
-      <th>edr_exe_path</th>
-      <td><p>If <code>img_path</code> is <code>NULL</code>, a full path to the EDR
-executable. Ignored otherwise.</p></td>
-    </tr>
-    <tr>
-      <th>output.path</th>
-      <td><p>Directory in which to execute the run. Defaults to
-<code>dirname(ed2in_path)</code>.</p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>PEcAn settings list. Default is <code>list(model = list(revision = "git", config.header = NULL))</code>.</p></td>
-    </tr>
-    <tr>
-      <th>singularity_args</th>
-      <td><p>Additional arguments to be passed to <code>singularity run</code> (before)</p></td>
-    </tr>
-    <tr>
-      <th>clean</th>
-      <td><p>Logical. If <code>TRUE</code>, remove all files generated by this function
-(e.g. cloned history file, ED2IN, output HDF files).</p></td>
-    </tr>
-    <tr>
-      <th>stderr</th>
-      <td><p>Logical. If <code>TRUE</code> (default), internalize <code>system2</code> results as
-R character vector. <code>TRUE</code> is recommended because it allows EDR to check its
-execution and to run more quietly.</p></td>
-    </tr>
-    <tr>
-      <th>verbose_error</th>
-      <td><p>Logical. If <code>TRUE</code> (default), spit out the full ED
-if EDR execution fails.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional arguments to <code>system2</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>img_path</th>
+              <td>
+                <p>
+                  Path to Singularity container (usually a
+                  <code>.simg</code> file)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ed2in_path</th>
+              <td><p>Path to ED2IN file.</p></td>
+            </tr>
+            <tr>
+              <th>spectra_list</th>
+              <td>
+                <p>
+                  List of spectral data matrices. Names must exactly match the
+                  PFTs given in <code>trait.values</code>. Each item must be a
+                  matrix of reflectance (labeled 'R' or 'reflectance') and
+                  transmittance (labeled 'T' or 'transmittance') values. If the
+                  matrix is not of class <code>spectra</code> (see
+                  <code><a href="spectra.html">spectra()</a></code
+                  >), it must also have a column of wavelength values (labeled
+                  'wl'). Such a matrix is returned by default by all versions of
+                  PROSPECT in this package.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>trait.values</th>
+              <td>
+                <p>
+                  Named, hierarchical list of trait values for generating
+                  config.xml file. Names must be PFTs, and must exactly match
+                  names of <code>spectra_list</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>soil_reflect_path</th>
+              <td>
+                <p>
+                  Path to soil reflectance file (defaults to spectra in package
+                  <code>extdata</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>wood_reflect_path</th>
+              <td>
+                <p>
+                  Path to wood reflectance file (defaults to spectra in package
+                  <code>extdata</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>par.wl</th>
+              <td><p>Vector of wavelengths defining PAR region</p></td>
+            </tr>
+            <tr>
+              <th>nir.wl</th>
+              <td><p>Vector of wavelengths defining NIR region</p></td>
+            </tr>
+            <tr>
+              <th>edr_exe_path</th>
+              <td>
+                <p>
+                  If <code>img_path</code> is <code>NULL</code>, a full path to
+                  the EDR executable. Ignored otherwise.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>output.path</th>
+              <td>
+                <p>
+                  Directory in which to execute the run. Defaults to
+                  <code>dirname(ed2in_path)</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>
+                  PEcAn settings list. Default is
+                  <code
+                    >list(model = list(revision = "git", config.header =
+                    NULL))</code
+                  >.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>singularity_args</th>
+              <td>
+                <p>
+                  Additional arguments to be passed to
+                  <code>singularity run</code> (before)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>clean</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code>, remove all files generated by
+                  this function (e.g. cloned history file, ED2IN, output HDF
+                  files).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>stderr</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code> (default), internalize
+                  <code>system2</code> results as R character vector.
+                  <code>TRUE</code> is recommended because it allows EDR to
+                  check its execution and to run more quietly.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose_error</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code> (default), spit out the full ED
+                  if EDR execution fails.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>Additional arguments to <code>system2</code></p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/rtm/docs/reference/EDR.preprocess.history.html b/modules/rtm/docs/reference/EDR.preprocess.history.html
index f45fea1..2ff6a93 100644
--- a/modules/rtm/docs/reference/EDR.preprocess.history.html
+++ b/modules/rtm/docs/reference/EDR.preprocess.history.html
@@ -2,167 +2,218 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Bootstrap -->
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-
-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Preprocess history file for EDR — EDR.preprocess.history • PEcAnRTM
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
+    <meta
+      property="og:title"
+      content="Preprocess history file for EDR — EDR.preprocess.history"
+    />
+
+    <meta
+      property="og:description"
+      content="Locate history file based on path and prefix, copy to specified output
+directory, and rename to correct time."
+    />
+    <meta name="twitter:card" content="summary" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
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+                type="button"
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAnRTM</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
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+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Preprocess history file for EDR</h1>
-    
-    <div class="hidden name"><code>EDR.preprocess.history.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Locate history file based on path and prefix, copy to specified output
-directory, and rename to correct time.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>EDR.preprocess.history</span>(<span class='no'>history.path</span>, <span class='no'>output.path</span>, <span class='no'>datetime</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Preprocess history file for EDR</h1>
+
+            <div class="hidden name">
+              <code>EDR.preprocess.history.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Locate history file based on path and prefix, copy to specified
+              output directory, and rename to correct time.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>EDR.preprocess.history</span>(<span class='no'>history.path</span>, <span class='no'>output.path</span>, <span class='no'>datetime</span>,
   <span class='kw'>history.prefix</span> <span class='kw'>=</span> <span class='st'>"history"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>history.path</th>
-      <td><p>Path to directory containing history file.</p></td>
-    </tr>
-    <tr>
-      <th>datetime</th>
-      <td><p>POSIX date and time for run</p></td>
-    </tr>
-    <tr>
-      <th>history.prefix</th>
-      <td><p>String describing the history file prefix in
-<code>history.path</code>. Default = 'history'</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>history.path</th>
+              <td><p>Path to directory containing history file.</p></td>
+            </tr>
+            <tr>
+              <th>datetime</th>
+              <td><p>POSIX date and time for run</p></td>
+            </tr>
+            <tr>
+              <th>history.prefix</th>
+              <td>
+                <p>
+                  String describing the history file prefix in
+                  <code>history.path</code>. Default = 'history'
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
   </body>
 </html>
-
diff --git a/modules/rtm/docs/reference/bt_check_convergence.html b/modules/rtm/docs/reference/bt_check_convergence.html
index 06ebcdc..dcd57b4 100644
--- a/modules/rtm/docs/reference/bt_check_convergence.html
+++ b/modules/rtm/docs/reference/bt_check_convergence.html
@@ -2,146 +2,184 @@
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 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
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-    <h1>Check convergence of BayesianTools output</h1>
-    
-    <div class="hidden name"><code>bt_check_convergence.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Check convergence of BayesianTools output</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check convergence of BayesianTools output</h1>
 
-    <pre class="usage"><span class='fu'>bt_check_convergence</span>(<span class='no'>samples</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.1</span>, <span class='kw'>use_CI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>use_mpsrf</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-        
+            <div class="hidden name"><code>bt_check_convergence.Rd</code></div>
+          </div>
 
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Check convergence of BayesianTools output</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>bt_check_convergence</span>(<span class='no'>samples</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.1</span>, <span class='kw'>use_CI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>use_mpsrf</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
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+        </div>
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diff --git a/modules/rtm/docs/reference/burnin.thin.html b/modules/rtm/docs/reference/burnin.thin.html
index 38c933d..8cc1219 100644
--- a/modules/rtm/docs/reference/burnin.thin.html
+++ b/modules/rtm/docs/reference/burnin.thin.html
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-<div class="row">
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-    <div class="page-header">
-    <h1>Burn-in and thinning of MCMC samples</h1>
-    
-    <div class="hidden name"><code>burnin.thin.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Burn-in and thinning of MCMC samples</h1>
 
-    <div class="ref-description">
-    
-    <p>Burn-in and thinning of MCMC samples</p>
-    
-    </div>
+            <div class="hidden name"><code>burnin.thin.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>burnin.thin</span>(<span class='no'>samples</span>, <span class='kw'>target</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>burnin.ratio</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>auto</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='kw'>burnin</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>samples</th>
-      <td><p>Matrix of MCMC samples</p></td>
-    </tr>
-    <tr>
-      <th>target</th>
-      <td><p>Target number of samples (default = 5000). Only applicable if
-auto=TRUE.</p></td>
-    </tr>
-    <tr>
-      <th>burnin.ratio</th>
-      <td><p>Fraction of samples to burn-in; i.e. 2 means to remove
-first 1/2 of samples, 3 means 1/3, etc. (default = 2). Only applicable if
-auto=TRUE.</p></td>
-    </tr>
-    <tr>
-      <th>auto</th>
-      <td><p>Whether or not to perform automatic burnin and thin based on
-target number of samples.</p></td>
-    </tr>
-    <tr>
-      <th>burnin</th>
-      <td><p>Number of samples to discard as burnin (auto must be FALSE)</p></td>
-    </tr>
-    <tr>
-      <th>thin</th>
-      <td><p>Thinning interval (auto must be FALSE)</p></td>
-    </tr>
-    </table>
-    
-
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Burn-in and thinning of MCMC samples</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>burnin.thin</span>(<span class='no'>samples</span>, <span class='kw'>target</span> <span class='kw'>=</span> <span class='fl'>5000</span>, <span class='kw'>burnin.ratio</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>auto</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>burnin</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>thin</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>samples</th>
+              <td><p>Matrix of MCMC samples</p></td>
+            </tr>
+            <tr>
+              <th>target</th>
+              <td>
+                <p>
+                  Target number of samples (default = 5000). Only applicable if
+                  auto=TRUE.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>burnin.ratio</th>
+              <td>
+                <p>
+                  Fraction of samples to burn-in; i.e. 2 means to remove first
+                  1/2 of samples, 3 means 1/3, etc. (default = 2). Only
+                  applicable if auto=TRUE.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>auto</th>
+              <td>
+                <p>
+                  Whether or not to perform automatic burnin and thin based on
+                  target number of samples.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>burnin</th>
+              <td>
+                <p>
+                  Number of samples to discard as burnin (auto must be FALSE)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>thin</th>
+              <td><p>Thinning interval (auto must be FALSE)</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
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+    </div>
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-
diff --git a/modules/rtm/docs/reference/cbind.spectra.html b/modules/rtm/docs/reference/cbind.spectra.html
index 12ffb70..35be7b2 100644
--- a/modules/rtm/docs/reference/cbind.spectra.html
+++ b/modules/rtm/docs/reference/cbind.spectra.html
@@ -2,156 +2,192 @@
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 <html>
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+
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    ></script>
+
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+    <script src="../pkgdown.js"></script>
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+    <meta name="twitter:card" content="summary" />
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+                        >The PEcAn RTM package</a
+                      >
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+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Combine spectra by wavelength</h1>
-    
-    <div class="hidden name"><code>cbind.spectra.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Combine spectra by wavelength</h1>
 
-    <div class="ref-description">
-    
-    <p>Combine spectra by wavelength</p>
-    
-    </div>
+            <div class="hidden name"><code>cbind.spectra.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for spectra</span>
-<span class='fu'>cbind</span>(<span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>...</th>
-      <td><p>Spectra to combine</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Combine spectra by wavelength</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for spectra</span>
+<span class='fu'>cbind</span>(<span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>...</th>
+              <td><p>Spectra to combine</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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-
diff --git a/modules/rtm/docs/reference/check.convergence.html b/modules/rtm/docs/reference/check.convergence.html
index 7daf234..ffbb66e 100644
--- a/modules/rtm/docs/reference/check.convergence.html
+++ b/modules/rtm/docs/reference/check.convergence.html
@@ -2,179 +2,242 @@
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 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+multiple MCMC chains have converged"
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+                  >1.6.0</span
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+                  <a href="../index.html">
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+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
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+            <!--/.nav-collapse -->
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Check convergence of multiple MCMC chains</h1>
-    
-    <div class="hidden name"><code>check.convergence.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Uses Gelman multivariate Gelman-Rubin diagnostic to check if
-multiple MCMC chains have converged</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>check.convergence</span>(<span class='no'>jags_out</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.1</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>jags_out</th>
-      <td><p>mcmc.list object (from coda package) containing
-samples from MCMC chains.</p></td>
-    </tr>
-    <tr>
-      <th>threshold</th>
-      <td><p>Gelman-Rubin diagnostic parameter threshold. Default = 1.1</p></td>
-    </tr>
-    <tr>
-      <th>verbose</th>
-      <td><p>If TRUE, print convergence result. Default = TRUE</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional arguments to <code>gelman.diag</code> (from coda package)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>List length 3 containing the following:
-* convergence: Logical. Whether or not convergence was achieved.
-* diagnostics: Numerical value of Gelman-Rubin diagnostics for each parameter and multivariate diagnostic
-* error: Logical. Whether or not an error occured in the Gelman-Rubin calculation.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Check convergence of multiple MCMC chains</h1>
+
+            <div class="hidden name"><code>check.convergence.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Uses Gelman multivariate Gelman-Rubin diagnostic to check if
+              multiple MCMC chains have converged
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>check.convergence</span>(<span class='no'>jags_out</span>, <span class='kw'>threshold</span> <span class='kw'>=</span> <span class='fl'>1.1</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>jags_out</th>
+              <td>
+                <p>
+                  mcmc.list object (from coda package) containing samples from
+                  MCMC chains.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>threshold</th>
+              <td>
+                <p>
+                  Gelman-Rubin diagnostic parameter threshold. Default = 1.1
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>verbose</th>
+              <td><p>If TRUE, print convergence result. Default = TRUE</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  Additional arguments to <code>gelman.diag</code> (from coda
+                  package)
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            List length 3 containing the following: * convergence: Logical.
+            Whether or not convergence was achieved. * diagnostics: Numerical
+            value of Gelman-Rubin diagnostics for each parameter and
+            multivariate diagnostic * error: Logical. Whether or not an error
+            occured in the Gelman-Rubin calculation.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
-</div>
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diff --git a/modules/rtm/docs/reference/corr_max_lag.html b/modules/rtm/docs/reference/corr_max_lag.html
index f36dd97..29ee0ec 100644
--- a/modules/rtm/docs/reference/corr_max_lag.html
+++ b/modules/rtm/docs/reference/corr_max_lag.html
@@ -2,145 +2,183 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate max ACF lag from correlation power analysis</h1>
-    
-    <div class="hidden name"><code>corr_max_lag.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate max ACF lag from correlation power analysis</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate max ACF lag from correlation power analysis</h1>
 
-    <pre class="usage"><span class='fu'>corr_max_lag</span>(<span class='no'>nx</span>, <span class='kw'>r</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>sig.level</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>power</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>corr_max_lag.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Calculate max ACF lag from correlation power analysis</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>corr_max_lag</span>(<span class='no'>nx</span>, <span class='kw'>r</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>sig.level</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>power</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/default.settings.prospect.html b/modules/rtm/docs/reference/default.settings.prospect.html
index 6d08710..d66ccd0 100644
--- a/modules/rtm/docs/reference/default.settings.prospect.html
+++ b/modules/rtm/docs/reference/default.settings.prospect.html
@@ -2,151 +2,193 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Defult inversion settings for PROSPECT 5 models</h1>
-    
-    <div class="hidden name"><code>default.settings.prospect.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Default settings for PROSPECT inversion</p>
-    
-    </div>
-
-    <pre class="usage"><span class='no'>default.settings.prospect</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
-
-    <p>An object of class <code>list</code> of length 18.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Defult inversion settings for PROSPECT 5 models</h1>
+
+            <div class="hidden name">
+              <code>default.settings.prospect.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Default settings for PROSPECT inversion</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='no'>default.settings.prospect</span></pre>
+
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
+
+          <p>An object of class <code>list</code> of length 18.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/defparam.html b/modules/rtm/docs/reference/defparam.html
index 0cbe484..68fd06a 100644
--- a/modules/rtm/docs/reference/defparam.html
+++ b/modules/rtm/docs/reference/defparam.html
@@ -2,161 +2,206 @@
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get default parameters</h1>
-    
-    <div class="hidden name"><code>defparam.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Extract default parameter values from <code>model.list</code></p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>defparam</span>(<span class='no'>modname</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>modname</th>
-      <td><p>Model name. Must match <code>modname</code> in <code>model.list</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Named vector of default parameter values</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get default parameters</h1>
+
+            <div class="hidden name"><code>defparam.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Extract default parameter values from <code>model.list</code></p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>defparam</span>(<span class='no'>modname</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>modname</th>
+              <td>
+                <p>
+                  Model name. Must match <code>modname</code> in
+                  <code>model.list</code>
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Named vector of default parameter values</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
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+        </div>
+      </div>
 
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index d4b6cca..e640372 100644
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@@ -2,177 +2,232 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Truncated normal distribution density</h1>
-    
-    <div class="hidden name"><code>dtnorm.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculates the log density of a univariate truncated normal variable</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>dtnorm</span>(<span class='no'>x</span>, <span class='no'>mu</span>, <span class='no'>sd</span>, <span class='no'>MIN</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>A random variable</p></td>
-    </tr>
-    <tr>
-      <th>mu</th>
-      <td><p>The mean parameter of the distribution; NOTE this is not equal to the mean</p></td>
-    </tr>
-    <tr>
-      <th>sd</th>
-      <td><p>The standard deviation parameter of the distribution</p></td>
-    </tr>
-    <tr>
-      <th>MIN</th>
-      <td><p>Value at which the truncation takes place</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Numeric; log density of the distribution, or -1e15 if the x &lt; MIN</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Truncated normal distribution density</h1>
+
+            <div class="hidden name"><code>dtnorm.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Calculates the log density of a univariate truncated normal
+              variable
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>dtnorm</span>(<span class='no'>x</span>, <span class='no'>mu</span>, <span class='no'>sd</span>, <span class='no'>MIN</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>A random variable</p></td>
+            </tr>
+            <tr>
+              <th>mu</th>
+              <td>
+                <p>
+                  The mean parameter of the distribution; NOTE this is not equal
+                  to the mean
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sd</th>
+              <td>
+                <p>The standard deviation parameter of the distribution</p>
+              </td>
+            </tr>
+            <tr>
+              <th>MIN</th>
+              <td><p>Value at which the truncation takes place</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Numeric; log density of the distribution, or -1e15 if the x &lt; MIN
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAnRTM</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
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+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>List to FORTRAN data module</h1>
-    
-    <div class="hidden name"><code>fortran_data_module.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convert R list to a Fortran <code>/data/</code> module block</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>fortran_data_module</span>(<span class='no'>dat</span>, <span class='no'>types</span>, <span class='no'>modname</span>, <span class='kw'>fname</span> <span class='kw'>=</span> <span class='fu'>paste0</span>(<span class='no'>modname</span>, <span class='st'>".f90"</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dat</th>
-      <td><p>Named list object for creating module. List names will be used
-to initialize FORTRAN variabiles.</p></td>
-    </tr>
-    <tr>
-      <th>types</th>
-      <td><p>Character vector of FORTAN types (e.g. real*8, integer)</p></td>
-    </tr>
-    <tr>
-      <th>modname</th>
-      <td><p>Name of the module. We suggest the format 'MOD_yourmodname'.</p></td>
-    </tr>
-    <tr>
-      <th>fname</th>
-      <td><p>Output file name. Defaults to 'yourmodname.f90'</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>For models with large constants (e.g. absorption features in the
-PROSPECT model), it may be preferable to store these in FORTRAN90
-modules. However, manually creating and formatting these files is
-tedious. This script allows you to automatically generate module files
-from R lists. It automatically interprets the object lengths as array
-dimensions (only vectors are supported right now -- higher dimension
-arrays may be in the future) and splits long data into rows of 10.
-Currently, only numeric data are supported (i.e. no characters).</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>List to FORTRAN data module</h1>
+
+            <div class="hidden name"><code>fortran_data_module.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convert R list to a Fortran <code>/data/</code> module block</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>fortran_data_module</span>(<span class='no'>dat</span>, <span class='no'>types</span>, <span class='no'>modname</span>, <span class='kw'>fname</span> <span class='kw'>=</span> <span class='fu'>paste0</span>(<span class='no'>modname</span>, <span class='st'>".f90"</span>))</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dat</th>
+              <td>
+                <p>
+                  Named list object for creating module. List names will be used
+                  to initialize FORTRAN variabiles.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>types</th>
+              <td>
+                <p>Character vector of FORTAN types (e.g. real*8, integer)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>modname</th>
+              <td>
+                <p>
+                  Name of the module. We suggest the format 'MOD_yourmodname'.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>fname</th>
+              <td><p>Output file name. Defaults to 'yourmodname.f90'</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            For models with large constants (e.g. absorption features in the
+            PROSPECT model), it may be preferable to store these in FORTRAN90
+            modules. However, manually creating and formatting these files is
+            tedious. This script allows you to automatically generate module
+            files from R lists. It automatically interprets the object lengths
+            as array dimensions (only vectors are supported right now -- higher
+            dimension arrays may be in the future) and splits long data into
+            rows of 10. Currently, only numeric data are supported (i.e. no
+            characters).
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
       <span class='no'>w</span> <span class='kw'>&lt;-</span> <span class='fl'>3.2</span>
       <span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fl'>1</span>:<span class='fl'>5</span>
       <span class='no'>y</span> <span class='kw'>&lt;-</span> <span class='fl'>6</span>:<span class='fl'>15</span>
@@ -168,38 +231,34 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examp
       <span class='no'>d.types</span> <span class='kw'>&lt;-</span> <span class='fu'>rep</span>(<span class='st'>'real*8'</span>, <span class='fu'>ncol</span>(<span class='no'>d</span>))
       <span class='fu'>fortran_data_module</span>(<span class='no'>d</span>, <span class='no'>d.types</span>, <span class='st'>'random'</span>)
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          Alexey Shiklomanov
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/rtm/docs/reference/foursail.html b/modules/rtm/docs/reference/foursail.html
index 496d025..e4f3b3c 100644
--- a/modules/rtm/docs/reference/foursail.html
+++ b/modules/rtm/docs/reference/foursail.html
@@ -2,192 +2,243 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+    <![endif]-->
   </head>
 
   <body>
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+                <li class="dropdown">
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
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+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>SAIL model</h1>
-    
-    <div class="hidden name"><code>foursail.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>R wrapper for 4SAIL model</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>foursail</span>(<span class='no'>refl</span>, <span class='no'>tran</span>, <span class='no'>rsoil</span>, <span class='no'>param</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>refl</th>
-      <td><p>input leaf reflectance from 400-2500nm (can be measured or modeled)</p></td>
-    </tr>
-    <tr>
-      <th>tran</th>
-      <td><p>input leaf transmittance from 400-2500nm (can be measured or modeled)</p></td>
-    </tr>
-    <tr>
-      <th>rsoil</th>
-      <td><p>input soil reflectance spectra from 400-2500nm (can be measured or modeled)</p></td>
-    </tr>
-    <tr>
-      <th>param</th>
-      <td><p>Vector of SAIL parameter values:
-* LIDFa: Leaf angle distribution function - parameter a
-* LIDFb: Leaf angle distribution function - parameter b
-* TypeLIDF: Leaf angle distribution function type (1 or 2)
-* LAI: Leaf area index
-* q: Hot spot effect parameter
-* tts: Solar zenith angle
-* tto: Observer zenith angle
-* psi: Sun-sensor azimuth angle</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Spectra matrix (see <code><a href='spectra.html'>spectra()</a></code>) (2101 x 4) of reflectance factors
-for wavelengths 400 to 2500nm:
-* bi-hemispherical reflectance (rddt)
-* hemispherical directional (rsdt)
-* directional hemispherical (rdot)
-* bi-directional (rsot)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>SAIL model</h1>
+
+            <div class="hidden name"><code>foursail.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>R wrapper for 4SAIL model</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>foursail</span>(<span class='no'>refl</span>, <span class='no'>tran</span>, <span class='no'>rsoil</span>, <span class='no'>param</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>refl</th>
+              <td>
+                <p>
+                  input leaf reflectance from 400-2500nm (can be measured or
+                  modeled)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>tran</th>
+              <td>
+                <p>
+                  input leaf transmittance from 400-2500nm (can be measured or
+                  modeled)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>rsoil</th>
+              <td>
+                <p>
+                  input soil reflectance spectra from 400-2500nm (can be
+                  measured or modeled)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>param</th>
+              <td>
+                <p>
+                  Vector of SAIL parameter values: * LIDFa: Leaf angle
+                  distribution function - parameter a * LIDFb: Leaf angle
+                  distribution function - parameter b * TypeLIDF: Leaf angle
+                  distribution function type (1 or 2) * LAI: Leaf area index *
+                  q: Hot spot effect parameter * tts: Solar zenith angle * tto:
+                  Observer zenith angle * psi: Sun-sensor azimuth angle
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Spectra matrix (see <code><a href="spectra.html">spectra()</a></code
+            >) (2101 x 4) of reflectance factors for wavelengths 400 to 2500nm:
+            * bi-hemispherical reflectance (rddt) * hemispherical directional
+            (rsdt) * directional hemispherical (rdot) * bi-directional (rsot)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Shawn Serbin
+          <h2>Author</h2>
 
-Alexey Shiklomanov
-
-  </div>
-</div>
+          Shawn Serbin Alexey Shiklomanov
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/rtm/docs/reference/generalized_plate_model.html b/modules/rtm/docs/reference/generalized_plate_model.html
index 53de8af..6309aaa 100644
--- a/modules/rtm/docs/reference/generalized_plate_model.html
+++ b/modules/rtm/docs/reference/generalized_plate_model.html
@@ -2,163 +2,215 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generalized plate model</h1>
-    
-    <div class="hidden name"><code>generalized_plate_model.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>This is the fundamental physical model underlying the PROSPECT family of leaf RTMs.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>generalized_plate_model</span>(<span class='no'>k</span>, <span class='no'>refractive</span>, <span class='no'>N</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>k</th>
-      <td><p>Specific absorption coefficient (400 - 2500nm)</p></td>
-    </tr>
-    <tr>
-      <th>refractive</th>
-      <td><p>Refractive index (400 - 2500nm)</p></td>
-    </tr>
-    <tr>
-      <th>N</th>
-      <td><p>Effective number of mesophyll layers (see <code><a href='prospect.html'>prospect()</a></code>)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generalized plate model</h1>
+
+            <div class="hidden name">
+              <code>generalized_plate_model.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              This is the fundamental physical model underlying the PROSPECT
+              family of leaf RTMs.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>generalized_plate_model</span>(<span class='no'>k</span>, <span class='no'>refractive</span>, <span class='no'>N</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>k</th>
+              <td><p>Specific absorption coefficient (400 - 2500nm)</p></td>
+            </tr>
+            <tr>
+              <th>refractive</th>
+              <td><p>Refractive index (400 - 2500nm)</p></td>
+            </tr>
+            <tr>
+              <th>N</th>
+              <td>
+                <p>
+                  Effective number of mesophyll layers (see
+                  <code><a href="prospect.html">prospect()</a></code
+                  >)
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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index 77f4216..b09e934 100644
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-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
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-    <span class="caret"></span>
-  </a>
-  <ul class="dropdown-menu" role="menu">
-    <li>
-      <a href="../articles/pecanrtm.vignette.html">The PEcAn RTM package</a>
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-</li>
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-      
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-        
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-      
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-  </div><!--/.container -->
-</div><!--/.navbar -->
-
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAnRTM</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate autocorrelated spectral noise</h1>
-    
-    <div class="hidden name"><code>generate.noise.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generate autocorrelated spectral noise</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>generate.noise</span>(<span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>2101</span>, <span class='kw'>sigma</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>, <span class='kw'>fw</span> <span class='kw'>=</span> <span class='fl'>201</span>, <span class='kw'>fsd</span> <span class='kw'>=</span> <span class='fl'>6</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>n</th>
-      <td><p>Length of output vector (default = 2101)</p></td>
-    </tr>
-    <tr>
-      <th>sigma</th>
-      <td><p>Gaussian noise standard deviation (default=1e-4)</p></td>
-    </tr>
-    <tr>
-      <th>fw</th>
-      <td><p>Filter width. Will be coerced to an odd number if even (default = 201).</p></td>
-    </tr>
-    <tr>
-      <th>fsd</th>
-      <td><p>Scaling factor for filter standard deviation (default = 6)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generate autocorrelated spectral noise</h1>
+
+            <div class="hidden name"><code>generate.noise.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Generate autocorrelated spectral noise</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>generate.noise</span>(<span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>2101</span>, <span class='kw'>sigma</span> <span class='kw'>=</span> <span class='fl'>1e-04</span>, <span class='kw'>fw</span> <span class='kw'>=</span> <span class='fl'>201</span>, <span class='kw'>fsd</span> <span class='kw'>=</span> <span class='fl'>6</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>n</th>
+              <td><p>Length of output vector (default = 2101)</p></td>
+            </tr>
+            <tr>
+              <th>sigma</th>
+              <td><p>Gaussian noise standard deviation (default=1e-4)</p></td>
+            </tr>
+            <tr>
+              <th>fw</th>
+              <td>
+                <p>
+                  Filter width. Will be coerced to an odd number if even
+                  (default = 201).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>fsd</th>
+              <td>
+                <p>
+                  Scaling factor for filter standard deviation (default = 6)
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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diff --git a/modules/rtm/docs/reference/generate.rsr.all.html b/modules/rtm/docs/reference/generate.rsr.all.html
index d47c33f..e59ecf6 100644
--- a/modules/rtm/docs/reference/generate.rsr.all.html
+++ b/modules/rtm/docs/reference/generate.rsr.all.html
@@ -2,147 +2,187 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      generate.rsr.all • PEcAnRTM
+    </title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    />
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+data"
+    />
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+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAnRTM</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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-<li>
-  <a href="../reference/index.html">Reference</a>
-</li>
-<li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    Articles
-     
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-      <a href="../articles/pecanrtm.vignette.html">The PEcAn RTM package</a>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAnRTM</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate RSR matrices for all sensors and return as list</h1>
-    
-    <div class="hidden name"><code>generate.rsr.all.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Only needs to be called when updating these funcitons with new
-data</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>generate.rsr.all</span>(<span class='kw'>path.to.licor</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-        
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generate RSR matrices for all sensors and return as list</h1>
+
+            <div class="hidden name"><code>generate.rsr.all.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Only needs to be called when updating these funcitons with new
+              data
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>generate.rsr.all</span>(<span class='kw'>path.to.licor</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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+    </div>
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 </html>
-
diff --git a/modules/rtm/docs/reference/get.EDR.output.html b/modules/rtm/docs/reference/get.EDR.output.html
index ba5dbf8..a7da9af 100644
--- a/modules/rtm/docs/reference/get.EDR.output.html
+++ b/modules/rtm/docs/reference/get.EDR.output.html
@@ -2,155 +2,195 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Read EDR output — get.EDR.output • PEcAnRTM</title>
-
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<![endif]-->
-
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read EDR output</h1>
-    
-    <div class="hidden name"><code>get.EDR.output.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Read EDR output</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.EDR.output</span>(<span class='kw'>path</span> <span class='kw'>=</span> <span class='fu'>getwd</span>())</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>path</th>
-      <td><p>Path to directory containing <code>albedo_par/nir.dat</code> files</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read EDR output</h1>
+
+            <div class="hidden name"><code>get.EDR.output.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Read EDR output</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.EDR.output</span>(<span class='kw'>path</span> <span class='kw'>=</span> <span class='fu'>getwd</span>())</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>path</th>
+              <td>
+                <p>
+                  Path to directory containing
+                  <code>albedo_par/nir.dat</code> files
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
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-    <colgroup>
-      
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-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="EDR.html">EDR()</a></code> </p>
-        </td>
-        <td><p>ED radiative transfer module (EDR) wrapper function</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="EDR.preprocess.history.html">EDR.preprocess.history()</a></code> </p>
-        </td>
-        <td><p>Preprocess history file for EDR</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="bt_check_convergence.html">bt_check_convergence()</a></code> </p>
-        </td>
-        <td><p>Check convergence of BayesianTools output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="burnin.thin.html">burnin.thin()</a></code> </p>
-        </td>
-        <td><p>Burn-in and thinning of MCMC samples</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="cbind.spectra.html">cbind(<i>&lt;spectra&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Combine spectra by wavelength</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="check.convergence.html">check.convergence()</a></code> </p>
-        </td>
-        <td><p>Check convergence of multiple MCMC chains</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="corr_max_lag.html">corr_max_lag()</a></code> </p>
-        </td>
-        <td><p>Calculate max ACF lag from correlation power analysis</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="default.settings.prospect.html">default.settings.prospect</a></code> </p>
-        </td>
-        <td><p>Defult inversion settings for PROSPECT 5 models</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="defparam.html">defparam()</a></code> </p>
-        </td>
-        <td><p>Get default parameters</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="dtnorm.html">dtnorm()</a></code> </p>
-        </td>
-        <td><p>Truncated normal distribution density</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="fortran_data_module.html">fortran_data_module()</a></code> </p>
-        </td>
-        <td><p>List to FORTRAN data module</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="foursail.html">foursail()</a></code> </p>
-        </td>
-        <td><p>SAIL model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="generalized_plate_model.html">generalized_plate_model()</a></code> </p>
-        </td>
-        <td><p>Generalized plate model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="generate.noise.html">generate.noise()</a></code> </p>
-        </td>
-        <td><p>Generate autocorrelated spectral noise</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="generate.rsr.all.html">generate.rsr.all()</a></code> </p>
-        </td>
-        <td><p>Generate RSR matrices for all sensors and return as list</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.EDR.output.html">get.EDR.output()</a></code> </p>
-        </td>
-        <td><p>Read EDR output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="invert.auto.html">invert.auto()</a></code> </p>
-        </td>
-        <td><p>Inversion with automatic convergence checking</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="invert.custom.html">invert.custom()</a></code> </p>
-        </td>
-        <td><p>Bayesian inversion of a model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="invert.lsq.html">invert.lsq()</a></code> </p>
-        </td>
-        <td><p>Least squares model inversion</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="invert_bt.html">invert_bt()</a></code> </p>
-        </td>
-        <td><p>Perform Bayesian inversion using BayesianTools package</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="load.from.name.html">load.from.name()</a></code> </p>
-        </td>
-        <td><p>Load object from an RData file</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="lognorm.mu.html">lognorm.mu()</a></code> </p>
-        </td>
-        <td><p>Functions for default priors
-Lognormal mean parameters</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="lognorm.sigma.html">lognorm.sigma()</a></code> </p>
-        </td>
-        <td><p>Lognormal sigma parameter</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="matplot.html">matplot()</a></code> </p>
-        </td>
-        <td><p>Matplot generic method</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="matplot.default.html">matplot(<i>&lt;default&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Matplot default method</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="matplot.spectra.html">matplot(<i>&lt;spectra&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Plot multiple spectra on same graph</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="neff.html">neff()</a></code> </p>
-        </td>
-        <td><p>Effective sample size</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="params.prospect4.html">params.prospect4</a></code> </p>
-        </td>
-        <td><p>PROSPECT 4 parameters</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="params.prospect5.html">params.prospect5</a></code> </p>
-        </td>
-        <td><p>PROSPECT 5 parameters</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="params.prospect5b.html">params.prospect5b</a></code> </p>
-        </td>
-        <td><p>PROSPECT 5B parameters</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="params2edr.html">params2edr()</a></code> </p>
-        </td>
-        <td><p>Convert named parameter vector to EDR-compatible inputs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot.spectra.html">plot(<i>&lt;spectra&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Plot spectra vs. wavelength</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="print.spectra.html">print(<i>&lt;spectra&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Print method for spectra S3 class</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="print_results_summary.html">print_results_summary()</a></code> </p>
-        </td>
-        <td><p>Neatly print inversion results summary</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="prior.defaultvals.prospect.html">prior.defaultvals.prospect()</a></code> </p>
-        </td>
-        <td><p>Default prior parameters for PROSPECT models</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="priorfunc.prospect.html">priorfunc.prospect()</a></code> </p>
-        </td>
-        <td><p>Default PROSPECT 5 prior function</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pro2s.html">pro2s()</a></code> </p>
-        </td>
-        <td><p>Coupled PROSPECT-Two-stream model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="pro4sail.html">pro4sail()</a></code> </p>
-        </td>
-        <td><p>PRO4SAIL model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="prospect.html">prospect()</a></code> </p>
-        </td>
-        <td><p>PROSPECT (4, 5, or 5B) model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="prospect_bt_prior.html">prospect_bt_prior()</a></code> </p>
-        </td>
-        <td><p>Quick BayesianTools prior creator for PROSPECT model</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.rsr.folder.html">read.rsr.folder()</a></code> </p>
-        </td>
-        <td><p>Read and process RSR data from directory</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="resample.html">resample()</a></code> </p>
-        </td>
-        <td><p>Resample vector, matrix, or spectra</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="rsr.from.fwhm.html">rsr.from.fwhm()</a></code> </p>
-        </td>
-        <td><p>Generate relative spectral response (RSR) matrix based on FWHM data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="rtm_loglike.html">rtm_loglike()</a></code> </p>
-        </td>
-        <td><p>Generic log-likelihood generator for RTMs</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="rtnorm.html">rtnorm()</a></code> </p>
-        </td>
-        <td><p>Random sampling from one-sided truncated normal distribution</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sensor.list.html">sensor.list</a></code> </p>
-        </td>
-        <td><p>Sensor spectral response functions</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sensor.proper.html">sensor.proper</a></code> </p>
-        </td>
-        <td><p>Sensor list with proper names</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="setup_edr.html">setup_edr()</a></code> </p>
-        </td>
-        <td><p>Setup EDR run</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="spectra.html">spectra()</a></code> <code><a href="spectra.html">is_spectra()</a></code> </p>
-        </td>
-        <td><p>Spectra S3 class</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="spectral.response.html">spectral.response()</a></code> </p>
-        </td>
-        <td><p>Convolution of spectra to sensor RSR</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="str.spectra.html">str(<i>&lt;spectra&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Structure of <code>spectra</code> object</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sub-.spectra.html">`[`(<i>&lt;spectra&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Select spectra</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sub-sub-.spectra.html">`[[`(<i>&lt;spectra&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Select spectra by wavelength</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sub-subset-.spectra.html">`[[<-`(<i>&lt;spectra&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Assign values to spectra by wavelength</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="summary_mvnorm.html">summary_mvnorm()</a></code> </p>
-        </td>
-        <td><p>Multivariate normal fit</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="summary_simple.html">summary_simple()</a></code> </p>
-        </td>
-        <td><p>Simple summary statistics on MCMC samples</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="trim.rsr.html">trim.rsr()</a></code> </p>
-        </td>
-        <td><p>Trim RSR matrix to wavelength limits</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="wavelengths.html">wavelengths()</a></code> </p>
-        </td>
-        <td><p>Retrieve wavelengths from spectra object</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="EDR.html">EDR()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>ED radiative transfer module (EDR) wrapper function</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="EDR.preprocess.history.html"
+                        >EDR.preprocess.history()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Preprocess history file for EDR</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="bt_check_convergence.html"
+                        >bt_check_convergence()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check convergence of BayesianTools output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="burnin.thin.html">burnin.thin()</a></code>
+                  </p>
+                </td>
+                <td><p>Burn-in and thinning of MCMC samples</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="cbind.spectra.html"
+                        >cbind(<i>&lt;spectra&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Combine spectra by wavelength</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="check.convergence.html"
+                        >check.convergence()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Check convergence of multiple MCMC chains</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="corr_max_lag.html">corr_max_lag()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Calculate max ACF lag from correlation power analysis</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="default.settings.prospect.html"
+                        >default.settings.prospect</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Defult inversion settings for PROSPECT 5 models</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="defparam.html">defparam()</a></code>
+                  </p>
+                </td>
+                <td><p>Get default parameters</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="dtnorm.html">dtnorm()</a></code>
+                  </p>
+                </td>
+                <td><p>Truncated normal distribution density</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="fortran_data_module.html"
+                        >fortran_data_module()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>List to FORTRAN data module</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="foursail.html">foursail()</a></code>
+                  </p>
+                </td>
+                <td><p>SAIL model</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="generalized_plate_model.html"
+                        >generalized_plate_model()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Generalized plate model</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="generate.noise.html">generate.noise()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Generate autocorrelated spectral noise</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="generate.rsr.all.html"
+                        >generate.rsr.all()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Generate RSR matrices for all sensors and return as list
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.EDR.output.html">get.EDR.output()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read EDR output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="invert.auto.html">invert.auto()</a></code>
+                  </p>
+                </td>
+                <td><p>Inversion with automatic convergence checking</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="invert.custom.html">invert.custom()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Bayesian inversion of a model</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="invert.lsq.html">invert.lsq()</a></code>
+                  </p>
+                </td>
+                <td><p>Least squares model inversion</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="invert_bt.html">invert_bt()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Perform Bayesian inversion using BayesianTools package</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="load.from.name.html">load.from.name()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Load object from an RData file</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="lognorm.mu.html">lognorm.mu()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Functions for default priors Lognormal mean parameters</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="lognorm.sigma.html">lognorm.sigma()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Lognormal sigma parameter</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="matplot.html">matplot()</a></code>
+                  </p>
+                </td>
+                <td><p>Matplot generic method</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="matplot.default.html"
+                        >matplot(<i>&lt;default&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Matplot default method</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="matplot.spectra.html"
+                        >matplot(<i>&lt;spectra&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Plot multiple spectra on same graph</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="neff.html">neff()</a></code>
+                  </p>
+                </td>
+                <td><p>Effective sample size</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="params.prospect4.html"
+                        >params.prospect4</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>PROSPECT 4 parameters</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="params.prospect5.html"
+                        >params.prospect5</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>PROSPECT 5 parameters</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="params.prospect5b.html"
+                        >params.prospect5b</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>PROSPECT 5B parameters</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="params2edr.html">params2edr()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>Convert named parameter vector to EDR-compatible inputs</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot.spectra.html"
+                        >plot(<i>&lt;spectra&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Plot spectra vs. wavelength</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="print.spectra.html"
+                        >print(<i>&lt;spectra&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Print method for spectra S3 class</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="print_results_summary.html"
+                        >print_results_summary()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Neatly print inversion results summary</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="prior.defaultvals.prospect.html"
+                        >prior.defaultvals.prospect()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Default prior parameters for PROSPECT models</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="priorfunc.prospect.html"
+                        >priorfunc.prospect()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Default PROSPECT 5 prior function</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pro2s.html">pro2s()</a></code>
+                  </p>
+                </td>
+                <td><p>Coupled PROSPECT-Two-stream model</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="pro4sail.html">pro4sail()</a></code>
+                  </p>
+                </td>
+                <td><p>PRO4SAIL model</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="prospect.html">prospect()</a></code>
+                  </p>
+                </td>
+                <td><p>PROSPECT (4, 5, or 5B) model</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="prospect_bt_prior.html"
+                        >prospect_bt_prior()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Quick BayesianTools prior creator for PROSPECT model</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.rsr.folder.html"
+                        >read.rsr.folder()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read and process RSR data from directory</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="resample.html">resample()</a></code>
+                  </p>
+                </td>
+                <td><p>Resample vector, matrix, or spectra</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="rsr.from.fwhm.html">rsr.from.fwhm()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Generate relative spectral response (RSR) matrix based on
+                    FWHM data
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="rtm_loglike.html">rtm_loglike()</a></code>
+                  </p>
+                </td>
+                <td><p>Generic log-likelihood generator for RTMs</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="rtnorm.html">rtnorm()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Random sampling from one-sided truncated normal distribution
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sensor.list.html">sensor.list</a></code>
+                  </p>
+                </td>
+                <td><p>Sensor spectral response functions</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sensor.proper.html">sensor.proper</a></code>
+                  </p>
+                </td>
+                <td><p>Sensor list with proper names</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="setup_edr.html">setup_edr()</a></code>
+                  </p>
+                </td>
+                <td><p>Setup EDR run</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="spectra.html">spectra()</a></code>
+                    <code><a href="spectra.html">is_spectra()</a></code>
+                  </p>
+                </td>
+                <td><p>Spectra S3 class</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="spectral.response.html"
+                        >spectral.response()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Convolution of spectra to sensor RSR</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="str.spectra.html"
+                        >str(<i>&lt;spectra&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>Structure of <code>spectra</code> object</p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="sub-.spectra.html"
+                        >`[`(<i>&lt;spectra&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Select spectra</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="sub-sub-.spectra.html"
+                        >`[[`(<i>&lt;spectra&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Select spectra by wavelength</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="sub-subset-.spectra.html"
+                        >`[[<-`(<i>&lt;spectra&gt;</i>)</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Assign values to spectra by wavelength</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="summary_mvnorm.html">summary_mvnorm()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Multivariate normal fit</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="summary_simple.html">summary_simple()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Simple summary statistics on MCMC samples</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="trim.rsr.html">trim.rsr()</a></code>
+                  </p>
+                </td>
+                <td><p>Trim RSR matrix to wavelength limits</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="wavelengths.html">wavelengths()</a></code>
+                  </p>
+                </td>
+                <td><p>Retrieve wavelengths from spectra object</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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index b53034b..0a0cf32 100644
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Inversion with automatic convergence checking</h1>
-    
-    <div class="hidden name"><code>invert.auto.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Inversion with automatic convergence checking</h1>
 
-    <div class="ref-description">
-    
-    <p>Inversion with automatic convergence checking</p>
-    
-    </div>
+            <div class="hidden name"><code>invert.auto.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Inversion with automatic convergence checking</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>invert.auto</span>(<span class='no'>observed</span>, <span class='no'>invert.options</span>, <span class='kw'>return.samples</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>invert.auto</span>(<span class='no'>observed</span>, <span class='no'>invert.options</span>, <span class='kw'>return.samples</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>save.samples</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>parallel</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
   <span class='kw'>parallel.cores</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>parallel.output</span> <span class='kw'>=</span> <span class='st'>"/dev/null"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>observed</th>
-      <td><p>Vector, matrix, or data frame (coerced to matrix) of
-observed values. For spectral data, wavelengths are rows and spectra are
-columns. Dimensions must align with the output of <code>model</code>.</p></td>
-    </tr>
-    <tr>
-      <th>invert.options</th>
-      <td><p>Parameters related to inversion.</p></td>
-    </tr>
-    <tr>
-      <th>return.samples</th>
-      <td><p>Include full samples list in output. Default = <code>TRUE.</code></p></td>
-    </tr>
-    <tr>
-      <th>save.samples</th>
-      <td><p>Save samples to file as the inversion proceeds (useful
-for debugging). If <code>NULL</code>, do not save samples. Default = <code>NULL</code>.</p></td>
-    </tr>
-    <tr>
-      <th>quiet</th>
-      <td><p>Suppress progress bar and status messages. Default=FALSE</p></td>
-    </tr>
-    <tr>
-      <th>parallel</th>
-      <td><p>Logical. Whether or not to run multiple chains in parallel
-on multiple cores (default = <code>TRUE</code>).</p></td>
-    </tr>
-    <tr>
-      <th>parallel.cores</th>
-      <td><p>Number of cores to use for parallelization. If
-<code>NULL</code> (default), allocate one fewer than detected number of cores.</p></td>
-    </tr>
-    <tr>
-      <th>parallel.output</th>
-      <td><p>Filename (or '' for stdout) for printing parallel
-outputs. Use with caution. Default = <code>'/dev/null'</code>.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>List including <code>results</code> (summary statistics), <code>samples</code>
-(<code>mcmc.list</code> object, or <code>NA</code> if <code>return.samples=FALSE</code>), and other
-information.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Performs an inversion via the <code>invert.custom</code> function with
-multiple chains and automatic convergence checking.  Convergence checks are
-performed using the multivariate Gelman-Rubin diagnostic.</p>
-<p>Parameters specific to <code>invert.auto</code> are described here.
-For the remaining parameters, see <code><a href='invert.custom.html'>invert.custom()</a></code>.</p><ul>
-<li><p><code>model</code> -- The model to be inverted. This should be an R function that
-takes <code>params</code> as input and returns one column of <code>observed</code>
-(nrows should be the same). Constants should be implicitly included here.</p></li>
-<li><p><code>nchains</code> -- Number of independent chains.</p></li>
-<li><p><code>inits.function</code> -- Function for generating initial conditions.</p></li>
-<li><p><code>ngibbs.max</code> -- Maximum number of total iterations (per chain). DEFAULT = 5e6</p></li>
-<li><p><code>ngibbs.min</code> -- Minimum number of total iterations (per chain). DEFAULT = 5000.</p></li>
-<li><p><code>ngibbs.step</code> -- Number of iterations between convergence checks. Default = 1000.</p></li>
-<li><p><code>run_first</code> -- Function to run before running sampling. Takes parallel
-inputs list containing runID, initial values, and resume (NULL) as an
-argument.</p></li>
-<li><p><code>calculate.burnin</code> -- If <code>TRUE</code>, use <code>PEcAn.assim.batch::autoburin</code>
-function to calculate burnin. Otherwise, assume burnin is <code>min(niter/2, iter_conv_check)</code>.</p></li>
-<li><p><code>threshold</code> -- Maximum value of the Gelman-Rubin diagnostic for
-determining convergence. Default = 1.1</p></li>
-</ul>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>observed</th>
+              <td>
+                <p>
+                  Vector, matrix, or data frame (coerced to matrix) of observed
+                  values. For spectral data, wavelengths are rows and spectra
+                  are columns. Dimensions must align with the output of
+                  <code>model</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>invert.options</th>
+              <td><p>Parameters related to inversion.</p></td>
+            </tr>
+            <tr>
+              <th>return.samples</th>
+              <td>
+                <p>
+                  Include full samples list in output. Default =
+                  <code>TRUE.</code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>save.samples</th>
+              <td>
+                <p>
+                  Save samples to file as the inversion proceeds (useful for
+                  debugging). If <code>NULL</code>, do not save samples. Default
+                  = <code>NULL</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>quiet</th>
+              <td>
+                <p>Suppress progress bar and status messages. Default=FALSE</p>
+              </td>
+            </tr>
+            <tr>
+              <th>parallel</th>
+              <td>
+                <p>
+                  Logical. Whether or not to run multiple chains in parallel on
+                  multiple cores (default = <code>TRUE</code>).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>parallel.cores</th>
+              <td>
+                <p>
+                  Number of cores to use for parallelization. If
+                  <code>NULL</code> (default), allocate one fewer than detected
+                  number of cores.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>parallel.output</th>
+              <td>
+                <p>
+                  Filename (or '' for stdout) for printing parallel outputs. Use
+                  with caution. Default = <code>'/dev/null'</code>.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            List including <code>results</code> (summary statistics),
+            <code>samples</code> (<code>mcmc.list</code> object, or
+            <code>NA</code> if <code>return.samples=FALSE</code>), and other
+            information.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Performs an inversion via the <code>invert.custom</code> function
+            with multiple chains and automatic convergence checking. Convergence
+            checks are performed using the multivariate Gelman-Rubin diagnostic.
+          </p>
+          <p>
+            Parameters specific to <code>invert.auto</code> are described here.
+            For the remaining parameters, see
+            <code><a href="invert.custom.html">invert.custom()</a></code
+            >.
+          </p>
+          <ul>
+            <li>
+              <p>
+                <code>model</code> -- The model to be inverted. This should be
+                an R function that takes <code>params</code> as input and
+                returns one column of <code>observed</code> (nrows should be the
+                same). Constants should be implicitly included here.
+              </p>
+            </li>
+            <li>
+              <p><code>nchains</code> -- Number of independent chains.</p>
+            </li>
+            <li>
+              <p>
+                <code>inits.function</code> -- Function for generating initial
+                conditions.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>ngibbs.max</code> -- Maximum number of total iterations
+                (per chain). DEFAULT = 5e6
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>ngibbs.min</code> -- Minimum number of total iterations
+                (per chain). DEFAULT = 5000.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>ngibbs.step</code> -- Number of iterations between
+                convergence checks. Default = 1000.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>run_first</code> -- Function to run before running
+                sampling. Takes parallel inputs list containing runID, initial
+                values, and resume (NULL) as an argument.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>calculate.burnin</code> -- If <code>TRUE</code>, use
+                <code>PEcAn.assim.batch::autoburin</code> function to calculate
+                burnin. Otherwise, assume burnin is
+                <code>min(niter/2, iter_conv_check)</code>.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>threshold</code> -- Maximum value of the Gelman-Rubin
+                diagnostic for determining convergence. Default = 1.1
+              </p>
+            </li>
           </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-  </div>
-</div>
+            <li><a href="#value">Value</a></li>
 
-      <footer>
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-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+            <li><a href="#details">Details</a></li>
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+      property="og:description"
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 Metropolis Hastings algorithm with block sampling. This may be slightly
 slower than the implementation in Fortran, but is much more customizable, as
-the model can be any R function." />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Bayesian inversion of a model</h1>
-    
-    <div class="hidden name"><code>invert.custom.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Performs an inversion of an arbitrary model using a modified
-Metropolis Hastings algorithm with block sampling. This may be slightly
-slower than the implementation in Fortran, but is much more customizable, as
-the model can be any R function.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>invert.custom</span>(<span class='no'>observed</span>, <span class='no'>invert.options</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Bayesian inversion of a model</h1>
+
+            <div class="hidden name"><code>invert.custom.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Performs an inversion of an arbitrary model using a modified
+              Metropolis Hastings algorithm with block sampling. This may be
+              slightly slower than the implementation in Fortran, but is much
+              more customizable, as the model can be any R function.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>invert.custom</span>(<span class='no'>observed</span>, <span class='no'>invert.options</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>return.resume</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>runID</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>observed</th>
-      <td><p>Vector, matrix, or data frame (coerced to matrix) of
-observed values. For spectral data, wavelengths are rows and spectra are
-columns. Dimensions must align with the output of <code>model</code>.</p></td>
-    </tr>
-    <tr>
-      <th>invert.options</th>
-      <td><p>R list object containing inversion settings. See details.</p></td>
-    </tr>
-    <tr>
-      <th>quiet</th>
-      <td><p>Suppress progress bar and status messages. Default=FALSE</p></td>
-    </tr>
-    <tr>
-      <th>return.resume</th>
-      <td><p>If <code>TRUE</code>, return results as list that includes current
-Jump distribution (useful for continuing an ongoing run) and acceptance
-rate. Default = <code>FALSE</code>.</p></td>
-    </tr>
-    <tr>
-      <th>runID</th>
-      <td><p>Run-unique ID. Useful for parallel runs. Default=NULL</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><code>inversion.options</code> contains the following:</p><ul>
-<li><p><code>inits</code> -- Vector of initial values of model parameters to be inverted.</p></li>
-<li><p><code>ngibbs</code> -- Number of MCMC iterations</p></li>
-<li><p><code>prior.function</code> -- Function for use as prior.
-Should take a vector of parameters as input and return a single value -- the
-sum of their log-densities -- as output.</p></li>
-<li><p><code>param.mins</code> -- Vector of minimum values for inversion parameters</p></li>
-<li><p><code>param.maxs</code> -- Vector of minimum values for inversion parameters</p></li>
-<li><p><code>model</code> -- The model to be inverted.
-This should be an R function that takes <code>params</code> and <code>runID</code> as input and
-returns one column of <code>observed</code> (nrows should be the same).
-Constants should be implicitly included here.</p></li>
-<li><p><code>adapt</code> -- Number of steps for adapting covariance matrix (i.e. adapt
-every 'n' steps). Default=100</p></li>
-<li><p><code>adj_min</code> -- Minimum threshold for rescaling Jump standard deviation.
-Default = 0.1.</p></li>
-<li><p><code>target</code> -- Target acceptance rate. Default=0.234, based on recommendation
-for multivariate block sampling in Haario et al. 2001</p></li>
-<li><p><code>do.lsq</code> -- Perform least squares optimization first (see <code>invert.lsq</code>),
-and use outputs to initialize Metropolis Hastings.
-This may improve mixing time, but risks getting caught in a local minimum.
-Default=FALSE</p></li>
-<li><p><code>catch_error</code> -- If <code>TRUE</code> (default), wrap model in <code>tryCatch</code> to prevent sampling termination on model execution error.</p></li>
-</ul>
-    
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
-    <ul>
-<li><p>Haario, Heikki; Saksman, Eero; Tamminen, Johanna.  An adaptive Metropolis
-algorithm. Bernoulli 7 (2001), no. 2, 223--242.
-http://projecteuclid.org/euclid.bj/1080222083.</p></li>
-</ul>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#references">References</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>observed</th>
+              <td>
+                <p>
+                  Vector, matrix, or data frame (coerced to matrix) of observed
+                  values. For spectral data, wavelengths are rows and spectra
+                  are columns. Dimensions must align with the output of
+                  <code>model</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>invert.options</th>
+              <td>
+                <p>R list object containing inversion settings. See details.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>quiet</th>
+              <td>
+                <p>Suppress progress bar and status messages. Default=FALSE</p>
+              </td>
+            </tr>
+            <tr>
+              <th>return.resume</th>
+              <td>
+                <p>
+                  If <code>TRUE</code>, return results as list that includes
+                  current Jump distribution (useful for continuing an ongoing
+                  run) and acceptance rate. Default = <code>FALSE</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>runID</th>
+              <td>
+                <p>Run-unique ID. Useful for parallel runs. Default=NULL</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p><code>inversion.options</code> contains the following:</p>
+          <ul>
+            <li>
+              <p>
+                <code>inits</code> -- Vector of initial values of model
+                parameters to be inverted.
+              </p>
+            </li>
+            <li>
+              <p><code>ngibbs</code> -- Number of MCMC iterations</p>
+            </li>
+            <li>
+              <p>
+                <code>prior.function</code> -- Function for use as prior. Should
+                take a vector of parameters as input and return a single value
+                -- the sum of their log-densities -- as output.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>param.mins</code> -- Vector of minimum values for
+                inversion parameters
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>param.maxs</code> -- Vector of minimum values for
+                inversion parameters
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>model</code> -- The model to be inverted. This should be
+                an R function that takes <code>params</code> and
+                <code>runID</code> as input and returns one column of
+                <code>observed</code> (nrows should be the same). Constants
+                should be implicitly included here.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>adapt</code> -- Number of steps for adapting covariance
+                matrix (i.e. adapt every 'n' steps). Default=100
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>adj_min</code> -- Minimum threshold for rescaling Jump
+                standard deviation. Default = 0.1.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>target</code> -- Target acceptance rate. Default=0.234,
+                based on recommendation for multivariate block sampling in
+                Haario et al. 2001
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>do.lsq</code> -- Perform least squares optimization first
+                (see <code>invert.lsq</code>), and use outputs to initialize
+                Metropolis Hastings. This may improve mixing time, but risks
+                getting caught in a local minimum. Default=FALSE
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>catch_error</code> -- If <code>TRUE</code> (default), wrap
+                model in <code>tryCatch</code> to prevent sampling termination
+                on model execution error.
+              </p>
+            </li>
           </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="references">
+            <a class="anchor" href="#references"></a>References
+          </h2>
+
+          <ul>
+            <li>
+              <p>
+                Haario, Heikki; Saksman, Eero; Tamminen, Johanna. An adaptive
+                Metropolis algorithm. Bernoulli 7 (2001), no. 2, 223--242.
+                http://projecteuclid.org/euclid.bj/1080222083.
+              </p>
+            </li>
+          </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#references">References</a></li>
+          </ul>
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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diff --git a/modules/rtm/docs/reference/invert.lsq.html b/modules/rtm/docs/reference/invert.lsq.html
index 63de724..989e981 100644
--- a/modules/rtm/docs/reference/invert.lsq.html
+++ b/modules/rtm/docs/reference/invert.lsq.html
@@ -2,184 +2,243 @@
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+      property="og:title"
+      content="Least squares model inversion — invert.lsq"
+    />
+
+    <meta
+      property="og:description"
+      content="Performs a least-squares inversion of an arbitrary radiative transfer model
 (passed as an R function). The inversion attempts to minimize the sum of
 residual least squares between modeled and observed spectra via the
 Levenberg-Marquardt algorithm (nls.lm function from the minpack.lm
-package)." />
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+package)."
+    />
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Least squares model inversion</h1>
-    
-    <div class="hidden name"><code>invert.lsq.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Performs a least-squares inversion of an arbitrary radiative transfer model
-(passed as an R function). The inversion attempts to minimize the sum of
-residual least squares between modeled and observed spectra via the
-Levenberg-Marquardt algorithm (<code>nls.lm</code> function from the <code>minpack.lm</code>
-package).</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>invert.lsq</span>(<span class='no'>observed</span>, <span class='no'>inits</span>, <span class='no'>model</span>, <span class='kw'>lower</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>upper</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>observed</th>
-      <td><p>Vector of observations (e.g. a reflectance spectrum).</p></td>
-    </tr>
-    <tr>
-      <th>inits</th>
-      <td><p>Vector of initial conditions for the parameters.</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>An R function that calls the RTM and returns the error to be
-minimized. Be sure to include constants here.</p></td>
-    </tr>
-    <tr>
-      <th>lower</th>
-      <td><p>Lower bounds on parameters (default=NULL, which means -Inf).</p></td>
-    </tr>
-    <tr>
-      <th>uppper</th>
-      <td><p>Upper bounds on parameters (default=NULL, which means +Inf).</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Least squares model inversion</h1>
+
+            <div class="hidden name"><code>invert.lsq.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Performs a least-squares inversion of an arbitrary radiative
+              transfer model (passed as an R function). The inversion attempts
+              to minimize the sum of residual least squares between modeled and
+              observed spectra via the Levenberg-Marquardt algorithm (<code
+                >nls.lm</code
+              >
+              function from the <code>minpack.lm</code> package).
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>invert.lsq</span>(<span class='no'>observed</span>, <span class='no'>inits</span>, <span class='no'>model</span>, <span class='kw'>lower</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>upper</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>observed</th>
+              <td>
+                <p>Vector of observations (e.g. a reflectance spectrum).</p>
+              </td>
+            </tr>
+            <tr>
+              <th>inits</th>
+              <td><p>Vector of initial conditions for the parameters.</p></td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td>
+                <p>
+                  An R function that calls the RTM and returns the error to be
+                  minimized. Be sure to include constants here.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>lower</th>
+              <td>
+                <p>
+                  Lower bounds on parameters (default=NULL, which means -Inf).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>uppper</th>
+              <td>
+                <p>
+                  Upper bounds on parameters (default=NULL, which means +Inf).
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/invert_bt.html b/modules/rtm/docs/reference/invert_bt.html
index e9a90c4..bce2d28 100644
--- a/modules/rtm/docs/reference/invert_bt.html
+++ b/modules/rtm/docs/reference/invert_bt.html
@@ -2,211 +2,347 @@
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 <html>
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+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+      Perform Bayesian inversion using BayesianTools package — invert_bt •
+      PEcAnRTM
+    </title>
+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
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+    />
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+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    ></script>
+
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
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+      property="og:title"
+      content="Perform Bayesian inversion using BayesianTools package — invert_bt"
+    />
+
+    <meta
+      property="og:description"
+      content="Use samplers from the BayesianTools package to fit models to data. Like
 invert.auto, this will continue to run until convergence is achieved
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-specified by the user; see Details)." />
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-<![endif]-->
+specified by the user; see Details)."
+    />
+    <meta name="twitter:card" content="summary" />
 
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+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Perform Bayesian inversion using BayesianTools package</h1>
-    
-    <div class="hidden name"><code>invert_bt.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Use samplers from the BayesianTools package to fit models to data. Like
-<code>invert.auto</code>, this will continue to run until convergence is achieved
-(based on Gelman diagnostic) <em>and</em> the result has enough samples (as
-specified by the user; see Details).</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>invert_bt</span>(<span class='no'>observed</span>, <span class='no'>model</span>, <span class='no'>prior</span>, <span class='kw'>custom_settings</span> <span class='kw'>=</span> <span class='fu'>list</span>(),
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Perform Bayesian inversion using BayesianTools package</h1>
+
+            <div class="hidden name"><code>invert_bt.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Use samplers from the BayesianTools package to fit models to data.
+              Like <code>invert.auto</code>, this will continue to run until
+              convergence is achieved (based on Gelman diagnostic)
+              <em>and</em> the result has enough samples (as specified by the
+              user; see Details).
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>invert_bt</span>(<span class='no'>observed</span>, <span class='no'>model</span>, <span class='no'>prior</span>, <span class='kw'>custom_settings</span> <span class='kw'>=</span> <span class='fu'>list</span>(),
   <span class='kw'>loglike</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>observed</th>
-      <td><p>Vector of observations. Ignored if <code>loglike</code> is not <code>NULL</code>.</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>Function called by log-likelihood. Must be <code>function(params)</code>
-and return a vector equal to <code>length(observed)</code> or <code>nrow(observed)</code>. Ignored
-if <code>loglike</code> is not <code>NULL</code>.</p></td>
-    </tr>
-    <tr>
-      <th>prior</th>
-      <td><p>BayesianTools prior object.</p></td>
-    </tr>
-    <tr>
-      <th>custom_settings</th>
-      <td><p>Nested settings list. See Details.</p></td>
-    </tr>
-    <tr>
-      <th>loglike</th>
-      <td><p>Custom log likelihood function. If <code>NULL</code>, use <a href='rtm_loglike.html'>rtm_loglike</a>
-with provided <code>observed</code> and <code>model</code>.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p><code>custom_settings</code> is a list of lists, containing the following:</p><ul>
-<li><p><code>common</code> -- BayesianTools settings common to both the initial and subsequent samples.</p></li>
-<li><p><code>init</code> -- BayesianTools settings for just the first round of sampling.
-This is most common for the initial number of iterations, which is the
-minimum expected for convergence.</p></li>
-<li><p><code>loop</code> -- BayesianTools settings for iterations inside the convergence
-checking <code>while</code> loop. This is most commonly for setting a smaller
-iteration count than in <code>init</code>.</p></li>
-<li><p><code>other</code> -- Miscellaneous (non-BayesianTools) settings, including:</p><ul>
-<li><p><code>sampler</code> -- String describing which sampler to use. Default is <code>DEzs</code></p></li>
-<li><p><code>use_mpsrf</code> -- Use the multivariate PSRF to check convergence.
-Default is <code>FALSE</code> because it may be an excessively conservative
-diagnostic.</p></li>
-<li><p><code>min_samp</code> -- Minimum number of samples after burnin before stopping.
-Default is 5000.</p></li>
-<li><p><code>max_iter</code> -- Maximum total number of iterations. Default is 1e6.</p></li>
-<li><p><code>lag.max</code> -- Maximum lag to use for autocorrelation normalization.
-Default is <code>10 * log10(n)</code> (same as <code><a href='http://www.rdocumentation.org/packages/stats/topics/acf'>stats::acf</a></code> function).</p></li>
-<li><p><code>save_progress</code> -- File name for saving samples between loop
-iterations. If <code>NULL</code> (default), do not save progress samples.</p></li>
-<li><p><code>threshold</code> -- Threshold for Gelman PSRF convergence diagnostic. Default is 1.1.</p></li>
-<li><p><code>verbose_loglike</code> -- Diagnostic messages in log likelihood output. Default is TRUE.</p></li>
-</ul></li>
-</ul>
-    <p>See the BayesianTools sampler documentation for what can go in the <code>BayesianTools</code> settings lists.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>observed</th>
+              <td>
+                <p>
+                  Vector of observations. Ignored if <code>loglike</code> is not
+                  <code>NULL</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td>
+                <p>
+                  Function called by log-likelihood. Must be
+                  <code>function(params)</code> and return a vector equal to
+                  <code>length(observed)</code> or <code>nrow(observed)</code>.
+                  Ignored if <code>loglike</code> is not <code>NULL</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prior</th>
+              <td><p>BayesianTools prior object.</p></td>
+            </tr>
+            <tr>
+              <th>custom_settings</th>
+              <td><p>Nested settings list. See Details.</p></td>
+            </tr>
+            <tr>
+              <th>loglike</th>
+              <td>
+                <p>
+                  Custom log likelihood function. If <code>NULL</code>, use
+                  <a href="rtm_loglike.html">rtm_loglike</a> with provided
+                  <code>observed</code> and <code>model</code>.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            <code>custom_settings</code> is a list of lists, containing the
+            following:
+          </p>
+          <ul>
+            <li>
+              <p>
+                <code>common</code> -- BayesianTools settings common to both the
+                initial and subsequent samples.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>init</code> -- BayesianTools settings for just the first
+                round of sampling. This is most common for the initial number of
+                iterations, which is the minimum expected for convergence.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>loop</code> -- BayesianTools settings for iterations
+                inside the convergence checking <code>while</code> loop. This is
+                most commonly for setting a smaller iteration count than in
+                <code>init</code>.
+              </p>
+            </li>
+            <li>
+              <p>
+                <code>other</code> -- Miscellaneous (non-BayesianTools)
+                settings, including:
+              </p>
+              <ul>
+                <li>
+                  <p>
+                    <code>sampler</code> -- String describing which sampler to
+                    use. Default is <code>DEzs</code>
+                  </p>
+                </li>
+                <li>
+                  <p>
+                    <code>use_mpsrf</code> -- Use the multivariate PSRF to check
+                    convergence. Default is <code>FALSE</code> because it may be
+                    an excessively conservative diagnostic.
+                  </p>
+                </li>
+                <li>
+                  <p>
+                    <code>min_samp</code> -- Minimum number of samples after
+                    burnin before stopping. Default is 5000.
+                  </p>
+                </li>
+                <li>
+                  <p>
+                    <code>max_iter</code> -- Maximum total number of iterations.
+                    Default is 1e6.
+                  </p>
+                </li>
+                <li>
+                  <p>
+                    <code>lag.max</code> -- Maximum lag to use for
+                    autocorrelation normalization. Default is
+                    <code>10 * log10(n)</code> (same as
+                    <code
+                      ><a
+                        href="http://www.rdocumentation.org/packages/stats/topics/acf"
+                        >stats::acf</a
+                      ></code
+                    >
+                    function).
+                  </p>
+                </li>
+                <li>
+                  <p>
+                    <code>save_progress</code> -- File name for saving samples
+                    between loop iterations. If <code>NULL</code> (default), do
+                    not save progress samples.
+                  </p>
+                </li>
+                <li>
+                  <p>
+                    <code>threshold</code> -- Threshold for Gelman PSRF
+                    convergence diagnostic. Default is 1.1.
+                  </p>
+                </li>
+                <li>
+                  <p>
+                    <code>verbose_loglike</code> -- Diagnostic messages in log
+                    likelihood output. Default is TRUE.
+                  </p>
+                </li>
+              </ul>
+            </li>
+          </ul>
+          <p>
+            See the BayesianTools sampler documentation for what can go in the
+            <code>BayesianTools</code> settings lists.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/load.from.name.html b/modules/rtm/docs/reference/load.from.name.html
index 272e921..edbc414 100644
--- a/modules/rtm/docs/reference/load.from.name.html
+++ b/modules/rtm/docs/reference/load.from.name.html
@@ -2,159 +2,197 @@
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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-<div class="row">
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-    <h1>Load object from an RData file</h1>
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-    <div class="hidden name"><code>load.from.name.Rd</code></div>
-    </div>
-
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-    
-    <p>Load object from an RData file</p>
-    
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-
-    <pre class="usage"><span class='fu'>load.from.name</span>(<span class='no'>filename</span>, <span class='kw'>filepath</span> <span class='kw'>=</span> <span class='st'>"."</span>)</pre>
-    
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-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>filename</th>
-      <td><p>Full name (without path!) of RData file</p></td>
-    </tr>
-    <tr>
-      <th>filepath</th>
-      <td><p>Path of RData file (default='.')</p></td>
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-      <li><a href="#arguments">Arguments</a></li>
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-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Load object from an RData file</h1>
+
+            <div class="hidden name"><code>load.from.name.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Load object from an RData file</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>load.from.name</span>(<span class='no'>filename</span>, <span class='kw'>filepath</span> <span class='kw'>=</span> <span class='st'>"."</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>filename</th>
+              <td><p>Full name (without path!) of RData file</p></td>
+            </tr>
+            <tr>
+              <th>filepath</th>
+              <td><p>Path of RData file (default='.')</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
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diff --git a/modules/rtm/docs/reference/lognorm.mu.html b/modules/rtm/docs/reference/lognorm.mu.html
index f578077..e8aeafa 100644
--- a/modules/rtm/docs/reference/lognorm.mu.html
+++ b/modules/rtm/docs/reference/lognorm.mu.html
@@ -2,164 +2,205 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Functions for default priors
-Lognormal mean parameters</h1>
-    
-    <div class="hidden name"><code>lognorm.mu.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Functions for default priors
-Lognormal mean parameters</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>lognorm.mu</span>(<span class='no'>mean</span>, <span class='no'>sd</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mean</th>
-      <td><p>Sample mean</p></td>
-    </tr>
-    <tr>
-      <th>sd</th>
-      <td><p>Sample standard deviation</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Functions for default priors Lognormal mean parameters</h1>
+
+            <div class="hidden name"><code>lognorm.mu.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Functions for default priors Lognormal mean parameters</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>lognorm.mu</span>(<span class='no'>mean</span>, <span class='no'>sd</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mean</th>
+              <td><p>Sample mean</p></td>
+            </tr>
+            <tr>
+              <th>sd</th>
+              <td><p>Sample standard deviation</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/lognorm.sigma.html b/modules/rtm/docs/reference/lognorm.sigma.html
index 91d39c9..e5acd6f 100644
--- a/modules/rtm/docs/reference/lognorm.sigma.html
+++ b/modules/rtm/docs/reference/lognorm.sigma.html
@@ -2,159 +2,197 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Lognormal sigma parameter</h1>
-    
-    <div class="hidden name"><code>lognorm.sigma.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Lognormal sigma parameter</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>lognorm.sigma</span>(<span class='no'>mean</span>, <span class='no'>sd</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mean</th>
-      <td><p>Sample mean</p></td>
-    </tr>
-    <tr>
-      <th>sd</th>
-      <td><p>Sample standard deviation</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Lognormal sigma parameter</h1>
+
+            <div class="hidden name"><code>lognorm.sigma.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Lognormal sigma parameter</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>lognorm.sigma</span>(<span class='no'>mean</span>, <span class='no'>sd</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mean</th>
+              <td><p>Sample mean</p></td>
+            </tr>
+            <tr>
+              <th>sd</th>
+              <td><p>Sample standard deviation</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/matplot.default.html b/modules/rtm/docs/reference/matplot.default.html
index 2783272..282b4da 100644
--- a/modules/rtm/docs/reference/matplot.default.html
+++ b/modules/rtm/docs/reference/matplot.default.html
@@ -2,146 +2,176 @@
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+                  </a>
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+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Matplot default method</h1>
-    
-    <div class="hidden name"><code>matplot.default.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Matplot default method</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Matplot default method</h1>
 
-    <pre class="usage"><span class='co'># S3 method for default</span>
-<span class='fu'><a href='matplot.html'>matplot</a></span>(<span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>matplot.default.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Matplot default method</p>
+          </div>
 
-  </div>
-</div>
+          <pre class="usage"><span class='co'># S3 method for default</span>
+<span class='fu'><a href='matplot.html'>matplot</a></span>(<span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index 161c25f..2c6a538 100644
--- a/modules/rtm/docs/reference/matplot.html
+++ b/modules/rtm/docs/reference/matplot.html
@@ -2,145 +2,174 @@
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-    <h1>Matplot generic method</h1>
-    
-    <div class="hidden name"><code>matplot.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Matplot generic method</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Matplot generic method</h1>
 
-    <pre class="usage"><span class='fu'>matplot</span>(<span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>matplot.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Matplot generic method</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>matplot</span>(<span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/matplot.spectra.html b/modules/rtm/docs/reference/matplot.spectra.html
index 425c8ab..7f3cbf5 100644
--- a/modules/rtm/docs/reference/matplot.spectra.html
+++ b/modules/rtm/docs/reference/matplot.spectra.html
@@ -2,160 +2,208 @@
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+                        >The PEcAn RTM package</a
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Plot multiple spectra on same graph</h1>
-    
-    <div class="hidden name"><code>matplot.spectra.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Plot multiple spectra on same graph</h1>
 
-    <div class="ref-description">
-    
-    <p>Plot multiple spectra on same graph</p>
-    
-    </div>
+            <div class="hidden name"><code>matplot.spectra.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for spectra</span>
-<span class='fu'><a href='matplot.html'>matplot</a></span>(<span class='no'>spectra</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spectra</th>
-      <td><p>Vector (<code>length = length(wavelengths)</code>) or matrix (<code>ncol = length(wavelengths)</code>)</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional arguments to <code>matplot</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Plot multiple spectra on same graph</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for spectra</span>
+<span class='fu'><a href='matplot.html'>matplot</a></span>(<span class='no'>spectra</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spectra</th>
+              <td>
+                <p>
+                  Vector (<code>length = length(wavelengths)</code>) or matrix
+                  (<code>ncol = length(wavelengths)</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>Additional arguments to <code>matplot</code></p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/rtm/docs/reference/neff.html b/modules/rtm/docs/reference/neff.html
index 05756ca..ce04073 100644
--- a/modules/rtm/docs/reference/neff.html
+++ b/modules/rtm/docs/reference/neff.html
@@ -2,155 +2,196 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Effective sample size</h1>
-    
-    <div class="hidden name"><code>neff.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate effective sample size of vector based on its autocorrelation.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>neff</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>A vector or time series</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Effective sample size</h1>
+
+            <div class="hidden name"><code>neff.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Calculate effective sample size of vector based on its
+              autocorrelation.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>neff</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>A vector or time series</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/params.prospect4.html b/modules/rtm/docs/reference/params.prospect4.html
index 6523967..e78205b 100644
--- a/modules/rtm/docs/reference/params.prospect4.html
+++ b/modules/rtm/docs/reference/params.prospect4.html
@@ -2,151 +2,186 @@
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-<div class="row">
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-    <div class="page-header">
-    <h1>PROSPECT 4 parameters</h1>
-    
-    <div class="hidden name"><code>params.prospect4.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>PROSPECT 4 parameters</h1>
 
-    <div class="ref-description">
-    
-    <p>Shortcut lists for PROSPECT parameter names</p>
-    
-    </div>
+            <div class="hidden name"><code>params.prospect4.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='no'>params.prospect4</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+          <div class="ref-description">
+            <p>Shortcut lists for PROSPECT parameter names</p>
+          </div>
 
-    <p>An object of class <code>character</code> of length 4.</p>
-    
+          <pre class="usage"><span class='no'>params.prospect4</span></pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
-          </ul>
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
 
-  </div>
-</div>
+          <p>An object of class <code>character</code> of length 4.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/rtm/docs/reference/params.prospect5.html b/modules/rtm/docs/reference/params.prospect5.html
index c50e35b..db5021d 100644
--- a/modules/rtm/docs/reference/params.prospect5.html
+++ b/modules/rtm/docs/reference/params.prospect5.html
@@ -2,151 +2,183 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
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+    />
+
+    <!-- clipboard.js -->
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+              <ul class="nav navbar-nav">
+                <li>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
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+                    role="button"
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+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
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+                </li>
+              </ul>
+
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>PROSPECT 5 parameters</h1>
-    
-    <div class="hidden name"><code>params.prospect5.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>PROSPECT 5 parameters</h1>
 
-    <div class="ref-description">
-    
-    <p>PROSPECT 5 parameters</p>
-    
-    </div>
+            <div class="hidden name"><code>params.prospect5.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='no'>params.prospect5</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+          <div class="ref-description">
+            <p>PROSPECT 5 parameters</p>
+          </div>
 
-    <p>An object of class <code>character</code> of length 5.</p>
-    
+          <pre class="usage"><span class='no'>params.prospect5</span></pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
-          </ul>
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
 
-  </div>
-</div>
+          <p>An object of class <code>character</code> of length 5.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/rtm/docs/reference/params.prospect5b.html b/modules/rtm/docs/reference/params.prospect5b.html
index 471fd3f..6e78c77 100644
--- a/modules/rtm/docs/reference/params.prospect5b.html
+++ b/modules/rtm/docs/reference/params.prospect5b.html
@@ -2,151 +2,183 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    />
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+      crossorigin="anonymous"
+    ></script>
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>PROSPECT 5B parameters</h1>
-    
-    <div class="hidden name"><code>params.prospect5b.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>PROSPECT 5B parameters</h1>
 
-    <div class="ref-description">
-    
-    <p>PROSPECT 5B parameters</p>
-    
-    </div>
+            <div class="hidden name"><code>params.prospect5b.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='no'>params.prospect5b</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+          <div class="ref-description">
+            <p>PROSPECT 5B parameters</p>
+          </div>
 
-    <p>An object of class <code>character</code> of length 6.</p>
-    
+          <pre class="usage"><span class='no'>params.prospect5b</span></pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
-          </ul>
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
 
-  </div>
-</div>
+          <p>An object of class <code>character</code> of length 6.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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diff --git a/modules/rtm/docs/reference/params2edr.html b/modules/rtm/docs/reference/params2edr.html
index 7247117..44ed9ea 100644
--- a/modules/rtm/docs/reference/params2edr.html
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@@ -2,201 +2,281 @@
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convert named parameter vector to EDR-compatible inputs</h1>
-    
-    <div class="hidden name"><code>params2edr.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Creates a nested list whose components are suitable for passing to EDR.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>params2edr</span>(<span class='no'>params</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>prospect</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='fl'>5</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>params</th>
-      <td><p>Named parameter vector</p></td>
-    </tr>
-    <tr>
-      <th>sep</th>
-      <td><p>Separator between PFT name and trait name. Must be a single
-character (default = ".").</p></td>
-    </tr>
-    <tr>
-      <th>prospect</th>
-      <td><p>Logical. If <code>TRUE</code> (default), scan for PROSPECT traits and
-pass them to PROSPECT.</p></td>
-    </tr>
-    <tr>
-      <th>version</th>
-      <td><p>PROSPECT version</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>List containing <code>spectra_list</code> and <code>trait.values</code>, both objects needed by <a href='EDR.html'>EDR</a>.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>If <code>prospect = TRUE</code>, parameters prefixed with <code>prospect_</code> are passed to
-<a href='prospect.html'>prospect</a> with the specified <code>version</code>, and other parameters are passed to
-<code>trait.values</code>.</p>
-<p>The regular expression defining the separation is greedy, i.e.
-<code>temperate.Early_Hardwood.SLA</code> will separate into <code>temperate.Early_Hardwood</code>
-and <code>SLA</code> (assuming the default <code>sep = "."</code>). Therefore, it is crucial that
-trait names not contain any <code>sep</code> characters (neither ED nor PROSPECT
-parameters should anyway). If this is a problem, use an alternate separator
-(e.g. <code>|</code>).</p>
-<p>Note that using <code>sep = "."</code> allows this function to directly invert the
-default behavior of <code>unlist</code>. That is, calling
-<code>unlist(params2edr(params, prospect = FALSE)$trait.values)</code> will return the input vector of
-trait values. This makes <code>unlist</code> a convenient way to go from a
-<code>trait.values</code> list to a properly formatted <code>params</code> vector.</p>
-<p>Because unused ED parameters in the <code>config.xml</code> are ignored, the PROSPECT
-parameters are saved in the <code>trait.values</code> object as well, which may be
-useful for debugging.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convert named parameter vector to EDR-compatible inputs</h1>
+
+            <div class="hidden name"><code>params2edr.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Creates a nested list whose components are suitable for passing to
+              EDR.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>params2edr</span>(<span class='no'>params</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>prospect</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='fl'>5</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>params</th>
+              <td><p>Named parameter vector</p></td>
+            </tr>
+            <tr>
+              <th>sep</th>
+              <td>
+                <p>
+                  Separator between PFT name and trait name. Must be a single
+                  character (default = ".").
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prospect</th>
+              <td>
+                <p>
+                  Logical. If <code>TRUE</code> (default), scan for PROSPECT
+                  traits and pass them to PROSPECT.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>version</th>
+              <td><p>PROSPECT version</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            List containing <code>spectra_list</code> and
+            <code>trait.values</code>, both objects needed by
+            <a href="EDR.html">EDR</a>.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            If <code>prospect = TRUE</code>, parameters prefixed with
+            <code>prospect_</code> are passed to
+            <a href="prospect.html">prospect</a> with the specified
+            <code>version</code>, and other parameters are passed to
+            <code>trait.values</code>.
+          </p>
+          <p>
+            The regular expression defining the separation is greedy, i.e.
+            <code>temperate.Early_Hardwood.SLA</code> will separate into
+            <code>temperate.Early_Hardwood</code> and <code>SLA</code> (assuming
+            the default <code>sep = "."</code>). Therefore, it is crucial that
+            trait names not contain any <code>sep</code> characters (neither ED
+            nor PROSPECT parameters should anyway). If this is a problem, use an
+            alternate separator (e.g. <code>|</code>).
+          </p>
+          <p>
+            Note that using <code>sep = "."</code> allows this function to
+            directly invert the default behavior of <code>unlist</code>. That
+            is, calling
+            <code
+              >unlist(params2edr(params, prospect = FALSE)$trait.values)</code
+            >
+            will return the input vector of trait values. This makes
+            <code>unlist</code> a convenient way to go from a
+            <code>trait.values</code> list to a properly formatted
+            <code>params</code> vector.
+          </p>
+          <p>
+            Because unused ED parameters in the <code>config.xml</code> are
+            ignored, the PROSPECT parameters are saved in the
+            <code>trait.values</code> object as well, which may be useful for
+            debugging.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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-
diff --git a/modules/rtm/docs/reference/plot.spectra.html b/modules/rtm/docs/reference/plot.spectra.html
index da18e0d..6e00cb1 100644
--- a/modules/rtm/docs/reference/plot.spectra.html
+++ b/modules/rtm/docs/reference/plot.spectra.html
@@ -2,160 +2,203 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Plot spectra vs. wavelength</h1>
-    
-    <div class="hidden name"><code>plot.spectra.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Plot spectra vs. wavelength</h1>
 
-    <div class="ref-description">
-    
-    <p>Plot spectra vs. wavelength</p>
-    
-    </div>
+            <div class="hidden name"><code>plot.spectra.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for spectra</span>
-<span class='fu'>plot</span>(<span class='no'>spectra</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"l"</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spectra</th>
-      <td><p>Vector (<code>length = length(wavelengths)</code>) or matrix (<code>ncol = length(wavelengths)</code>)</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional arguments to <code>plot</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Plot spectra vs. wavelength</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for spectra</span>
+<span class='fu'>plot</span>(<span class='no'>spectra</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"l"</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spectra</th>
+              <td>
+                <p>
+                  Vector (<code>length = length(wavelengths)</code>) or matrix
+                  (<code>ncol = length(wavelengths)</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>Additional arguments to <code>plot</code></p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/print.spectra.html b/modules/rtm/docs/reference/print.spectra.html
index 4917a58..a404664 100644
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Print method for spectra S3 class</h1>
-    
-    <div class="hidden name"><code>print.spectra.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Print method for spectra S3 class</h1>
 
-    <div class="ref-description">
-    
-    <p>Print method for spectra S3 class</p>
-    
-    </div>
+            <div class="hidden name"><code>print.spectra.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for spectra</span>
-<span class='fu'>print</span>(<span class='no'>spectra</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spectra</th>
-      <td><p>Object of class <code>spectra</code></p></td>
-    </tr>
-    <tr>
-      <th>n</th>
-      <td><p>Max number of rows to print (show first <code>n/2</code> and last <code>n/2</code> rows)</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional arguments to <code>print</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Print method for spectra S3 class</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for spectra</span>
+<span class='fu'>print</span>(<span class='no'>spectra</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spectra</th>
+              <td>
+                <p>Object of class <code>spectra</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>n</th>
+              <td>
+                <p>
+                  Max number of rows to print (show first <code>n/2</code> and
+                  last <code>n/2</code> rows)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>Additional arguments to <code>print</code></p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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-
diff --git a/modules/rtm/docs/reference/print_results_summary.html b/modules/rtm/docs/reference/print_results_summary.html
index 9c5e022..be48b2e 100644
--- a/modules/rtm/docs/reference/print_results_summary.html
+++ b/modules/rtm/docs/reference/print_results_summary.html
@@ -2,159 +2,204 @@
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+      Neatly print inversion results summary — print_results_summary • PEcAnRTM
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+
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+    ></script>
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
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+    />
+    <meta name="twitter:card" content="summary" />
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+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
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+
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Neatly print inversion results summary</h1>
-    
-    <div class="hidden name"><code>print_results_summary.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Neatly print inversion results summary</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>print_results_summary</span>(<span class='no'>output</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>output</th>
-      <td><p>Output from <code>invert.auto</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Neatly print inversion results summary</h1>
+
+            <div class="hidden name"><code>print_results_summary.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Neatly print inversion results summary</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>print_results_summary</span>(<span class='no'>output</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>output</th>
+              <td>
+                <p>Output from <code>invert.auto</code></p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/rtm/docs/reference/prior.defaultvals.prospect.html b/modules/rtm/docs/reference/prior.defaultvals.prospect.html
index 7452e8c..b6e1f6f 100644
--- a/modules/rtm/docs/reference/prior.defaultvals.prospect.html
+++ b/modules/rtm/docs/reference/prior.defaultvals.prospect.html
@@ -2,155 +2,201 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+      • PEcAnRTM
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+
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Default prior parameters for PROSPECT models</h1>
-    
-    <div class="hidden name"><code>prior.defaultvals.prospect.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Default prior parameters for PROSPECT models</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>prior.defaultvals.prospect</span>(<span class='kw'>sd.inflate</span> <span class='kw'>=</span> <span class='fl'>3</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sd.inflate</th>
-      <td><p>Standard deviation multiplier (default = 3)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Default prior parameters for PROSPECT models</h1>
+
+            <div class="hidden name">
+              <code>prior.defaultvals.prospect.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Default prior parameters for PROSPECT models</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>prior.defaultvals.prospect</span>(<span class='kw'>sd.inflate</span> <span class='kw'>=</span> <span class='fl'>3</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sd.inflate</th>
+              <td><p>Standard deviation multiplier (default = 3)</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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diff --git a/modules/rtm/docs/reference/priorfunc.prospect.html b/modules/rtm/docs/reference/priorfunc.prospect.html
index a350d84..f33117b 100644
--- a/modules/rtm/docs/reference/priorfunc.prospect.html
+++ b/modules/rtm/docs/reference/priorfunc.prospect.html
@@ -2,166 +2,213 @@
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Default PROSPECT 5 prior function</h1>
-    
-    <div class="hidden name"><code>priorfunc.prospect.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Default PROSPECT 5 prior function</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>priorfunc.prospect</span>(<span class='no'>pmu</span>, <span class='no'>psigma</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pmu</th>
-      <td><p>Lognormal mu parameter</p></td>
-    </tr>
-    <tr>
-      <th>psigma</th>
-      <td><p>Lognormal sigma parameter</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Assumes lognormal distribution for all parameters. NOTE that prior
-on N is shifted by 1.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Default PROSPECT 5 prior function</h1>
+
+            <div class="hidden name"><code>priorfunc.prospect.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Default PROSPECT 5 prior function</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>priorfunc.prospect</span>(<span class='no'>pmu</span>, <span class='no'>psigma</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pmu</th>
+              <td><p>Lognormal mu parameter</p></td>
+            </tr>
+            <tr>
+              <th>psigma</th>
+              <td><p>Lognormal sigma parameter</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Assumes lognormal distribution for all parameters. NOTE that prior
+            on N is shifted by 1.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
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-</div>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/pro2s.html b/modules/rtm/docs/reference/pro2s.html
index c2013b2..c76bb45 100644
--- a/modules/rtm/docs/reference/pro2s.html
+++ b/modules/rtm/docs/reference/pro2s.html
@@ -2,174 +2,238 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Coupled PROSPECT-Two-stream model</h1>
-    
-    <div class="hidden name"><code>pro2s.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Coupled PROSPECT-Two-stream model</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pro2s</span>(<span class='no'>param</span>, <span class='kw'>prospect.version</span> <span class='kw'>=</span> <span class='fl'>5</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>param</th>
-      <td><p>Model parameters, in the following order: N, Cab, (Car,
-Cbrown), Cw, Cm, solar zenith angle, LAI, soil_moisture</p></td>
-    </tr>
-    <tr>
-      <th>prospect.version</th>
-      <td><p>Version of PROSPECT to use (4, 5, or '5B'; default=5)</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Spectra matrix (see <code><a href='spectra.html'>spectra()</a></code>) for wavelengths 400 to 2500nm containing the following columns:</p><ul>
-<li><p><code>alpha.c</code> -- Direct ("collimated") reflectance</p></li>
-<li><p><code>alpha.i</code> -- Diffuse ("isotropic") reflectance</p></li>
-<li><p><code>Tc</code> -- Direct transmittance to background</p></li>
-<li><p><code>Ti</code> -- Diffuse reflectance to background</p></li>
-<li><p><code>Ac</code> -- Direct absorbance by canopy</p></li>
-<li><p><code>Ai</code> -- Diffuse absorbance by canopy</p></li>
-</ul>
-
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Coupled PROSPECT-Two-stream model</h1>
+
+            <div class="hidden name"><code>pro2s.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Coupled PROSPECT-Two-stream model</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pro2s</span>(<span class='no'>param</span>, <span class='kw'>prospect.version</span> <span class='kw'>=</span> <span class='fl'>5</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>param</th>
+              <td>
+                <p>
+                  Model parameters, in the following order: N, Cab, (Car,
+                  Cbrown), Cw, Cm, solar zenith angle, LAI, soil_moisture
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prospect.version</th>
+              <td>
+                <p>Version of PROSPECT to use (4, 5, or '5B'; default=5)</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Spectra matrix (see <code><a href="spectra.html">spectra()</a></code
+            >) for wavelengths 400 to 2500nm containing the following columns:
+          </p>
+          <ul>
+            <li>
+              <p><code>alpha.c</code> -- Direct ("collimated") reflectance</p>
+            </li>
+            <li>
+              <p><code>alpha.i</code> -- Diffuse ("isotropic") reflectance</p>
+            </li>
+            <li>
+              <p><code>Tc</code> -- Direct transmittance to background</p>
+            </li>
+            <li>
+              <p><code>Ti</code> -- Diffuse reflectance to background</p>
+            </li>
+            <li>
+              <p><code>Ac</code> -- Direct absorbance by canopy</p>
+            </li>
+            <li>
+              <p><code>Ai</code> -- Diffuse absorbance by canopy</p>
+            </li>
           </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-  </div>
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+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
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diff --git a/modules/rtm/docs/reference/pro4sail.html b/modules/rtm/docs/reference/pro4sail.html
index 1f40f42..98d9a70 100644
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+++ b/modules/rtm/docs/reference/pro4sail.html
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>PRO4SAIL model</h1>
-    
-    <div class="hidden name"><code>pro4sail.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>R wrapper for PRO4SAIL model</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>pro4sail</span>(<span class='no'>param</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>param</th>
-      <td><p>Vector of PRO4SAIL parameter values:
-* N: Effective number of leaf layers (&gt;1)
-* Cab: Leaf chlorophyll content (ug/cm2) (&gt;0)
-* Car: Leaf carotenoid content (ug/cm2) (&gt;0)
-* Cbrown: Leaf brown matter content (ug/cm2) (&gt;0)
-* Cw: Leaf water content (cm) (&gt;0)
-* Cm: Leaf dry matter content (ug/cm2) (&gt;0)
-* LIDFa: Leaf angle distribution function - parameter a
-* LIDFb: Leaf angle distribution function - parameter b
-* TypeLIDF: Leaf angle distribution function type (1 or 2)
-* LAI: Leaf area index
-* q: Hot spot effect parameter
-* tts: Solar zenith angle
-* tto: Observer zenith angle
-* psi: Sun-sensor azimuth angle
-* psoil: Fraction of soil moisture</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Spectra matrix (see <code><a href='spectra.html'>spectra()</a></code>) (2101 x 4) of reflectance factors
-for wavelengths 400 to 2500nm:
-* bi-hemispherical reflectance (rddt)
-* hemispherical directional (rsdt)
-* directional hemispherical (rdot)
-* bi-directional (rsot)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>PRO4SAIL model</h1>
+
+            <div class="hidden name"><code>pro4sail.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>R wrapper for PRO4SAIL model</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>pro4sail</span>(<span class='no'>param</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>param</th>
+              <td>
+                <p>
+                  Vector of PRO4SAIL parameter values: * N: Effective number of
+                  leaf layers (&gt;1) * Cab: Leaf chlorophyll content (ug/cm2)
+                  (&gt;0) * Car: Leaf carotenoid content (ug/cm2) (&gt;0) *
+                  Cbrown: Leaf brown matter content (ug/cm2) (&gt;0) * Cw: Leaf
+                  water content (cm) (&gt;0) * Cm: Leaf dry matter content
+                  (ug/cm2) (&gt;0) * LIDFa: Leaf angle distribution function -
+                  parameter a * LIDFb: Leaf angle distribution function -
+                  parameter b * TypeLIDF: Leaf angle distribution function type
+                  (1 or 2) * LAI: Leaf area index * q: Hot spot effect parameter
+                  * tts: Solar zenith angle * tto: Observer zenith angle * psi:
+                  Sun-sensor azimuth angle * psoil: Fraction of soil moisture
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Spectra matrix (see <code><a href="spectra.html">spectra()</a></code
+            >) (2101 x 4) of reflectance factors for wavelengths 400 to 2500nm:
+            * bi-hemispherical reflectance (rddt) * hemispherical directional
+            (rsdt) * directional hemispherical (rdot) * bi-directional (rsot)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
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-</div>
-
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+          <p>Developed by .</p>
+        </div>
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diff --git a/modules/rtm/docs/reference/prospect.html b/modules/rtm/docs/reference/prospect.html
index 292dbf8..1cca2a0 100644
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@@ -2,176 +2,223 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>PROSPECT (4, 5, or 5B) model</h1>
-    
-    <div class="hidden name"><code>prospect.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>R wrapper for PROSPECT models</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>prospect</span>(<span class='no'>param</span>, <span class='no'>version</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>param</th>
-      <td><p>Vector of PROSPECT parameter values:
-* N: Effective number of leaf layers (&gt;1)
-* Cab: Leaf chlorophyll content (ug/cm2) (&gt;0)
-* (5) Car: Leaf carotenoid content (ug/cm2) (&gt;0)
-* (5B) Cbrown: Leaf brown matter content (ug/cm2) (&gt;0)
-* Cw: Leaf water content (cm) (&gt;0)
-* Cm: Leaf dry matter content (ug/cm2) (&gt;0)</p></td>
-    </tr>
-    <tr>
-      <th>version</th>
-      <td><p>PROSPECT version: 4, 5, or '5B'</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Object of class <code>spectra</code> (see <code><a href='spectra.html'>spectra()</a></code>) with simulated
-reflectance (column 1) and transmittance (column 2) from 400 to 2500 nm</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>PROSPECT (4, 5, or 5B) model</h1>
+
+            <div class="hidden name"><code>prospect.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>R wrapper for PROSPECT models</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>prospect</span>(<span class='no'>param</span>, <span class='no'>version</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>param</th>
+              <td>
+                <p>
+                  Vector of PROSPECT parameter values: * N: Effective number of
+                  leaf layers (&gt;1) * Cab: Leaf chlorophyll content (ug/cm2)
+                  (&gt;0) * (5) Car: Leaf carotenoid content (ug/cm2) (&gt;0) *
+                  (5B) Cbrown: Leaf brown matter content (ug/cm2) (&gt;0) * Cw:
+                  Leaf water content (cm) (&gt;0) * Cm: Leaf dry matter content
+                  (ug/cm2) (&gt;0)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>version</th>
+              <td><p>PROSPECT version: 4, 5, or '5B'</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Object of class <code>spectra</code> (see
+            <code><a href="spectra.html">spectra()</a></code
+            >) with simulated reflectance (column 1) and transmittance (column
+            2) from 400 to 2500 nm
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/prospect_bt_prior.html b/modules/rtm/docs/reference/prospect_bt_prior.html
index 8c68b45..942cd80 100644
--- a/modules/rtm/docs/reference/prospect_bt_prior.html
+++ b/modules/rtm/docs/reference/prospect_bt_prior.html
@@ -2,159 +2,209 @@
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+
+    <!-- clipboard.js -->
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+          <!--/.container -->
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Quick BayesianTools prior creator for PROSPECT model</h1>
-    
-    <div class="hidden name"><code>prospect_bt_prior.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Quick BayesianTools prior creator for PROSPECT model</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>prospect_bt_prior</span>(<span class='no'>version</span>, <span class='kw'>custom_prior</span> <span class='kw'>=</span> <span class='fu'>list</span>())</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>version</th>
-      <td><p>PROSPECT version: 4, 5, or '5B'</p></td>
-    </tr>
-    <tr>
-      <th>custom_prior</th>
-      <td><p>List containing <code>param_name</code>, <code>distn</code>, <code>parama</code>, <code>paramb</code>, and <code>lower</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Quick BayesianTools prior creator for PROSPECT model</h1>
+
+            <div class="hidden name"><code>prospect_bt_prior.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Quick BayesianTools prior creator for PROSPECT model</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>prospect_bt_prior</span>(<span class='no'>version</span>, <span class='kw'>custom_prior</span> <span class='kw'>=</span> <span class='fu'>list</span>())</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>version</th>
+              <td><p>PROSPECT version: 4, 5, or '5B'</p></td>
+            </tr>
+            <tr>
+              <th>custom_prior</th>
+              <td>
+                <p>
+                  List containing <code>param_name</code>, <code>distn</code>,
+                  <code>parama</code>, <code>paramb</code>, and
+                  <code>lower</code>
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/rtm/docs/reference/read.rsr.folder.html b/modules/rtm/docs/reference/read.rsr.folder.html
index 8523013..ed8b2fa 100644
--- a/modules/rtm/docs/reference/read.rsr.folder.html
+++ b/modules/rtm/docs/reference/read.rsr.folder.html
@@ -2,159 +2,202 @@
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-
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-<![endif]-->
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
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+    <script
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+                <span
+                  class="label label-default"
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+                  >1.6.0</span
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+              <ul class="nav navbar-nav">
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
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+                    role="button"
+                    aria-expanded="false"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read and process RSR data from directory</h1>
-    
-    <div class="hidden name"><code>read.rsr.folder.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Read and process RSR data from directory</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>read.rsr.folder</span>(<span class='no'>dir.path</span>, <span class='no'>type</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>dir.path</th>
-      <td><p>Directory containing RSR data</p></td>
-    </tr>
-    <tr>
-      <th>type</th>
-      <td><p>Type of sensor. Options are: landsat, avhrr</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read and process RSR data from directory</h1>
+
+            <div class="hidden name"><code>read.rsr.folder.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Read and process RSR data from directory</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read.rsr.folder</span>(<span class='no'>dir.path</span>, <span class='no'>type</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>dir.path</th>
+              <td><p>Directory containing RSR data</p></td>
+            </tr>
+            <tr>
+              <th>type</th>
+              <td><p>Type of sensor. Options are: landsat, avhrr</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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+    </div>
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 </html>
-
diff --git a/modules/rtm/docs/reference/resample.html b/modules/rtm/docs/reference/resample.html
index 582eca8..412f410 100644
--- a/modules/rtm/docs/reference/resample.html
+++ b/modules/rtm/docs/reference/resample.html
@@ -2,124 +2,182 @@
 <!DOCTYPE html>
 <html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-
-<title>Resample vector, matrix, or spectra — resample • PEcAnRTM</title>
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+      content="Resample vector, matrix, or spectra — resample"
+    />
+
+    <meta
+      property="og:description"
+      content="Convenient wrapper around base R's splinefun and approxfun. See
 stats::splinefun() and stats::approxfun() documentation for information
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+                        >The PEcAn RTM package</a
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Resample vector, matrix, or spectra</h1>
-    
-    <div class="hidden name"><code>resample.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convenient wrapper around base R's <code>splinefun</code> and <code>approxfun</code>. See
-<code><a href='http://www.rdocumentation.org/packages/stats/topics/splinefun'>stats::splinefun()</a></code> and <code><a href='http://www.rdocumentation.org/packages/stats/topics/approxfun'>stats::approxfun()</a></code> documentation for information
-on different spline methods and additional arguments.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>resample</span>(<span class='no'>values</span>, <span class='no'>...</span>)
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Resample vector, matrix, or spectra</h1>
+
+            <div class="hidden name"><code>resample.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Convenient wrapper around base R's <code>splinefun</code> and
+              <code>approxfun</code>. See
+              <code
+                ><a
+                  href="http://www.rdocumentation.org/packages/stats/topics/splinefun"
+                  >stats::splinefun()</a
+                ></code
+              >
+              and
+              <code
+                ><a
+                  href="http://www.rdocumentation.org/packages/stats/topics/approxfun"
+                  >stats::approxfun()</a
+                ></code
+              >
+              documentation for information on different spline methods and
+              additional arguments.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>resample</span>(<span class='no'>values</span>, <span class='no'>...</span>)
 
 <span class='co'># S3 method for default</span>
 <span class='fu'>resample</span>(<span class='no'>values</span>, <span class='no'>from</span>, <span class='no'>to</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"fmm"</span>, <span class='no'>...</span>)
@@ -129,71 +187,122 @@ <h1>Resample vector, matrix, or spectra</h1>
 
 <span class='co'># S3 method for spectra</span>
 <span class='fu'>resample</span>(<span class='no'>values</span>, <span class='no'>to</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>values</th>
-      <td><p>Vector or matrix of values, or object of class <code><a href='spectra.html'>spectra()</a></code>.
-Length of vector, or <code>nrow</code> of matrix must match length of <code>from</code>. For
-<code>spectra</code>, <code>from</code> argument is omitted because it is taken from
-<code>wavelengths</code>.</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Additional arguments to <code><a href='http://www.rdocumentation.org/packages/stats/topics/splinefun'>stats::splinefun()</a></code> or
-<code><a href='http://www.rdocumentation.org/packages/stats/topics/approxfun'>stats::approxfun()</a></code></p></td>
-    </tr>
-    <tr>
-      <th>from</th>
-      <td><p>X values for interpolation (for <code>spectra</code> objects, this is
-assumed to be the <code>wavelengths</code> attribute.)</p></td>
-    </tr>
-    <tr>
-      <th>to</th>
-      <td><p>Y values onto which to interpolate. For <code>spectra</code> objects, this
-should be new wavelengths.</p></td>
-    </tr>
-    <tr>
-      <th>method</th>
-      <td><p>One of the methods for <code><a href='http://www.rdocumentation.org/packages/stats/topics/splinefun'>stats::splinefun()</a></code> (for polynomial
-and periodic splines) or <code><a href='http://www.rdocumentation.org/packages/stats/topics/approxfun'>stats::approxfun()</a></code> (for constant or linear).
-Default is <code>"fmm"</code> (same as splinefun).</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Object of the same class as <code>values</code>, resampled to the <code>to</code> values.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>values</th>
+              <td>
+                <p>
+                  Vector or matrix of values, or object of class
+                  <code><a href="spectra.html">spectra()</a></code
+                  >. Length of vector, or <code>nrow</code> of matrix must match
+                  length of <code>from</code>. For <code>spectra</code>,
+                  <code>from</code> argument is omitted because it is taken from
+                  <code>wavelengths</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  Additional arguments to
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/stats/topics/splinefun"
+                      >stats::splinefun()</a
+                    ></code
+                  >
+                  or
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/stats/topics/approxfun"
+                      >stats::approxfun()</a
+                    ></code
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>from</th>
+              <td>
+                <p>
+                  X values for interpolation (for <code>spectra</code> objects,
+                  this is assumed to be the <code>wavelengths</code> attribute.)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>to</th>
+              <td>
+                <p>
+                  Y values onto which to interpolate. For
+                  <code>spectra</code> objects, this should be new wavelengths.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>method</th>
+              <td>
+                <p>
+                  One of the methods for
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/stats/topics/splinefun"
+                      >stats::splinefun()</a
+                    ></code
+                  >
+                  (for polynomial and periodic splines) or
+                  <code
+                    ><a
+                      href="http://www.rdocumentation.org/packages/stats/topics/approxfun"
+                      >stats::approxfun()</a
+                    ></code
+                  >
+                  (for constant or linear). Default is <code>"fmm"</code> (same
+                  as splinefun).
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            Object of the same class as <code>values</code>, resampled to the
+            <code>to</code> values.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+          </ul>
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
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diff --git a/modules/rtm/docs/reference/rsr.from.fwhm.html b/modules/rtm/docs/reference/rsr.from.fwhm.html
index b1e83aa..8c77ad0 100644
--- a/modules/rtm/docs/reference/rsr.from.fwhm.html
+++ b/modules/rtm/docs/reference/rsr.from.fwhm.html
@@ -2,160 +2,216 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generate relative spectral response (RSR) matrix based on FWHM data</h1>
-    
-    <div class="hidden name"><code>rsr.from.fwhm.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generate relative spectral response (RSR) matrix based on FWHM data</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>rsr.from.fwhm</span>(<span class='no'>wavelength</span>, <span class='no'>fwhm</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>wavelength</th>
-      <td><p>Vector of average band widths, as reported in FWHM data.</p></td>
-    </tr>
-    <tr>
-      <th>fwhm</th>
-      <td><p>Vector of full-width half maximum (FWHM) bandwidths, as reported
-in FWHM data.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Generate relative spectral response (RSR) matrix based on FWHM
+              data
+            </h1>
+
+            <div class="hidden name"><code>rsr.from.fwhm.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Generate relative spectral response (RSR) matrix based on FWHM
+              data
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>rsr.from.fwhm</span>(<span class='no'>wavelength</span>, <span class='no'>fwhm</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>wavelength</th>
+              <td>
+                <p>Vector of average band widths, as reported in FWHM data.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>fwhm</th>
+              <td>
+                <p>
+                  Vector of full-width half maximum (FWHM) bandwidths, as
+                  reported in FWHM data.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/rtm_loglike.html b/modules/rtm/docs/reference/rtm_loglike.html
index e6c33c6..c68be23 100644
--- a/modules/rtm/docs/reference/rtm_loglike.html
+++ b/modules/rtm/docs/reference/rtm_loglike.html
@@ -2,146 +2,183 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Generic log-likelihood generator for RTMs</h1>
-    
-    <div class="hidden name"><code>rtm_loglike.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generic log-likelihood generator for RTMs</p>
-    
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Generic log-likelihood generator for RTMs</h1>
 
-    <pre class="usage"><span class='fu'>rtm_loglike</span>(<span class='no'>nparams</span>, <span class='no'>model</span>, <span class='no'>observed</span>, <span class='kw'>lag.max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
-  <span class='no'>...</span>)</pre>
-        
+            <div class="hidden name"><code>rtm_loglike.Rd</code></div>
+          </div>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-                </ul>
+          <div class="ref-description">
+            <p>Generic log-likelihood generator for RTMs</p>
+          </div>
 
-  </div>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>rtm_loglike</span>(<span class='no'>nparams</span>, <span class='no'>model</span>, <span class='no'>observed</span>, <span class='kw'>lag.max</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='no'>...</span>)</pre>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked"></ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/rtm/docs/reference/rtnorm.html b/modules/rtm/docs/reference/rtnorm.html
index 8be3cc3..bbacf9e 100644
--- a/modules/rtm/docs/reference/rtnorm.html
+++ b/modules/rtm/docs/reference/rtnorm.html
@@ -2,185 +2,245 @@
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Random sampling from one-sided truncated normal distribution</h1>
-    
-    <div class="hidden name"><code>rtnorm.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Random sampling from one-sided truncated normal distribution</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>rtnorm</span>(<span class='no'>mu</span>, <span class='no'>sd</span>, <span class='no'>MIN</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>mu</th>
-      <td><p>The mean parameter of the truncated normal. NOTE that this is NOT
-equal to the mean of the distribution</p></td>
-    </tr>
-    <tr>
-      <th>sd</th>
-      <td><p>The standard deviation parameter of the truncated normal. Again, NOTE
-tht this is not the SD of the distribution.</p></td>
-    </tr>
-    <tr>
-      <th>MIN</th>
-      <td><p>The minimum value, which defines the truncation.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Numeric length one.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Draws a random number and, if it doesn't fall within the
-specified range, resample using an adjusted Normal CDF. This isn't
-performed immediately because CDF sampling calls three functions --
-qnorm, runif, and pnorm--and therefore is much less efficient than a
-simple random sample.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Random sampling from one-sided truncated normal distribution
+            </h1>
+
+            <div class="hidden name"><code>rtnorm.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Random sampling from one-sided truncated normal distribution</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>rtnorm</span>(<span class='no'>mu</span>, <span class='no'>sd</span>, <span class='no'>MIN</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>mu</th>
+              <td>
+                <p>
+                  The mean parameter of the truncated normal. NOTE that this is
+                  NOT equal to the mean of the distribution
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sd</th>
+              <td>
+                <p>
+                  The standard deviation parameter of the truncated normal.
+                  Again, NOTE tht this is not the SD of the distribution.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>MIN</th>
+              <td><p>The minimum value, which defines the truncation.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Numeric length one.</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Draws a random number and, if it doesn't fall within the specified
+            range, resample using an adjusted Normal CDF. This isn't performed
+            immediately because CDF sampling calls three functions -- qnorm,
+            runif, and pnorm--and therefore is much less efficient than a simple
+            random sample.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
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index c4b7079..9e7ffa5 100644
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-    
-    <div class="hidden name"><code>sensor.list.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Sensor spectral response functions</h1>
 
-    <div class="ref-description">
-    
-    <p>Sensor spectral response functions</p>
-    
-    </div>
+            <div class="hidden name"><code>sensor.list.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='no'>sensor.list</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+          <div class="ref-description">
+            <p>Sensor spectral response functions</p>
+          </div>
 
-    <p>An object of class <code>character</code> of length 12.</p>
-    
+          <pre class="usage"><span class='no'>sensor.list</span></pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
-          </ul>
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
 
-  </div>
-</div>
+          <p>An object of class <code>character</code> of length 12.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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 </html>
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diff --git a/modules/rtm/docs/reference/sensor.proper.html b/modules/rtm/docs/reference/sensor.proper.html
index 1e6188e..4b6d3b7 100644
--- a/modules/rtm/docs/reference/sensor.proper.html
+++ b/modules/rtm/docs/reference/sensor.proper.html
@@ -2,151 +2,183 @@
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 <html>
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
+    <!-- Bootstrap -->
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+    <!-- sticky kit -->
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+    <script src="../pkgdown.js"></script>
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+                <span
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+                  >1.6.0</span
+                >
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
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+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Sensor list with proper names</h1>
-    
-    <div class="hidden name"><code>sensor.proper.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Sensor list with proper names</h1>
 
-    <div class="ref-description">
-    
-    <p>Sensor list with proper names</p>
-    
-    </div>
+            <div class="hidden name"><code>sensor.proper.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='no'>sensor.proper</span></pre>
-        
-    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+          <div class="ref-description">
+            <p>Sensor list with proper names</p>
+          </div>
 
-    <p>An object of class <code>character</code> of length 12.</p>
-    
+          <pre class="usage"><span class='no'>sensor.proper</span></pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#format">Format</a></li>
-          </ul>
+          <h2 class="hasAnchor" id="format">
+            <a class="anchor" href="#format"></a>Format
+          </h2>
 
-  </div>
-</div>
+          <p>An object of class <code>character</code> of length 12.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#format">Format</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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 </html>
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diff --git a/modules/rtm/docs/reference/setup_edr.html b/modules/rtm/docs/reference/setup_edr.html
index c4a59f5..8f7251c 100644
--- a/modules/rtm/docs/reference/setup_edr.html
+++ b/modules/rtm/docs/reference/setup_edr.html
@@ -2,177 +2,231 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-
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-<!-- Font Awesome icons -->
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-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+file configured for running EDR."
+    />
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
+
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Setup EDR run</h1>
-    
-    <div class="hidden name"><code>setup_edr.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Setup EDR run</h1>
 
-    <div class="ref-description">
-    
-    <p>Using an existing ED2IN file as a template, create a new ED2IN and history
-file configured for running EDR.</p>
-    
-    </div>
+            <div class="hidden name"><code>setup_edr.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Using an existing ED2IN file as a template, create a new ED2IN and
+              history file configured for running EDR.
+            </p>
+          </div>
 
-    <pre class="usage"><span class='fu'>setup_edr</span>(<span class='no'>ed2in</span>, <span class='no'>output_dir</span>, <span class='kw'>datetime</span> <span class='kw'>=</span> <span class='fu'>ISOdatetime</span>(<span class='no'>ed2in</span><span class='kw'>[[</span><span class='st'>"IYEARA"</span>]],
+          <pre
+            class="usage"
+          ><span class='fu'>setup_edr</span>(<span class='no'>ed2in</span>, <span class='no'>output_dir</span>, <span class='kw'>datetime</span> <span class='kw'>=</span> <span class='fu'>ISOdatetime</span>(<span class='no'>ed2in</span><span class='kw'>[[</span><span class='st'>"IYEARA"</span>]],
   <span class='no'>ed2in</span><span class='kw'>[[</span><span class='st'>"IMONTHA"</span>]], <span class='no'>ed2in</span><span class='kw'>[[</span><span class='st'>"IDATEA"</span>]], <span class='fl'>12</span>, <span class='fl'>0</span>, <span class='fl'>0</span>, <span class='kw'>tz</span> <span class='kw'>=</span> <span class='st'>"UTC"</span>), <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ed2in</th>
-      <td><p>ED2IN list object (see <a href='http://www.rdocumentation.org/packages/PEcAn.ED2/topics/read_ed2in'>PEcAn.ED2::read_ed2in</a>).</p></td>
-    </tr>
-    <tr>
-      <th>output_dir</th>
-      <td><p>Directory in which run files will be stored</p></td>
-    </tr>
-    <tr>
-      <th>datetime</th>
-      <td><p>Date time object (or compliant string) at which to run EDR.
-Defaults to 12 noon on start date in ED2IN.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>Path to EDR-configured ED2IN file.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ed2in</th>
+              <td>
+                <p>
+                  ED2IN list object (see
+                  <a
+                    href="http://www.rdocumentation.org/packages/PEcAn.ED2/topics/read_ed2in"
+                    >PEcAn.ED2::read_ed2in</a
+                  >).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>output_dir</th>
+              <td><p>Directory in which run files will be stored</p></td>
+            </tr>
+            <tr>
+              <th>datetime</th>
+              <td>
+                <p>
+                  Date time object (or compliant string) at which to run EDR.
+                  Defaults to 12 noon on start date in ED2IN.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Path to EDR-configured ED2IN file.</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Alexey Shiklomanov
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Alexey Shiklomanov
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
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   </body>
 </html>
-
diff --git a/modules/rtm/docs/reference/spectra.html b/modules/rtm/docs/reference/spectra.html
index 061a541..aa21698 100644
--- a/modules/rtm/docs/reference/spectra.html
+++ b/modules/rtm/docs/reference/spectra.html
@@ -2,169 +2,216 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
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+
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+      crossorigin="anonymous"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
+
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   </head>
 
   <body>
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
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+              >
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAnRTM</a>
+                <span
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+            </div>
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
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+                <li class="dropdown">
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+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
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+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Spectra S3 class</h1>
-    
-    <div class="hidden name"><code>spectra.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Spectra S3 class</h1>
 
-    <div class="ref-description">
-    
-    <p>Spectra S3 class</p>
-    
-    </div>
+            <div class="hidden name"><code>spectra.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>spectra</span>(<span class='no'>spectra</span>, <span class='kw'>wavelengths</span> <span class='kw'>=</span> <span class='fl'>400</span>:<span class='fl'>2500</span>)
+          <div class="ref-description">
+            <p>Spectra S3 class</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>spectra</span>(<span class='no'>spectra</span>, <span class='kw'>wavelengths</span> <span class='kw'>=</span> <span class='fl'>400</span>:<span class='fl'>2500</span>)
 
 <span class='fu'>is_spectra</span>(<span class='no'>spectra</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spectra</th>
-      <td><p>Vector (<code>length = length(wavelengths)</code>) or matrix (<code>ncol = length(wavelengths)</code>)</p></td>
-    </tr>
-    <tr>
-      <th>wavelengths</th>
-      <td><p>Wavelengths of spectra.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="functions"><a class="anchor" href="#functions"></a>Functions</h2>
-
-    <ul>
-<li><p><code>is_spectra</code>: Test if object is class <code>spectra</code></p></li>
-</ul>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#functions">Functions</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spectra</th>
+              <td>
+                <p>
+                  Vector (<code>length = length(wavelengths)</code>) or matrix
+                  (<code>ncol = length(wavelengths)</code>)
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>wavelengths</th>
+              <td><p>Wavelengths of spectra.</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="functions">
+            <a class="anchor" href="#functions"></a>Functions
+          </h2>
+
+          <ul>
+            <li>
+              <p>
+                <code>is_spectra</code>: Test if object is class
+                <code>spectra</code>
+              </p>
+            </li>
           </ul>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-  </div>
-</div>
+            <li><a href="#functions">Functions</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
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-  <p>Developed by .</p>
-</div>
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diff --git a/modules/rtm/docs/reference/spectral.response.html b/modules/rtm/docs/reference/spectral.response.html
index 9c2dbb2..e74f9e3 100644
--- a/modules/rtm/docs/reference/spectral.response.html
+++ b/modules/rtm/docs/reference/spectral.response.html
@@ -2,159 +2,202 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Convolution of spectra to sensor RSR</h1>
-    
-    <div class="hidden name"><code>spectral.response.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Convolution of spectra to sensor RSR</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>spectral.response</span>(<span class='no'>spec</span>, <span class='no'>sensor</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spec</th>
-      <td><p>Full (1 nm) spectrum (vector)</p></td>
-    </tr>
-    <tr>
-      <th>sensor</th>
-      <td><p>Sensor name (string). See sensor.list</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Convolution of spectra to sensor RSR</h1>
+
+            <div class="hidden name"><code>spectral.response.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Convolution of spectra to sensor RSR</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>spectral.response</span>(<span class='no'>spec</span>, <span class='no'>sensor</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spec</th>
+              <td><p>Full (1 nm) spectrum (vector)</p></td>
+            </tr>
+            <tr>
+              <th>sensor</th>
+              <td><p>Sensor name (string). See sensor.list</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/str.spectra.html b/modules/rtm/docs/reference/str.spectra.html
index 577085e..b3541de 100644
--- a/modules/rtm/docs/reference/str.spectra.html
+++ b/modules/rtm/docs/reference/str.spectra.html
@@ -2,156 +2,196 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Structure of <code>spectra</code> object</h1>
-    
-    <div class="hidden name"><code>str.spectra.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Structure of <code>spectra</code> object</h1>
 
-    <div class="ref-description">
-    
-    <p>Structure of <code>spectra</code> object</p>
-    
-    </div>
+            <div class="hidden name"><code>str.spectra.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='co'># S3 method for spectra</span>
-<span class='fu'>str</span>(<span class='no'>spectra</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spectra</th>
-      <td><p>Object of class <code>spectra</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>Structure of <code>spectra</code> object</p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre class="usage"><span class='co'># S3 method for spectra</span>
+<span class='fu'>str</span>(<span class='no'>spectra</span>, <span class='no'>...</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spectra</th>
+              <td>
+                <p>Object of class <code>spectra</code></p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/rtm/docs/reference/sub-.spectra.html b/modules/rtm/docs/reference/sub-.spectra.html
index f42aab1..9c6e522 100644
--- a/modules/rtm/docs/reference/sub-.spectra.html
+++ b/modules/rtm/docs/reference/sub-.spectra.html
@@ -2,203 +2,274 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-<title>Select spectra — [.spectra • PEcAnRTM</title>
+    <title>Select spectra — [.spectra • PEcAnRTM</title>
 
-<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
 
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
 
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
 
-<!-- clipboard.js -->
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+    <!-- clipboard.js -->
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+      crossorigin="anonymous"
+    ></script>
 
-<!-- sticky kit -->
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+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
 
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
+    <!-- pkgdown -->
+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
 
+    <meta property="og:title" content="Select spectra — [.spectra" />
 
+    <meta property="og:description" content="Select spectra" />
+    <meta name="twitter:card" content="summary" />
 
-<meta property="og:title" content="Select spectra — [.spectra" />
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-<![endif]-->
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+    <!-- mathjax -->
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+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-reference-topic">
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-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <a class="navbar-link" href="../index.html">PEcAnRTM</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html">PEcAnRTM</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fa fa-home fa-lg"></span>
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+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+                <li class="dropdown">
+                  <a
+                    href="#"
+                    class="dropdown-toggle"
+                    data-toggle="dropdown"
+                    role="button"
+                    aria-expanded="false"
+                  >
+                    Articles
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Select spectra</h1>
-    
-    <div class="hidden name"><code>sub-.spectra.Rd</code></div>
-    </div>
+                    <span class="caret"></span>
+                  </a>
+                  <ul class="dropdown-menu" role="menu">
+                    <li>
+                      <a href="../articles/pecanrtm.vignette.html"
+                        >The PEcAn RTM package</a
+                      >
+                    </li>
+                  </ul>
+                </li>
+              </ul>
 
-    <div class="ref-description">
-    
-    <p>Select spectra</p>
-    
-    </div>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
 
-    <pre class="usage"># S3 method for spectra
-[(spectra, i, j, drop = FALSE)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spectra</th>
-      <td><p>Object of class <code>spectra</code></p></td>
-    </tr>
-    <tr>
-      <th>i</th>
-      <td><p>indices specifying elements to extract or replace.  Indices are
-    <code>numeric</code> or <code>character</code> vectors or empty (missing) or
-    <code>NULL</code>.  Numeric values are coerced to integer as by
-    <code>as.integer</code> (and hence truncated towards zero).
-    Character vectors will be matched to the <code>names</code> of the
-    object (or for matrices/arrays, the <code>dimnames</code>):
-    see &#8216;Character indices&#8217; below for further details.</p>
-<p>For <code>[</code>-indexing only: <code>i</code>, <code>j</code>, <code>&#8230;</code> can be
-    logical vectors, indicating elements/slices to select.  Such vectors
-    are recycled if necessary to match the corresponding extent.
-    <code>i</code>, <code>j</code>, <code>&#8230;</code> can also be negative integers,
-    indicating elements/slices to leave out of the selection.</p>
-<p>When indexing arrays by <code>[</code> a single argument <code>i</code> can be a
-    matrix with as many columns as there are dimensions of <code>x</code>; the
-    result is then a vector with elements corresponding to the sets of
-    indices in each row of <code>i</code>.</p>
-<p>An index value of <code>NULL</code> is treated as if it were <code>integer(0)</code>.</p></td>
-    </tr>
-    <tr>
-      <th>j</th>
-      <td><p>indices specifying elements to extract or replace.  Indices are
-    <code>numeric</code> or <code>character</code> vectors or empty (missing) or
-    <code>NULL</code>.  Numeric values are coerced to integer as by
-    <code>as.integer</code> (and hence truncated towards zero).
-    Character vectors will be matched to the <code>names</code> of the
-    object (or for matrices/arrays, the <code>dimnames</code>):
-    see &#8216;Character indices&#8217; below for further details.</p>
-<p>For <code>[</code>-indexing only: <code>i</code>, <code>j</code>, <code>&#8230;</code> can be
-    logical vectors, indicating elements/slices to select.  Such vectors
-    are recycled if necessary to match the corresponding extent.
-    <code>i</code>, <code>j</code>, <code>&#8230;</code> can also be negative integers,
-    indicating elements/slices to leave out of the selection.</p>
-<p>When indexing arrays by <code>[</code> a single argument <code>i</code> can be a
-    matrix with as many columns as there are dimensions of <code>x</code>; the
-    result is then a vector with elements corresponding to the sets of
-    indices in each row of <code>i</code>.</p>
-<p>An index value of <code>NULL</code> is treated as if it were <code>integer(0)</code>.</p></td>
-    </tr>
-    <tr>
-      <th>drop</th>
-      <td><p>For matrices and arrays.  If <code>TRUE</code> the result is
-    coerced to the lowest possible dimension (see the examples).  This
-    only works for extracting elements, not for the replacement.  See
-    <code>drop</code> for further details.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Select spectra</h1>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <div class="hidden name"><code>sub-.spectra.Rd</code></div>
+          </div>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <div class="ref-description">
+            <p>Select spectra</p>
+          </div>
 
-      </footer>
-   </div>
+          <pre class="usage">
+# S3 method for spectra
+[(spectra, i, j, drop = FALSE)</pre
+          >
 
-  
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spectra</th>
+              <td>
+                <p>Object of class <code>spectra</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>i</th>
+              <td>
+                <p>
+                  indices specifying elements to extract or replace. Indices are
+                  <code>numeric</code> or <code>character</code> vectors or
+                  empty (missing) or <code>NULL</code>. Numeric values are
+                  coerced to integer as by <code>as.integer</code> (and hence
+                  truncated towards zero). Character vectors will be matched to
+                  the <code>names</code> of the object (or for matrices/arrays,
+                  the <code>dimnames</code>): see &#8216;Character
+                  indices&#8217; below for further details.
+                </p>
+                <p>
+                  For <code>[</code>-indexing only: <code>i</code>,
+                  <code>j</code>, <code>&#8230;</code> can be logical vectors,
+                  indicating elements/slices to select. Such vectors are
+                  recycled if necessary to match the corresponding extent.
+                  <code>i</code>, <code>j</code>, <code>&#8230;</code> can also
+                  be negative integers, indicating elements/slices to leave out
+                  of the selection.
+                </p>
+                <p>
+                  When indexing arrays by <code>[</code> a single argument
+                  <code>i</code> can be a matrix with as many columns as there
+                  are dimensions of <code>x</code>; the result is then a vector
+                  with elements corresponding to the sets of indices in each row
+                  of <code>i</code>.
+                </p>
+                <p>
+                  An index value of <code>NULL</code> is treated as if it were
+                  <code>integer(0)</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>j</th>
+              <td>
+                <p>
+                  indices specifying elements to extract or replace. Indices are
+                  <code>numeric</code> or <code>character</code> vectors or
+                  empty (missing) or <code>NULL</code>. Numeric values are
+                  coerced to integer as by <code>as.integer</code> (and hence
+                  truncated towards zero). Character vectors will be matched to
+                  the <code>names</code> of the object (or for matrices/arrays,
+                  the <code>dimnames</code>): see &#8216;Character
+                  indices&#8217; below for further details.
+                </p>
+                <p>
+                  For <code>[</code>-indexing only: <code>i</code>,
+                  <code>j</code>, <code>&#8230;</code> can be logical vectors,
+                  indicating elements/slices to select. Such vectors are
+                  recycled if necessary to match the corresponding extent.
+                  <code>i</code>, <code>j</code>, <code>&#8230;</code> can also
+                  be negative integers, indicating elements/slices to leave out
+                  of the selection.
+                </p>
+                <p>
+                  When indexing arrays by <code>[</code> a single argument
+                  <code>i</code> can be a matrix with as many columns as there
+                  are dimensions of <code>x</code>; the result is then a vector
+                  with elements corresponding to the sets of indices in each row
+                  of <code>i</code>.
+                </p>
+                <p>
+                  An index value of <code>NULL</code> is treated as if it were
+                  <code>integer(0)</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>drop</th>
+              <td>
+                <p>
+                  For matrices and arrays. If <code>TRUE</code> the result is
+                  coerced to the lowest possible dimension (see the examples).
+                  This only works for extracting elements, not for the
+                  replacement. See <code>drop</code> for further details.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/rtm/docs/reference/sub-sub-.spectra.html b/modules/rtm/docs/reference/sub-sub-.spectra.html
index 88a1be3..8f53168 100644
--- a/modules/rtm/docs/reference/sub-sub-.spectra.html
+++ b/modules/rtm/docs/reference/sub-sub-.spectra.html
@@ -2,180 +2,235 @@
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 <html>
   <head>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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-
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-
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-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
-
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+    <title>Select spectra by wavelength — [[.spectra • PEcAnRTM</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Select spectra by wavelength</h1>
-    
-    <div class="hidden name"><code>sub-sub-.spectra.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Select spectra by wavelength</p>
-    
-    </div>
-
-    <pre class="usage"># S3 method for spectra
-[[(spectra, wavelength, j)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spectra</th>
-      <td><p>Object of class <code>spectra</code></p></td>
-    </tr>
-    <tr>
-      <th>wavelength</th>
-      <td><p>Wavelength vector to select</p></td>
-    </tr>
-    <tr>
-      <th>j</th>
-      <td><p>indices specifying elements to extract or replace.  Indices are
-    <code>numeric</code> or <code>character</code> vectors or empty (missing) or
-    <code>NULL</code>.  Numeric values are coerced to integer as by
-    <code>as.integer</code> (and hence truncated towards zero).
-    Character vectors will be matched to the <code>names</code> of the
-    object (or for matrices/arrays, the <code>dimnames</code>):
-    see &#8216;Character indices&#8217; below for further details.</p>
-<p>For <code>[</code>-indexing only: <code>i</code>, <code>j</code>, <code>&#8230;</code> can be
-    logical vectors, indicating elements/slices to select.  Such vectors
-    are recycled if necessary to match the corresponding extent.
-    <code>i</code>, <code>j</code>, <code>&#8230;</code> can also be negative integers,
-    indicating elements/slices to leave out of the selection.</p>
-<p>When indexing arrays by <code>[</code> a single argument <code>i</code> can be a
-    matrix with as many columns as there are dimensions of <code>x</code>; the
-    result is then a vector with elements corresponding to the sets of
-    indices in each row of <code>i</code>.</p>
-<p>An index value of <code>NULL</code> is treated as if it were <code>integer(0)</code>.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Select spectra by wavelength</h1>
+
+            <div class="hidden name"><code>sub-sub-.spectra.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Select spectra by wavelength</p>
+          </div>
+
+          <pre class="usage">
+# S3 method for spectra
+[[(spectra, wavelength, j)</pre
+          >
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spectra</th>
+              <td>
+                <p>Object of class <code>spectra</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>wavelength</th>
+              <td><p>Wavelength vector to select</p></td>
+            </tr>
+            <tr>
+              <th>j</th>
+              <td>
+                <p>
+                  indices specifying elements to extract or replace. Indices are
+                  <code>numeric</code> or <code>character</code> vectors or
+                  empty (missing) or <code>NULL</code>. Numeric values are
+                  coerced to integer as by <code>as.integer</code> (and hence
+                  truncated towards zero). Character vectors will be matched to
+                  the <code>names</code> of the object (or for matrices/arrays,
+                  the <code>dimnames</code>): see &#8216;Character
+                  indices&#8217; below for further details.
+                </p>
+                <p>
+                  For <code>[</code>-indexing only: <code>i</code>,
+                  <code>j</code>, <code>&#8230;</code> can be logical vectors,
+                  indicating elements/slices to select. Such vectors are
+                  recycled if necessary to match the corresponding extent.
+                  <code>i</code>, <code>j</code>, <code>&#8230;</code> can also
+                  be negative integers, indicating elements/slices to leave out
+                  of the selection.
+                </p>
+                <p>
+                  When indexing arrays by <code>[</code> a single argument
+                  <code>i</code> can be a matrix with as many columns as there
+                  are dimensions of <code>x</code>; the result is then a vector
+                  with elements corresponding to the sets of indices in each row
+                  of <code>i</code>.
+                </p>
+                <p>
+                  An index value of <code>NULL</code> is treated as if it were
+                  <code>integer(0)</code>.
+                </p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/sub-subset-.spectra.html b/modules/rtm/docs/reference/sub-subset-.spectra.html
index fab8225..c1918d8 100644
--- a/modules/rtm/docs/reference/sub-subset-.spectra.html
+++ b/modules/rtm/docs/reference/sub-subset-.spectra.html
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Assign values to spectra by wavelength</h1>
-    
-    <div class="hidden name"><code>sub-subset-.spectra.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Assign values to spectra by wavelength</p>
-    
-    </div>
-
-    <pre class="usage"># S3 method for spectra
-[[(spectra, wavelength, j, values) <- value</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spectra</th>
-      <td><p>Object of class <code>spectra</code></p></td>
-    </tr>
-    <tr>
-      <th>wavelength</th>
-      <td><p>Wavelength vector to select</p></td>
-    </tr>
-    <tr>
-      <th>j</th>
-      <td><p>indices specifying elements to extract or replace.  Indices are
-    <code>numeric</code> or <code>character</code> vectors or empty (missing) or
-    <code>NULL</code>.  Numeric values are coerced to integer as by
-    <code>as.integer</code> (and hence truncated towards zero).
-    Character vectors will be matched to the <code>names</code> of the
-    object (or for matrices/arrays, the <code>dimnames</code>):
-    see &#8216;Character indices&#8217; below for further details.</p>
-<p>For <code>[</code>-indexing only: <code>i</code>, <code>j</code>, <code>&#8230;</code> can be
-    logical vectors, indicating elements/slices to select.  Such vectors
-    are recycled if necessary to match the corresponding extent.
-    <code>i</code>, <code>j</code>, <code>&#8230;</code> can also be negative integers,
-    indicating elements/slices to leave out of the selection.</p>
-<p>When indexing arrays by <code>[</code> a single argument <code>i</code> can be a
-    matrix with as many columns as there are dimensions of <code>x</code>; the
-    result is then a vector with elements corresponding to the sets of
-    indices in each row of <code>i</code>.</p>
-<p>An index value of <code>NULL</code> is treated as if it were <code>integer(0)</code>.</p></td>
-    </tr>
-    <tr>
-      <th>values</th>
-      <td><p>Vector or matrix of values to assign</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Assign values to spectra by wavelength</h1>
+
+            <div class="hidden name"><code>sub-subset-.spectra.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Assign values to spectra by wavelength</p>
+          </div>
+
+          <pre class="usage">
+# S3 method for spectra
+[[(spectra, wavelength, j, values) <- value</pre
+          >
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spectra</th>
+              <td>
+                <p>Object of class <code>spectra</code></p>
+              </td>
+            </tr>
+            <tr>
+              <th>wavelength</th>
+              <td><p>Wavelength vector to select</p></td>
+            </tr>
+            <tr>
+              <th>j</th>
+              <td>
+                <p>
+                  indices specifying elements to extract or replace. Indices are
+                  <code>numeric</code> or <code>character</code> vectors or
+                  empty (missing) or <code>NULL</code>. Numeric values are
+                  coerced to integer as by <code>as.integer</code> (and hence
+                  truncated towards zero). Character vectors will be matched to
+                  the <code>names</code> of the object (or for matrices/arrays,
+                  the <code>dimnames</code>): see &#8216;Character
+                  indices&#8217; below for further details.
+                </p>
+                <p>
+                  For <code>[</code>-indexing only: <code>i</code>,
+                  <code>j</code>, <code>&#8230;</code> can be logical vectors,
+                  indicating elements/slices to select. Such vectors are
+                  recycled if necessary to match the corresponding extent.
+                  <code>i</code>, <code>j</code>, <code>&#8230;</code> can also
+                  be negative integers, indicating elements/slices to leave out
+                  of the selection.
+                </p>
+                <p>
+                  When indexing arrays by <code>[</code> a single argument
+                  <code>i</code> can be a matrix with as many columns as there
+                  are dimensions of <code>x</code>; the result is then a vector
+                  with elements corresponding to the sets of indices in each row
+                  of <code>i</code>.
+                </p>
+                <p>
+                  An index value of <code>NULL</code> is treated as if it were
+                  <code>integer(0)</code>.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>values</th>
+              <td><p>Vector or matrix of values to assign</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/rtm/docs/reference/summary_mvnorm.html b/modules/rtm/docs/reference/summary_mvnorm.html
index 9d1adcc..8ec30fc 100644
--- a/modules/rtm/docs/reference/summary_mvnorm.html
+++ b/modules/rtm/docs/reference/summary_mvnorm.html
@@ -2,157 +2,200 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    />
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+
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+    />
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+long list (for easy construction of data.tables)"
+    />
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+
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Multivariate normal fit</h1>
-    
-    <div class="hidden name"><code>summary_mvnorm.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Fit multivariate normal to samples. Return means and covariance matrix as a
-long list (for easy construction of data.tables)</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>summary_mvnorm</span>(<span class='no'>samples</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>samples</th>
-      <td><p>Matrix of MCMC samples.</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Multivariate normal fit</h1>
+
+            <div class="hidden name"><code>summary_mvnorm.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Fit multivariate normal to samples. Return means and covariance
+              matrix as a long list (for easy construction of data.tables)
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>summary_mvnorm</span>(<span class='no'>samples</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>samples</th>
+              <td><p>Matrix of MCMC samples.</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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diff --git a/modules/rtm/docs/reference/summary_simple.html b/modules/rtm/docs/reference/summary_simple.html
index 3665de5..275e0cd 100644
--- a/modules/rtm/docs/reference/summary_simple.html
+++ b/modules/rtm/docs/reference/summary_simple.html
@@ -2,155 +2,201 @@
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-    </div>
-
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-    
-    <p>Calculate simple univariate summary statistics and return as named list</p>
-    
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-
-    <pre class="usage"><span class='fu'>summary_simple</span>(<span class='no'>samples</span>)</pre>
-    
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-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>samples</th>
-      <td><p>Matrix of MCMC samples</p></td>
-    </tr>
-    </table>
-    
-
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-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Simple summary statistics on MCMC samples</h1>
+
+            <div class="hidden name"><code>summary_simple.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Calculate simple univariate summary statistics and return as named
+              list
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>summary_simple</span>(<span class='no'>samples</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>samples</th>
+              <td><p>Matrix of MCMC samples</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/trim.rsr.html b/modules/rtm/docs/reference/trim.rsr.html
index bce5012..600d4aa 100644
--- a/modules/rtm/docs/reference/trim.rsr.html
+++ b/modules/rtm/docs/reference/trim.rsr.html
@@ -2,163 +2,204 @@
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Trim RSR matrix to wavelength limits</h1>
-    
-    <div class="hidden name"><code>trim.rsr.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Trim RSR matrix to wavelength limits</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>trim.rsr</span>(<span class='no'>rsr</span>, <span class='kw'>wl.min</span> <span class='kw'>=</span> <span class='fl'>400</span>, <span class='kw'>wl.max</span> <span class='kw'>=</span> <span class='fl'>2500</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>rsr</th>
-      <td><p>RSR matrix</p></td>
-    </tr>
-    <tr>
-      <th>wl.min</th>
-      <td><p>Minimum wavelength (inclusive, default = 400)</p></td>
-    </tr>
-    <tr>
-      <th>wl.max</th>
-      <td><p>Maximum wavelength (inclusive, default = 2500)</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Trim RSR matrix to wavelength limits</h1>
+
+            <div class="hidden name"><code>trim.rsr.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Trim RSR matrix to wavelength limits</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>trim.rsr</span>(<span class='no'>rsr</span>, <span class='kw'>wl.min</span> <span class='kw'>=</span> <span class='fl'>400</span>, <span class='kw'>wl.max</span> <span class='kw'>=</span> <span class='fl'>2500</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>rsr</th>
+              <td><p>RSR matrix</p></td>
+            </tr>
+            <tr>
+              <th>wl.min</th>
+              <td><p>Minimum wavelength (inclusive, default = 400)</p></td>
+            </tr>
+            <tr>
+              <th>wl.max</th>
+              <td><p>Maximum wavelength (inclusive, default = 2500)</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/rtm/docs/reference/wavelengths.html b/modules/rtm/docs/reference/wavelengths.html
index 72f1229..696ce60 100644
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+++ b/modules/rtm/docs/reference/wavelengths.html
@@ -2,155 +2,200 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Retrieve wavelengths from spectra object</h1>
-    
-    <div class="hidden name"><code>wavelengths.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Retrieve wavelengths from spectra object</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>wavelengths</span>(<span class='no'>spectra</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>spectra</th>
-      <td><p>Object of class <code>spectra</code></p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Retrieve wavelengths from spectra object</h1>
+
+            <div class="hidden name"><code>wavelengths.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Retrieve wavelengths from spectra object</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>wavelengths</span>(<span class='no'>spectra</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>spectra</th>
+              <td>
+                <p>Object of class <code>spectra</code></p>
+              </td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+        </div>
+      </div>
 
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index 1b9878a..096d513 100644
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+                  >1.6.0</span
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+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>License</h1>
+          </div>
 
-<pre>## This is the master copy of the PEcAn License
+          <pre>
+## This is the master copy of the PEcAn License
 
 University of Illinois/NCSA Open Source License
 
@@ -126,27 +155,22 @@ <h1>License</h1>
 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
 
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+          >
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index acce303..05add31 100644
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
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-<meta property="og:title" content="Authors" />
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+    <title>Authors • PEcAn.uncertainty</title>
+
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+
+    <meta property="og:title" content="Authors" />
+
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
   </head>
 
   <body>
     <div class="container template-authors">
       <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
-  <div class="container">
-    <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-        <span class="icon-bar"></span>
-      </button>
-      <span class="navbar-brand">
-        <a class="navbar-link" href="index.html">PEcAn.uncertainty</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
-      </span>
-    </div>
-
-    <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="index.html">
-    <span class="fa fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
-  <a href="reference/index.html">Reference</a>
-</li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        
-      </ul>
-      
-    </div><!--/.nav-collapse -->
-  </div><!--/.container -->
-</div><!--/.navbar -->
-
-      
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
+            <div class="navbar-header">
+              <button
+                type="button"
+                class="navbar-toggle collapsed"
+                data-toggle="collapse"
+                data-target="#navbar"
+              >
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.uncertainty</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Authors</h1>
-    </div>
-
-    <ul class="list-unstyled">
-      <li>
-        <p><strong>Mike Dietze</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>David LeBauer</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Xiaohui Feng</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Dan  Wang</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Carl Davidson</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Rob Kooper</strong>. . 
-        </p>
-      </li>
-      <li>
-        <p><strong>Shawn Serbin</strong>. . 
-        </p>
-      </li>
-    </ul>
-
-  </div>
-
-</div>
-
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Authors</h1>
+          </div>
+
+          <ul class="list-unstyled">
+            <li>
+              <p><strong>Mike Dietze</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>David LeBauer</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Xiaohui Feng</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Dan Wang</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Carl Davidson</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Rob Kooper</strong>. .</p>
+            </li>
+            <li>
+              <p><strong>Shawn Serbin</strong>. .</p>
+            </li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/uncertainty/docs/docsearch.css b/modules/uncertainty/docs/docsearch.css
index e5f1fe1..b8f6963 100644
--- a/modules/uncertainty/docs/docsearch.css
+++ b/modules/uncertainty/docs/docsearch.css
@@ -8,106 +8,110 @@
   display: block;
   -webkit-box-flex: 1;
   -ms-flex: 1;
-  flex: 1
+  flex: 1;
 }
 
 .algolia-autocomplete .ds-dropdown-menu {
   width: 100%;
   min-width: none;
   max-width: none;
-  padding: .75rem 0;
+  padding: 0.75rem 0;
   background-color: #fff;
   background-clip: padding-box;
-  border: 1px solid rgba(0, 0, 0, .1);
-  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+  border: 1px solid rgba(0, 0, 0, 0.1);
+  box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.175);
 }
 
-@media (min-width:768px) {
+@media (min-width: 768px) {
   .algolia-autocomplete .ds-dropdown-menu {
-      width: 175%
+    width: 175%;
   }
 }
 
 .algolia-autocomplete .ds-dropdown-menu::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+.algolia-autocomplete .ds-dropdown-menu [class^="ds-dataset-"] {
   padding: 0;
-  background-color: rgb(255,255,255);
+  background-color: rgb(255, 255, 255);
   border: 0;
   max-height: 80vh;
 }
 
 .algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
-  margin-top: 0
+  margin-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion {
   padding: 0;
-  overflow: visible
+  overflow: visible;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--category-header {
-  padding: .125rem 1rem;
+  padding: 0.125rem 1rem;
   margin-top: 0;
   font-size: 1.3em;
   font-weight: 500;
-  color: #00008B;
-  border-bottom: 0
+  color: #00008b;
+  border-bottom: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
-    float: none;
-    padding-top: 0
+  float: none;
+  padding-top: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
   float: none;
   width: auto;
   padding: 0;
-  text-align: left
+  text-align: left;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content {
   float: none;
   width: auto;
-  padding: 0
+  padding: 0;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--content::before {
-  display: none
+  display: none;
 }
 
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
-  padding-top: .75rem;
-  margin-top: .75rem;
-  border-top: 1px solid rgba(0, 0, 0, .1)
+.algolia-autocomplete
+  .ds-suggestion:not(:first-child)
+  .algolia-docsearch-suggestion--category-header {
+  padding-top: 0.75rem;
+  margin-top: 0.75rem;
+  border-top: 1px solid rgba(0, 0, 0, 0.1);
 }
 
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+.algolia-autocomplete
+  .ds-suggestion
+  .algolia-docsearch-suggestion--subcategory-column {
   display: block;
-  padding: .1rem 1rem;
+  padding: 0.1rem 1rem;
   margin-bottom: 0.1;
-  font-size: 1.0em;
-  font-weight: 400
+  font-size: 1em;
+  font-weight: 400;
   /* display: none */
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--title {
   display: block;
-  padding: .25rem 1rem;
+  padding: 0.25rem 1rem;
   margin-bottom: 0;
   font-size: 0.9em;
-  font-weight: 400
+  font-weight: 400;
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--text {
-  padding: 0 1rem .5rem;
-  margin-top: -.25rem;
+  padding: 0 1rem 0.5rem;
+  margin-top: -0.25rem;
   font-size: 0.8em;
   font-weight: 400;
-  line-height: 1.25
+  line-height: 1.25;
 }
 
 .algolia-autocomplete .algolia-docsearch-footer {
@@ -134,15 +138,18 @@
 }
 
 .algolia-autocomplete .algolia-docsearch-suggestion--highlight {
-  color: #FF8C00;
-  background: rgba(232, 189, 54, 0.1)
+  color: #ff8c00;
+  background: rgba(232, 189, 54, 0.1);
 }
 
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
-  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+.algolia-autocomplete
+  .algolia-docsearch-suggestion--text
+  .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, 0.5);
 }
 
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
-  background-color: rgba(192, 192, 192, .15)
+.algolia-autocomplete
+  .ds-suggestion.ds-cursor
+  .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, 0.15);
 }
diff --git a/modules/uncertainty/docs/docsearch.js b/modules/uncertainty/docs/docsearch.js
index b35504c..bab6d00 100644
--- a/modules/uncertainty/docs/docsearch.js
+++ b/modules/uncertainty/docs/docsearch.js
@@ -1,8 +1,7 @@
 $(function() {
-
   // register a handler to move the focus to the search bar
   // upon pressing shift + "/" (i.e. "?")
-  $(document).on('keydown', function(e) {
+  $(document).on("keydown", function(e) {
     if (e.shiftKey && e.keyCode == 191) {
       e.preventDefault();
       $("#search-input").focus();
@@ -13,18 +12,17 @@ $(function() {
     // do keyword highlighting
     /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
     var mark = function() {
-
-      var referrer = document.URL ;
-      var paramKey = "q" ;
+      var referrer = document.URL;
+      var paramKey = "q";
 
       if (referrer.indexOf("?") !== -1) {
-        var qs = referrer.substr(referrer.indexOf('?') + 1);
-        var qs_noanchor = qs.split('#')[0];
-        var qsa = qs_noanchor.split('&');
+        var qs = referrer.substr(referrer.indexOf("?") + 1);
+        var qs_noanchor = qs.split("#")[0];
+        var qsa = qs_noanchor.split("&");
         var keyword = "";
 
         for (var i = 0; i < qsa.length; i++) {
-          var currentParam = qsa[i].split('=');
+          var currentParam = qsa[i].split("=");
 
           if (currentParam.length !== 2) {
             continue;
@@ -71,14 +69,18 @@ function matchedWords(hit) {
 }
 
 function updateHitURL(hit) {
-
   var words = matchedWords(hit);
   var url = "";
 
   if (hit.anchor) {
-    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+    url =
+      hit.url_without_anchor +
+      "?q=" +
+      escape(words.join(" ")) +
+      "#" +
+      hit.anchor;
   } else {
-    url = hit.url + '?q=' + escape(words.join(" "));
+    url = hit.url + "?q=" + escape(words.join(" "));
   }
 
   return url;
diff --git a/modules/uncertainty/docs/index.html b/modules/uncertainty/docs/index.html
index 0b5d6f6..344b1b9 100644
--- a/modules/uncertainty/docs/index.html
+++ b/modules/uncertainty/docs/index.html
@@ -1,117 +1,172 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>PEcAn functions used for ecological forecasts and
-    reanalysis • PEcAn.uncertainty</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="pkgdown.js"></script><meta property="og:title" content="PEcAn functions used for ecological forecasts and
-    reanalysis">
-<meta property="og:description" content="The Predictive Ecosystem Carbon Analyzer
+<!-- Generated by pkgdown: do not edit by hand -->
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>
+      PEcAn functions used for ecological forecasts and reanalysis •
+      PEcAn.uncertainty
+    </title>
+    <!-- jquery -->
+    <script
+      src="https://code.jquery.com/jquery-3.1.0.min.js"
+      integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
+      rel="stylesheet"
+      integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1"
+      crossorigin="anonymous"
+    />
+    <!-- clipboard.js -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js"
+      integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3"
+      crossorigin="anonymous"
+    ></script>
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
+      integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw="
+      crossorigin="anonymous"
+    ></script>
+    <!-- pkgdown -->
+    <link href="pkgdown.css" rel="stylesheet" />
+    <script src="pkgdown.js"></script>
+    <meta
+      property="og:title"
+      content="PEcAn functions used for ecological forecasts and
+    reanalysis"
+    />
+    <meta
+      property="og:description"
+      content="The Predictive Ecosystem Carbon Analyzer
     (PEcAn) is a scientific workflow management tool that
     is designed to simplify the management of model
     parameterization, execution, and analysis. The goal of
     PECAn is to streamline the interaction between data and
     models, and to improve the efficacy of scientific
-    investigation.">
-<meta name="twitter:card" content="summary">
-<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-</head>
-<body>
+    investigation."
+    />
+    <meta name="twitter:card" content="summary" />
+    <!-- mathjax -->
+    <script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <!--[if lt IE 9]>
+      <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+      <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+    <![endif]-->
+  </head>
+  <body>
     <div class="container template-home">
-      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">1.6.0</span>
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+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="index.html">PEcAn.uncertainty</a>
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
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-      
-      </header><div class="row">
-  <div class="contents col-md-9">
-    The Predictive Ecosystem Carbon Analyzer
-    (PEcAn) is a scientific workflow management tool that
-    is designed to simplify the management of model
-    parameterization, execution, and analysis. The goal of
-    PECAn is to streamline the interaction between data and
-    models, and to improve the efficacy of scientific
-    investigation.
-  </div>
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                <li>
+                  <a href="reference/index.html">Reference</a>
+                </li>
+              </ul>
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
+      </header>
+      <div class="row">
+        <div class="contents col-md-9">
+          The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
+          workflow management tool that is designed to simplify the management
+          of model parameterization, execution, and analysis. The goal of PECAn
+          is to streamline the interaction between data and models, and to
+          improve the efficacy of scientific investigation.
+        </div>
 
-  <div class="col-md-3" id="sidebar">
-    <div class="links">
-<h2>Links</h2>
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-<h2>License</h2>
-<ul class="list-unstyled">
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-<a href="https://www.freebsd.org/copyright/freebsd-license.html">FreeBSD</a> + file <a href="LICENSE-text.html">LICENSE</a>
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-<h2>Developers</h2>
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+        <div class="col-md-3" id="sidebar">
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+            <ul class="list-unstyled">
+              <li>Report a bug at <br /><a href="NA">NA</a></li>
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+            <h2>License</h2>
+            <ul class="list-unstyled">
+              <li>
+                <a href="https://www.freebsd.org/copyright/freebsd-license.html"
+                  >FreeBSD</a
+                >
+                + file <a href="LICENSE-text.html">LICENSE</a>
+              </li>
+            </ul>
+          </div>
+          <div class="developers">
+            <h2>Developers</h2>
+            <ul class="list-unstyled">
+              <li><a href="authors.html">All authors...</a></li>
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+          </div>
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-  <p>Developed by .</p>
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-</div>
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
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       </footer>
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   </body>
 </html>
diff --git a/modules/uncertainty/docs/pkgdown.css b/modules/uncertainty/docs/pkgdown.css
index 6ca2f37..ffd8e39 100644
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+                <span
+                  class="label label-default"
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Plots an ensemble time-series from PEcAn for the selected target variable</h1>
-    
-    <div class="hidden name"><code>ensemble.ts.Rd</code></div>
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-
-    <div class="ref-description">
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-    <p>Plots an ensemble time-series from PEcAn for the selected target variable</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>ensemble.ts</span>(<span class='no'>ensemble.ts</span>, <span class='kw'>observations</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>...</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing, generates an ensemble time-series plot</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Plots an ensemble time-series from PEcAn for the selected target
+              variable
+            </h1>
+
+            <div class="hidden name"><code>ensemble.ts.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Plots an ensemble time-series from PEcAn for the selected target
+              variable
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>ensemble.ts</span>(<span class='no'>ensemble.ts</span>, <span class='kw'>observations</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing, generates an ensemble time-series plot</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze, Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze, Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
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diff --git a/modules/uncertainty/docs/reference/flux.uncertainty.html b/modules/uncertainty/docs/reference/flux.uncertainty.html
index 13ab7cb..23cf787 100644
--- a/modules/uncertainty/docs/reference/flux.uncertainty.html
+++ b/modules/uncertainty/docs/reference/flux.uncertainty.html
@@ -2,175 +2,221 @@
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+    </title>
+
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate parameters for heteroskedastic flux uncertainty</h1>
-    
-    <div class="hidden name"><code>flux.uncertainty.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate parameters for heteroskedastic flux uncertainty</h1>
 
-    <div class="ref-description">
-    
-    <p>Calculate parameters for heteroskedastic flux uncertainty</p>
-    
-    </div>
+            <div class="hidden name"><code>flux.uncertainty.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate parameters for heteroskedastic flux uncertainty</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>flux.uncertainty</span>(<span class='no'>measurement</span>, <span class='kw'>QC</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>flags</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>bin.num</span> <span class='kw'>=</span> <span class='fl'>10</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>flux.uncertainty</span>(<span class='no'>measurement</span>, <span class='kw'>QC</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>flags</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>bin.num</span> <span class='kw'>=</span> <span class='fl'>10</span>,
   <span class='kw'>transform</span> <span class='kw'>=</span> <span class='no'>identity</span>, <span class='kw'>minBin</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>measurement</th>
-      <td><p>= flux time-series</p></td>
-    </tr>
-    <tr>
-      <th>QC</th>
-      <td><p>= quality control flag time series (0 = best)</p></td>
-    </tr>
-    <tr>
-      <th>flags</th>
-      <td><p>= additional flags on flux filtering of PAIRS (length = 1/2 that of the 
-time series, TRUE = use).</p></td>
-    </tr>
-    <tr>
-      <th>bin.num</th>
-      <td><p>= number of bins (default = 10)</p></td>
-    </tr>
-    <tr>
-      <th>transform</th>
-      <td><p>= transformation of magnitude (default = identity)</p></td>
-    </tr>
-    <tr>
-      <th>minBin</th>
-      <td><p>= minimum number of points allowed in a bin</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>return.list List of parameters from the fitted uncertainty model</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>measurement</th>
+              <td><p>= flux time-series</p></td>
+            </tr>
+            <tr>
+              <th>QC</th>
+              <td><p>= quality control flag time series (0 = best)</p></td>
+            </tr>
+            <tr>
+              <th>flags</th>
+              <td>
+                <p>
+                  = additional flags on flux filtering of PAIRS (length = 1/2
+                  that of the time series, TRUE = use).
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>bin.num</th>
+              <td><p>= number of bins (default = 10)</p></td>
+            </tr>
+            <tr>
+              <th>transform</th>
+              <td><p>= transformation of magnitude (default = identity)</p></td>
+            </tr>
+            <tr>
+              <th>minBin</th>
+              <td><p>= minimum number of points allowed in a bin</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            return.list List of parameters from the fitted uncertainty model
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze, Carl Davidson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze, Carl Davidson
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/uncertainty/docs/reference/get.change.html b/modules/uncertainty/docs/reference/get.change.html
index 57c2899..b797933 100644
--- a/modules/uncertainty/docs/reference/get.change.html
+++ b/modules/uncertainty/docs/reference/get.change.html
@@ -2,143 +2,177 @@
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+      PEcAn.uncertainty
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+
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-<div class="row">
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-    <h1>Get delta between sequential flux datapoints</h1>
-    
-    <div class="hidden name"><code>get.change.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get delta between sequential flux datapoints</h1>
 
-    <div class="ref-description">
-    
-    <p>Get delta between sequential flux datapoints</p>
-    
-    </div>
+            <div class="hidden name"><code>get.change.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>get.change</span>(<span class='no'>measurement</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <div class="ref-description">
+            <p>Get delta between sequential flux datapoints</p>
+          </div>
 
-    <p>Difference between consecutive measurements</p>
-    
+          <pre
+            class="usage"
+          ><span class='fu'>get.change</span>(<span class='no'>measurement</span>)</pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Difference between consecutive measurements</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze, Carl Davidson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze, Carl Davidson
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
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diff --git a/modules/uncertainty/docs/reference/get.coef.var.html b/modules/uncertainty/docs/reference/get.coef.var.html
index ccadedb..7f8a19c 100644
--- a/modules/uncertainty/docs/reference/get.coef.var.html
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get coefficient of variance</h1>
-    
-    <div class="hidden name"><code>get.coef.var.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Given a set of numbers (a numeric vector), this returns the set's coefficient of variance.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.coef.var</span>(<span class='no'>set</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>set</th>
-      <td><p>numeric vector of trait values</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>coeficient of variance</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get coefficient of variance</h1>
+
+            <div class="hidden name"><code>get.coef.var.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Given a set of numbers (a numeric vector), this returns the set's
+              coefficient of variance.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.coef.var</span>(<span class='no'>set</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>set</th>
+              <td><p>numeric vector of trait values</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>coeficient of variance</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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+        </div>
+
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diff --git a/modules/uncertainty/docs/reference/get.elasticity.html b/modules/uncertainty/docs/reference/get.elasticity.html
index 9049b95..8c8edb4 100644
--- a/modules/uncertainty/docs/reference/get.elasticity.html
+++ b/modules/uncertainty/docs/reference/get.elasticity.html
@@ -2,163 +2,210 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
+      integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u"
+      crossorigin="anonymous"
+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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-<div class="row">
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-    <div class="page-header">
-    <h1>Get Elasticity</h1>
-    
-    <div class="hidden name"><code>get.elasticity.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Generic function for the elasticity</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.elasticity</span>(<span class='no'>sensitivity</span>, <span class='no'>samples</span>, <span class='no'>outputs</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sensitivity</th>
-      <td><p>univariate sensitivity of model to a parameter, can be calculated by <code><a href='get.sensitivity.html'>get.sensitivity</a></code></p></td>
-    </tr>
-    <tr>
-      <th>samples</th>
-      <td><p>samples from trait distribution</p></td>
-    </tr>
-    <tr>
-      <th>outputs</th>
-      <td><p>model output from ensemble runs</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>elasticity = normalized sensitivity</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Given the sensitivity, samples, and outputs for a single trait, return elasticity</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get Elasticity</h1>
+
+            <div class="hidden name"><code>get.elasticity.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Generic function for the elasticity</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.elasticity</span>(<span class='no'>sensitivity</span>, <span class='no'>samples</span>, <span class='no'>outputs</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sensitivity</th>
+              <td>
+                <p>
+                  univariate sensitivity of model to a parameter, can be
+                  calculated by
+                  <code
+                    ><a href="get.sensitivity.html">get.sensitivity</a></code
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>samples</th>
+              <td><p>samples from trait distribution</p></td>
+            </tr>
+            <tr>
+              <th>outputs</th>
+              <td><p>model output from ensemble runs</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>elasticity = normalized sensitivity</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Given the sensitivity, samples, and outputs for a single trait,
+            return elasticity
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
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-</div>
+        </div>
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diff --git a/modules/uncertainty/docs/reference/get.ensemble.samples.html b/modules/uncertainty/docs/reference/get.ensemble.samples.html
index f9d85cc..b90e2d6 100644
--- a/modules/uncertainty/docs/reference/get.ensemble.samples.html
+++ b/modules/uncertainty/docs/reference/get.ensemble.samples.html
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get Ensemble Samples</h1>
-    
-    <div class="hidden name"><code>get.ensemble.samples.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get Ensemble Samples</h1>
 
-    <div class="ref-description">
-    
-    <p>Get parameter values used in ensemble</p>
-    
-    </div>
+            <div class="hidden name"><code>get.ensemble.samples.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Get parameter values used in ensemble</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>get.ensemble.samples</span>(<span class='no'>ensemble.size</span>, <span class='no'>pft.samples</span>, <span class='no'>env.samples</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>get.ensemble.samples</span>(<span class='no'>ensemble.size</span>, <span class='no'>pft.samples</span>, <span class='no'>env.samples</span>,
   <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"uniform"</span>, <span class='kw'>param.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ensemble.size</th>
-      <td><p>number of runs in model ensemble</p></td>
-    </tr>
-    <tr>
-      <th>pft.samples</th>
-      <td><p>random samples from parameter distribution, e.g. from a MCMC chain</p></td>
-    </tr>
-    <tr>
-      <th>env.samples</th>
-      <td><p>env samples</p></td>
-    </tr>
-    <tr>
-      <th>method</th>
-      <td><p>the method used to generate the ensemble samples. Random generators: uniform, uniform with latin hypercube permutation. Quasi-random generators: halton, sobol, torus. Random generation draws random variates whereas quasi-random generation is deterministic but well equidistributed. Default is uniform. For small ensemble size with relatively large parameter number (e.g ensemble size &lt; 5 and # of traits &gt; 5) use methods other than halton.</p></td>
-    </tr>
-    <tr>
-      <th>param.names</th>
-      <td><p>a list of parameter names that were fitted either by MA or PDA, important argument, if NULL parameters will be resampled independently</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Other arguments passed on to the sampling method</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>matrix of (quasi-)random samples from trait distributions</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Returns a matrix of randomly or quasi-randomly sampled trait values 
-to be assigned to traits over several model runs.
-given the number of model runs and a list of sample distributions for traits
-The model run is indexed first by model run, then by trait</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ensemble.size</th>
+              <td><p>number of runs in model ensemble</p></td>
+            </tr>
+            <tr>
+              <th>pft.samples</th>
+              <td>
+                <p>
+                  random samples from parameter distribution, e.g. from a MCMC
+                  chain
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>env.samples</th>
+              <td><p>env samples</p></td>
+            </tr>
+            <tr>
+              <th>method</th>
+              <td>
+                <p>
+                  the method used to generate the ensemble samples. Random
+                  generators: uniform, uniform with latin hypercube permutation.
+                  Quasi-random generators: halton, sobol, torus. Random
+                  generation draws random variates whereas quasi-random
+                  generation is deterministic but well equidistributed. Default
+                  is uniform. For small ensemble size with relatively large
+                  parameter number (e.g ensemble size &lt; 5 and # of traits
+                  &gt; 5) use methods other than halton.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>param.names</th>
+              <td>
+                <p>
+                  a list of parameter names that were fitted either by MA or
+                  PDA, important argument, if NULL parameters will be resampled
+                  independently
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>Other arguments passed on to the sampling method</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>matrix of (quasi-)random samples from trait distributions</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Returns a matrix of randomly or quasi-randomly sampled trait values
+            to be assigned to traits over several model runs. given the number
+            of model runs and a list of sample distributions for traits The
+            model run is indexed first by model run, then by trait
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Istem Fer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Istem Fer
+        </div>
+      </div>
 
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+          <p>Developed by .</p>
+        </div>
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diff --git a/modules/uncertainty/docs/reference/get.gi.phii.html b/modules/uncertainty/docs/reference/get.gi.phii.html
index 863773b..13498df 100644
--- a/modules/uncertainty/docs/reference/get.gi.phii.html
+++ b/modules/uncertainty/docs/reference/get.gi.phii.html
@@ -2,168 +2,229 @@
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+                  <a href="../index.html">
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+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Get g_i(phi_i)</h1>
-    
-    <div class="hidden name"><code>get.gi.phii.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate distribution of function of a variable</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.gi.phii</span>(<span class='no'>splinefuns</span>, <span class='no'>trait.samples</span>, <span class='kw'>maxn</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>splinefuns</th>
-      <td><p>univariate spline functions created for each trait, e.g. by the <code><a href='sensitivity.analysis.html'>sensitivity.analysis</a></code> function.</p></td>
-    </tr>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>n x m matrix (or list with m vectors of length n) of n parameter sets, each with a sample from m traits</p></td>
-    </tr>
-    <tr>
-      <th>maxn</th>
-      <td><p>maximum number of parameter sets to evaluate</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>matrix of spline estimates of model output for each of n parameter sets</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Transform trait parameter through trait-specific univariate model emulator spline function
-Given a matrix of parameter sets, calculates a matrix of model output by applying appropriate spline function to each parameter. Output is use with <code>variance.decomposition</code> and <code><a href='spline.ensemble.html'>spline.ensemble</a></code></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Get g_i(phi_i)</h1>
+
+            <div class="hidden name"><code>get.gi.phii.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate distribution of function of a variable</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.gi.phii</span>(<span class='no'>splinefuns</span>, <span class='no'>trait.samples</span>, <span class='kw'>maxn</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>splinefuns</th>
+              <td>
+                <p>
+                  univariate spline functions created for each trait, e.g. by
+                  the
+                  <code
+                    ><a href="sensitivity.analysis.html"
+                      >sensitivity.analysis</a
+                    ></code
+                  >
+                  function.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>trait.samples</th>
+              <td>
+                <p>
+                  n x m matrix (or list with m vectors of length n) of n
+                  parameter sets, each with a sample from m traits
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>maxn</th>
+              <td><p>maximum number of parameter sets to evaluate</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            matrix of spline estimates of model output for each of n parameter
+            sets
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Transform trait parameter through trait-specific univariate model
+            emulator spline function Given a matrix of parameter sets,
+            calculates a matrix of model output by applying appropriate spline
+            function to each parameter. Output is use with
+            <code>variance.decomposition</code> and
+            <code><a href="spline.ensemble.html">spline.ensemble</a></code>
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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index 7480292..6fd3971 100644
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+++ b/modules/uncertainty/docs/reference/get.parameter.samples.html
@@ -2,148 +2,189 @@
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+    <link href="../pkgdown.css" rel="stylesheet" />
+    <script src="../pkgdown.js"></script>
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+      property="og:title"
+      content="Sample from priors or posteriors — get.parameter.samples"
+    />
+
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+      property="og:description"
+      content="Convert priors / MCMC samples to chains that can be sampled for model parameters"
+    />
+    <meta name="twitter:card" content="summary" />
+
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.uncertainty</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Sample from priors or posteriors</h1>
-    
-    <div class="hidden name"><code>get.parameter.samples.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Sample from priors or posteriors</h1>
 
-    <div class="ref-description">
-    
-    <p>Convert priors / MCMC samples to chains that can be sampled for model parameters</p>
-    
-    </div>
+            <div class="hidden name"><code>get.parameter.samples.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>get.parameter.samples</span>(<span class='no'>settings</span>, <span class='kw'>posterior.files</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>NA</span>,
-  <span class='fu'>length</span>(<span class='no'>settings</span>$<span class='no'>pfts</span>)), <span class='kw'>ens.sample.method</span> <span class='kw'>=</span> <span class='st'>"uniform"</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>pfts</th>
-      <td><p>the pfts node of the list of pecan settings</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Istem Fer
-
-  </div>
-</div>
+          <div class="ref-description">
+            <p>
+              Convert priors / MCMC samples to chains that can be sampled for
+              model parameters
+            </p>
+          </div>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+          <pre
+            class="usage"
+          ><span class='fu'>get.parameter.samples</span>(<span class='no'>settings</span>, <span class='kw'>posterior.files</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fl'>NA</span>,
+  <span class='fu'>length</span>(<span class='no'>settings</span>$<span class='no'>pfts</span>)), <span class='kw'>ens.sample.method</span> <span class='kw'>=</span> <span class='st'>"uniform"</span>)</pre>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>pfts</th>
+              <td><p>the pfts node of the list of pecan settings</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          David LeBauer, Shawn Serbin, Istem Fer
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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 </html>
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diff --git a/modules/uncertainty/docs/reference/get.sensitivity.html b/modules/uncertainty/docs/reference/get.sensitivity.html
index 82683ba..c2f9b0d 100644
--- a/modules/uncertainty/docs/reference/get.sensitivity.html
+++ b/modules/uncertainty/docs/reference/get.sensitivity.html
@@ -2,161 +2,202 @@
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 <html>
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+    <!-- clipboard.js -->
+    <script
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
+    <script
+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+    />
+    <meta name="twitter:card" content="summary" />
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                type="button"
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+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.uncertainty</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
+            <div id="navbar" class="navbar-collapse collapse">
+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
+              <ul class="nav navbar-nav navbar-right"></ul>
+            </div>
+            <!--/.nav-collapse -->
+          </div>
+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate Sensitivity</h1>
-    
-    <div class="hidden name"><code>get.sensitivity.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculate the sensitivity of a function at the median</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>get.sensitivity</span>(<span class='no'>trait.samples</span>, <span class='no'>sa.splinefun</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.samples</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>sa.splinefun</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>numeric estimate of model sensitivity to parameter</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This function evaluates the sensitivity of a model to a parameter.
-This is done by evaluating the first derivative of the univariate spline estimate
-of the model response at the parameter median.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate Sensitivity</h1>
+
+            <div class="hidden name"><code>get.sensitivity.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculate the sensitivity of a function at the median</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>get.sensitivity</span>(<span class='no'>trait.samples</span>, <span class='no'>sa.splinefun</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.samples</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>sa.splinefun</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>numeric estimate of model sensitivity to parameter</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This function evaluates the sensitivity of a model to a parameter.
+            This is done by evaluating the first derivative of the univariate
+            spline estimate of the model response at the parameter median.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
-  </div>
-</div>
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
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   </body>
 </html>
-
diff --git a/modules/uncertainty/docs/reference/index.html b/modules/uncertainty/docs/reference/index.html
index 95fae6e..9632bbb 100644
--- a/modules/uncertainty/docs/reference/index.html
+++ b/modules/uncertainty/docs/reference/index.html
@@ -2,306 +2,486 @@
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-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-<title>Function reference • PEcAn.uncertainty</title>
+    <title>Function reference • PEcAn.uncertainty</title>
 
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+    ></script>
+    <!-- Bootstrap -->
 
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.uncertainty</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
 
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-<div class="row">
-  <div class="contents col-md-9">
-    <div class="page-header">
-      <h1>Reference</h1>
-    </div>
-
-    <table class="ref-index">
+      <div class="row">
+        <div class="contents col-md-9">
+          <div class="page-header">
+            <h1>Reference</h1>
+          </div>
 
-    <colgroup>
-      
-      <col class="alias" />
-      <col class="title" />
-    </colgroup>
+          <table class="ref-index">
+            <colgroup>
+              <col class="alias" />
+              <col class="title" />
+            </colgroup>
 
-    <tbody>
-      <tr>
-        <th colspan="2">
-          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-          <p class="section-desc"></p>
-        </th>
-      </tr>
-      <tr>
-        
-        <td>
-          <p><code><a href="ensemble.ts.html">ensemble.ts()</a></code> </p>
-        </td>
-        <td><p>Plots an ensemble time-series from PEcAn for the selected target variable</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="flux.uncertainty.html">flux.uncertainty()</a></code> </p>
-        </td>
-        <td><p>Calculate parameters for heteroskedastic flux uncertainty</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.change.html">get.change()</a></code> </p>
-        </td>
-        <td><p>Get delta between sequential flux datapoints</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.coef.var.html">get.coef.var()</a></code> </p>
-        </td>
-        <td><p>Get coefficient of variance</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.elasticity.html">get.elasticity()</a></code> </p>
-        </td>
-        <td><p>Get Elasticity</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.ensemble.samples.html">get.ensemble.samples()</a></code> </p>
-        </td>
-        <td><p>Get Ensemble Samples</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.gi.phii.html">get.gi.phii()</a></code> </p>
-        </td>
-        <td><p>Get g_i(phi_i)</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.parameter.samples.html">get.parameter.samples()</a></code> </p>
-        </td>
-        <td><p>Sample from priors or posteriors</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="get.sensitivity.html">get.sensitivity()</a></code> </p>
-        </td>
-        <td><p>Calculate Sensitivity</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="input.ens.gen.html">input.ens.gen()</a></code> </p>
-        </td>
-        <td><p>Function for generating samples based on sampling method, parent or etc</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="kurtosis.html">kurtosis()</a></code> </p>
-        </td>
-        <td><p>Calculate excess kurtosis from a vector</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot_flux_uncertainty.html">plot_flux_uncertainty()</a></code> </p>
-        </td>
-        <td><p>Plot fit for heteroskedastic flux uncertainty</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot_sensitivities.html">plot_sensitivities()</a></code> </p>
-        </td>
-        <td><p>Plot Sensitivities</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot_sensitivity.html">plot_sensitivity()</a></code> </p>
-        </td>
-        <td><p>Sensitivity plot</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="plot_variance_decomposition.html">plot_variance_decomposition()</a></code> </p>
-        </td>
-        <td><p>Variance Decomposition Plots</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="prep.data.assim.html">prep.data.assim()</a></code> </p>
-        </td>
-        <td><p>prep.data.assim</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.ameriflux.L2.html">read.ameriflux.L2()</a></code> </p>
-        </td>
-        <td><p>Read Ameriflux L2 Data</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.ensemble.output.html">read.ensemble.output()</a></code> </p>
-        </td>
-        <td><p>Read ensemble output</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="read.ensemble.ts.html">read.ensemble.ts()</a></code> </p>
-        </td>
-        <td><p>Reads an ensemble time-series from PEcAn for the selected target variable</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="run.ensemble.analysis.html">run.ensemble.analysis()</a></code> </p>
-        </td>
-        <td><p>run ensemble.analysis</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="run.sensitivity.analysis.html">run.sensitivity.analysis()</a></code> </p>
-        </td>
-        <td><p>run sensitivity.analysis</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sa.splinefun.html">sa.splinefun()</a></code> </p>
-        </td>
-        <td><p>Sensitivity spline function</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sd.var.html">sd.var()</a></code> </p>
-        </td>
-        <td><p>Standard deviation of sample variance</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="sensitivity.analysis.html">sensitivity.analysis()</a></code> </p>
-        </td>
-        <td><p>Sensitivity Analysis</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="spline.ensemble.html">spline.ensemble()</a></code> </p>
-        </td>
-        <td><p>Spline Ensemble</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="spline.truncate.html">spline.truncate()</a></code> </p>
-        </td>
-        <td><p>Truncate spline</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="variance.stats.html">variance.stats()</a></code> </p>
-        </td>
-        <td><p>variance statistics</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="write.ensemble.configs.html">write.ensemble.configs()</a></code> </p>
-        </td>
-        <td><p>Write ensemble config files</p></td>
-      </tr>
-    </tbody>
-    </table>
-  </div>
+            <tbody>
+              <tr>
+                <th colspan="2">
+                  <h2 id="section-all-functions" class="hasAnchor">
+                    <a href="#section-all-functions" class="anchor"></a>All
+                    functions
+                  </h2>
+                  <p class="section-desc"></p>
+                </th>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="ensemble.ts.html">ensemble.ts()</a></code>
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Plots an ensemble time-series from PEcAn for the selected
+                    target variable
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="flux.uncertainty.html"
+                        >flux.uncertainty()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Calculate parameters for heteroskedastic flux uncertainty
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.change.html">get.change()</a></code>
+                  </p>
+                </td>
+                <td><p>Get delta between sequential flux datapoints</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.coef.var.html">get.coef.var()</a></code>
+                  </p>
+                </td>
+                <td><p>Get coefficient of variance</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.elasticity.html">get.elasticity()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get Elasticity</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.ensemble.samples.html"
+                        >get.ensemble.samples()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Get Ensemble Samples</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="get.gi.phii.html">get.gi.phii()</a></code>
+                  </p>
+                </td>
+                <td><p>Get g_i(phi_i)</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.parameter.samples.html"
+                        >get.parameter.samples()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Sample from priors or posteriors</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="get.sensitivity.html"
+                        >get.sensitivity()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Calculate Sensitivity</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="input.ens.gen.html">input.ens.gen()</a></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Function for generating samples based on sampling method,
+                    parent or etc
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="kurtosis.html">kurtosis()</a></code>
+                  </p>
+                </td>
+                <td><p>Calculate excess kurtosis from a vector</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot_flux_uncertainty.html"
+                        >plot_flux_uncertainty()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Plot fit for heteroskedastic flux uncertainty</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot_sensitivities.html"
+                        >plot_sensitivities()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Plot Sensitivities</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot_sensitivity.html"
+                        >plot_sensitivity()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Sensitivity plot</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="plot_variance_decomposition.html"
+                        >plot_variance_decomposition()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Variance Decomposition Plots</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="prep.data.assim.html"
+                        >prep.data.assim()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>prep.data.assim</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.ameriflux.L2.html"
+                        >read.ameriflux.L2()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read Ameriflux L2 Data</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.ensemble.output.html"
+                        >read.ensemble.output()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Read ensemble output</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="read.ensemble.ts.html"
+                        >read.ensemble.ts()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td>
+                  <p>
+                    Reads an ensemble time-series from PEcAn for the selected
+                    target variable
+                  </p>
+                </td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="run.ensemble.analysis.html"
+                        >run.ensemble.analysis()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>run ensemble.analysis</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="run.sensitivity.analysis.html"
+                        >run.sensitivity.analysis()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>run sensitivity.analysis</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sa.splinefun.html">sa.splinefun()</a></code>
+                  </p>
+                </td>
+                <td><p>Sensitivity spline function</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code><a href="sd.var.html">sd.var()</a></code>
+                  </p>
+                </td>
+                <td><p>Standard deviation of sample variance</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="sensitivity.analysis.html"
+                        >sensitivity.analysis()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Sensitivity Analysis</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="spline.ensemble.html"
+                        >spline.ensemble()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Spline Ensemble</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="spline.truncate.html"
+                        >spline.truncate()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Truncate spline</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="variance.stats.html">variance.stats()</a></code
+                    >
+                  </p>
+                </td>
+                <td><p>variance statistics</p></td>
+              </tr>
+              <tr>
+                <td>
+                  <p>
+                    <code
+                      ><a href="write.ensemble.configs.html"
+                        >write.ensemble.configs()</a
+                      ></code
+                    >
+                  </p>
+                </td>
+                <td><p>Write ensemble config files</p></td>
+              </tr>
+            </tbody>
+          </table>
+        </div>
 
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#section-all-functions">All functions</a></li>
-    </ul>
-  </div>
-</div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#section-all-functions">All functions</a></li>
+          </ul>
+        </div>
+      </div>
 
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-  <p>Developed by .</p>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
 
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index c3c3f29..4b506d1 100644
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Function for generating samples based on sampling method, parent or etc</h1>
-    
-    <div class="hidden name"><code>input.ens.gen.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Function for generating samples based on sampling method, parent or etc</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>input.ens.gen</span>(<span class='no'>settings</span>, <span class='no'>input</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"sampling"</span>, <span class='kw'>parent_ids</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>list of PEcAn settings</p></td>
-    </tr>
-    <tr>
-      <th>method</th>
-      <td><p>Method for sampling - For now looping or sampling with replacement is implemented</p></td>
-    </tr>
-    <tr>
-      <th>parent_ids</th>
-      <td><p>This is basically the order of the paths that the parent is sampled.See Details.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>For a given input/tag in the pecan xml and a method, this function returns a list with $id showing the order of sampling and $samples with samples of that input.</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>If for example met was a parent and it's sampling method resulted in choosing the first, third and fourth samples, these are the ids that need to be sent as
-parent_ids to this function.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Function for generating samples based on sampling method, parent
+              or etc
+            </h1>
+
+            <div class="hidden name"><code>input.ens.gen.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Function for generating samples based on sampling method, parent
+              or etc
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>input.ens.gen</span>(<span class='no'>settings</span>, <span class='no'>input</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"sampling"</span>, <span class='kw'>parent_ids</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td><p>list of PEcAn settings</p></td>
+            </tr>
+            <tr>
+              <th>method</th>
+              <td>
+                <p>
+                  Method for sampling - For now looping or sampling with
+                  replacement is implemented
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>parent_ids</th>
+              <td>
+                <p>
+                  This is basically the order of the paths that the parent is
+                  sampled.See Details.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            For a given input/tag in the pecan xml and a method, this function
+            returns a list with $id showing the order of sampling and $samples
+            with samples of that input.
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            If for example met was a parent and it's sampling method resulted in
+            choosing the first, third and fourth samples, these are the ids that
+            need to be sent as parent_ids to this function.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>input.ens.gen</span>(<span class='no'>settings</span>,<span class='st'>"met"</span>,<span class='st'>"sampling"</span>)
 <span class='co'># }</span># NOT RUN {
  
 # }
 </pre>
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-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
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+            <li><a href="#value">Value</a></li>
 
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+            <li><a href="#details">Details</a></li>
 
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diff --git a/modules/uncertainty/docs/reference/kurtosis.html b/modules/uncertainty/docs/reference/kurtosis.html
index 0c2adec..ce8eec2 100644
--- a/modules/uncertainty/docs/reference/kurtosis.html
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+                <span class="icon-bar"></span>
+              </button>
+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.uncertainty</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
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+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
+                  </a>
+                </li>
+                <li>
+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+            <!--/.nav-collapse -->
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Calculate excess kurtosis from a vector</h1>
-    
-    <div class="hidden name"><code>kurtosis.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculates the excess kurtosis of a vector</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>kurtosis</span>(<span class='no'>x</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>vector of values</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>numeric value of kurtosis</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Note that this calculates the 'excess kurtosis', which is defined as kurtosis - 3.
-This statistic is used in the calculation of the standard deviation of sample variance
-in the function <code><a href='sd.var.html'>sd.var</a></code>.  
-Additional details</p>
-    
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
-    <p>NIST/SEMATECH e-Handbook of Statistical Methods, <a href='http://www.itl.nist.gov/div898/handbook/eda/section3/eda35b.htm'>http://www.itl.nist.gov/div898/handbook/eda/section3/eda35b.htm</a>, 2011-06-20.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#references">References</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Calculate excess kurtosis from a vector</h1>
+
+            <div class="hidden name"><code>kurtosis.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculates the excess kurtosis of a vector</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>kurtosis</span>(<span class='no'>x</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>vector of values</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>numeric value of kurtosis</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Note that this calculates the 'excess kurtosis', which is defined as
+            kurtosis - 3. This statistic is used in the calculation of the
+            standard deviation of sample variance in the function
+            <code><a href="sd.var.html">sd.var</a></code
+            >. Additional details
+          </p>
+
+          <h2 class="hasAnchor" id="references">
+            <a class="anchor" href="#references"></a>References
+          </h2>
+
+          <p>
+            NIST/SEMATECH e-Handbook of Statistical Methods,
+            <a
+              href="http://www.itl.nist.gov/div898/handbook/eda/section3/eda35b.htm"
+              >http://www.itl.nist.gov/div898/handbook/eda/section3/eda35b.htm</a
+            >, 2011-06-20.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#references">References</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index c78669f..b6e5f3a 100644
--- a/modules/uncertainty/docs/reference/plot_flux_uncertainty.html
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Plot fit for heteroskedastic flux uncertainty</h1>
-    
-    <div class="hidden name"><code>plot_flux_uncertainty.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Plot fit for heteroskedastic flux uncertainty</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>plot_flux_uncertainty</span>(<span class='no'>f</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>f</th>
-      <td><p>output of flux.uncertainty functions</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>optional graphical paramters</p></td>
-    </tr>
-    </table>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-                </ul>
-
-    <h2>Author</h2>
-    
-Mike Dietze, Carl Davidson
-
-  </div>
-</div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Plot fit for heteroskedastic flux uncertainty</h1>
+
+            <div class="hidden name"><code>plot_flux_uncertainty.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Plot fit for heteroskedastic flux uncertainty</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>plot_flux_uncertainty</span>(<span class='no'>f</span>, <span class='no'>...</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>f</th>
+              <td><p>output of flux.uncertainty functions</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td><p>optional graphical paramters</p></td>
+            </tr>
+          </table>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+          </ul>
+
+          <h2>Author</h2>
+
+          Mike Dietze, Carl Davidson
+        </div>
+      </div>
 
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diff --git a/modules/uncertainty/docs/reference/plot_sensitivities.html b/modules/uncertainty/docs/reference/plot_sensitivities.html
index f717586..cfd6045 100644
--- a/modules/uncertainty/docs/reference/plot_sensitivities.html
+++ b/modules/uncertainty/docs/reference/plot_sensitivities.html
@@ -2,168 +2,218 @@
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+      content="Plot functions and quantiles used in sensitivity analysis"
+    />
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-<div class="row">
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-    <h1>Plot Sensitivities</h1>
-    
-    <div class="hidden name"><code>plot_sensitivities.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Plot Sensitivities</h1>
 
-    <div class="ref-description">
-    
-    <p>Plot functions and quantiles used in sensitivity analysis</p>
-    
-    </div>
+            <div class="hidden name"><code>plot_sensitivities.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>plot_sensitivities</span>(<span class='no'>sensitivity.plot.inputs</span>,
+          <div class="ref-description">
+            <p>Plot functions and quantiles used in sensitivity analysis</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>plot_sensitivities</span>(<span class='no'>sensitivity.plot.inputs</span>,
   <span class='kw'>prior.sensitivity.plot.inputs</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sensitivity.plot.inputs</th>
-      <td><p>inputs</p></td>
-    </tr>
-    <tr>
-      <th>prior.sensitivity.plot.inputs</th>
-      <td><p>priors</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>arguments passed to <code><a href='plot_sensitivity.html'>plot_sensitivity</a></code></p></td>
-    </tr>
-    <tr>
-      <th>sensitivity.results</th>
-      <td><p>list containing sa.samples and sa.splines</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list of plots, one per trait</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Generates a plot using <code><a href='plot_sensitivity.html'>plot_sensitivity</a></code> for multiple traits.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sensitivity.plot.inputs</th>
+              <td><p>inputs</p></td>
+            </tr>
+            <tr>
+              <th>prior.sensitivity.plot.inputs</th>
+              <td><p>priors</p></td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  arguments passed to
+                  <code
+                    ><a href="plot_sensitivity.html">plot_sensitivity</a></code
+                  >
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sensitivity.results</th>
+              <td><p>list containing sa.samples and sa.splines</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list of plots, one per trait</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Generates a plot using
+            <code><a href="plot_sensitivity.html">plot_sensitivity</a></code>
+            for multiple traits.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+          </ul>
+        </div>
+      </div>
 
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diff --git a/modules/uncertainty/docs/reference/plot_sensitivity.html b/modules/uncertainty/docs/reference/plot_sensitivity.html
index 4a9468e..9e04c1b 100644
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-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Sensitivity plot</h1>
-    
-    <div class="hidden name"><code>plot_sensitivity.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Sensitivity plot</h1>
 
-    <div class="ref-description">
-    
-    <p>Plot univariate response of model output to a trait parameter.</p>
-    
-    </div>
+            <div class="hidden name"><code>plot_sensitivity.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>plot_sensitivity</span>(<span class='no'>sa.sample</span>, <span class='no'>sa.spline</span>, <span class='no'>trait</span>, <span class='kw'>y.range</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>50</span>),
+          <div class="ref-description">
+            <p>
+              Plot univariate response of model output to a trait parameter.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>plot_sensitivity</span>(<span class='no'>sa.sample</span>, <span class='no'>sa.spline</span>, <span class='no'>trait</span>, <span class='kw'>y.range</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>50</span>),
   <span class='kw'>median.i</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>prior.sa.sample</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>prior.sa.spline</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>fontsize</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>12</span>, <span class='kw'>axis</span> <span class='kw'>=</span> <span class='fl'>8</span>), <span class='kw'>linesize</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>dotsize</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>sa.sample</th>
-      <td><p>trait quantiles used in sensitivity analysis</p></td>
-    </tr>
-    <tr>
-      <th>sa.spline</th>
-      <td><p>spline function estimated from sensitivity analysis</p></td>
-    </tr>
-    <tr>
-      <th>trait</th>
-      <td><p>trait name for title</p></td>
-    </tr>
-    <tr>
-      <th>y.range</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>median.i</th>
-      <td><p>index of median value in sa.sample; <code>median.i == which(as.numeric(rownames(sa.sample)) == 50) </code></p></td>
-    </tr>
-    <tr>
-      <th>prior.sa.sample</th>
-      <td><p>similar to sa.sample, but for prior distribution. If given, plots sensitivity for prior run</p></td>
-    </tr>
-    <tr>
-      <th>prior.sa.spline</th>
-      <td><p>similar to sa.spline, but for prior trait distribution.</p></td>
-    </tr>
-    <tr>
-      <th>fontsize</th>
-      <td><p>(optional) list with three arguments that can be set to vary the fontsize of the title, axis labels, and axis title in the sensitivity plots</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>object of class ggplot</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Plots for a single trait; called by <code><a href='plot_sensitivities.html'>plot_sensitivities</a></code>
-to plot sensitivity plots for multiple traits.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-          </ul>
 
-  </div>
-</div>
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>sa.sample</th>
+              <td><p>trait quantiles used in sensitivity analysis</p></td>
+            </tr>
+            <tr>
+              <th>sa.spline</th>
+              <td>
+                <p>spline function estimated from sensitivity analysis</p>
+              </td>
+            </tr>
+            <tr>
+              <th>trait</th>
+              <td><p>trait name for title</p></td>
+            </tr>
+            <tr>
+              <th>y.range</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>median.i</th>
+              <td>
+                <p>
+                  index of median value in sa.sample;
+                  <code
+                    >median.i == which(as.numeric(rownames(sa.sample)) == 50)
+                  </code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prior.sa.sample</th>
+              <td>
+                <p>
+                  similar to sa.sample, but for prior distribution. If given,
+                  plots sensitivity for prior run
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>prior.sa.spline</th>
+              <td>
+                <p>similar to sa.spline, but for prior trait distribution.</p>
+              </td>
+            </tr>
+            <tr>
+              <th>fontsize</th>
+              <td>
+                <p>
+                  (optional) list with three arguments that can be set to vary
+                  the fontsize of the title, axis labels, and axis title in the
+                  sensitivity plots
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>object of class ggplot</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Plots for a single trait; called by
+            <code
+              ><a href="plot_sensitivities.html">plot_sensitivities</a></code
+            >
+            to plot sensitivity plots for multiple traits.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+          </ul>
+        </div>
+      </div>
 
       <footer>
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-</div>
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-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
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+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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index 646ccee..ad9a920 100644
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    <!-- clipboard.js -->
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+    ></script>
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Variance Decomposition Plots</h1>
-    
-    <div class="hidden name"><code>plot_variance_decomposition.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Variance Decomposition Plots</h1>
 
-    <div class="ref-description">
-    
-    <p>Plot results of variance decomposition</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>plot_variance_decomposition.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>Plot results of variance decomposition</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>plot_variance_decomposition</span>(<span class='no'>plot.inputs</span>, <span class='kw'>fontsize</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>18</span>, <span class='kw'>axis</span>
+          <pre
+            class="usage"
+          ><span class='fu'>plot_variance_decomposition</span>(<span class='no'>plot.inputs</span>, <span class='kw'>fontsize</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>title</span> <span class='kw'>=</span> <span class='fl'>18</span>, <span class='kw'>axis</span>
   <span class='kw'>=</span> <span class='fl'>14</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>fontsize</th>
-      <td><p>list specifying the font size of the titles and axes of the graph</p></td>
-    </tr>
-    <tr>
-      <th>...</th>
-      <td><p>Output from any number of sensitivity analyses. Output must be of the form 
-given by sensitivity.results$variance.decomposition.output in model output</p></td>
-    </tr>
-    <tr>
-      <th>all.plot.inputs</th>
-      <td><p>Optional argument allowing output from sensitivity analyses to be specified in a list</p></td>
-    </tr>
-    <tr>
-      <th>exclude</th>
-      <td><p>vector of strings specifying parameters to omit from the variance decomposition graph</p></td>
-    </tr>
-    <tr>
-      <th>convert.var</th>
-      <td><p>function transforming variances to the value displayed in the graph</p></td>
-    </tr>
-    <tr>
-      <th>var.label</th>
-      <td><p>label to displayed over variance column</p></td>
-    </tr>
-    <tr>
-      <th>order.plot.input</th>
-      <td><p>Output from a sensitivity analysis that is to be used to order parameters.
-Parameters are ordered by variance. Defaults to the first sensitivity analysis output given</p></td>
-    </tr>
-    <tr>
-      <th>ticks.plot.input</th>
-      <td><p>Output from a sensitivity analysis that is to be used.
-Defaults to the first sensitivity analysis output given</p></td>
-    </tr>
-    <tr>
-      <th>col</th>
-      <td><p>Color of each sensitivity analysis. Equivalent to col parameter of the plot function.</p></td>
-    </tr>
-    <tr>
-      <th>pch</th>
-      <td><p>Shape of each sensitivity analysis. Equivalent to pch parameter of the plot function.</p></td>
-    </tr>
-    <tr>
-      <th>main</th>
-      <td><p>Plot title. Useful for multi-pft variance decompositions.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Plots variance decomposition tryptich</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>fontsize</th>
+              <td>
+                <p>
+                  list specifying the font size of the titles and axes of the
+                  graph
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>...</th>
+              <td>
+                <p>
+                  Output from any number of sensitivity analyses. Output must be
+                  of the form given by
+                  sensitivity.results$variance.decomposition.output in model
+                  output
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>all.plot.inputs</th>
+              <td>
+                <p>
+                  Optional argument allowing output from sensitivity analyses to
+                  be specified in a list
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>exclude</th>
+              <td>
+                <p>
+                  vector of strings specifying parameters to omit from the
+                  variance decomposition graph
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>convert.var</th>
+              <td>
+                <p>
+                  function transforming variances to the value displayed in the
+                  graph
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>var.label</th>
+              <td><p>label to displayed over variance column</p></td>
+            </tr>
+            <tr>
+              <th>order.plot.input</th>
+              <td>
+                <p>
+                  Output from a sensitivity analysis that is to be used to order
+                  parameters. Parameters are ordered by variance. Defaults to
+                  the first sensitivity analysis output given
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>ticks.plot.input</th>
+              <td>
+                <p>
+                  Output from a sensitivity analysis that is to be used.
+                  Defaults to the first sensitivity analysis output given
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>col</th>
+              <td>
+                <p>
+                  Color of each sensitivity analysis. Equivalent to col
+                  parameter of the plot function.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>pch</th>
+              <td>
+                <p>
+                  Shape of each sensitivity analysis. Equivalent to pch
+                  parameter of the plot function.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>main</th>
+              <td>
+                <p>Plot title. Useful for multi-pft variance decompositions.</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Plots variance decomposition tryptich</p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>trait.labels</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>'a'</span>, <span class='st'>'b'</span>, <span class='st'>'c'</span>),
           <span class='kw'>coef.vars</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>a</span><span class='kw'>=</span><span class='fl'>1</span>,<span class='kw'>b</span><span class='kw'>=</span><span class='fl'>0.5</span>, <span class='kw'>c</span><span class='kw'>=</span><span class='fl'>0.1</span>),
           <span class='kw'>elasticities</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>a</span><span class='kw'>=</span><span class='fl'>1</span>,<span class='kw'>b</span><span class='kw'>=</span><span class='fl'>2</span>,<span class='kw'>c</span><span class='kw'>=</span><span class='fl'>0.5</span>),
           <span class='kw'>variances</span>    <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>a</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>b</span><span class='kw'>=</span><span class='fl'>30</span>, <span class='kw'>c</span> <span class='kw'>=</span> <span class='fl'>10</span>))
 <span class='fu'>do.call</span>(<span class='no'>grid.arrange</span>, <span class='fu'>c</span>(<span class='fu'>plot_variance_decomposition</span>(<span class='no'>x</span>), <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fl'>4</span>))
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-      </footer>
-   </div>
+          <h2>Author</h2>
 
-  
+          David LeBauer, Carl Davidson
+        </div>
+      </div>
 
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
+      </footer>
+    </div>
   </body>
 </html>
-
diff --git a/modules/uncertainty/docs/reference/prep.data.assim.html b/modules/uncertainty/docs/reference/prep.data.assim.html
index ba86494..92ba3b8 100644
--- a/modules/uncertainty/docs/reference/prep.data.assim.html
+++ b/modules/uncertainty/docs/reference/prep.data.assim.html
@@ -2,164 +2,202 @@
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+
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+    ></script>
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
+
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.uncertainty</a
+                >
+                <span
+                  class="label label-default"
+                  data-toggle="tooltip"
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+                  title="Released package"
+                  >1.6.0</span
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>prep.data.assim</h1>
-    
-    <div class="hidden name"><code>prep.data.assim.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>prep.data.assim</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>prep.data.assim</span>(<span class='no'>settings</span>, <span class='no'>numvals</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>settings</th>
-      <td><p>the PEcAn settings object (a collection of nested lists)</p></td>
-    </tr>
-    <tr>
-      <th>numvals</th>
-      <td><p>number of simulated data points for each time point</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>None</p>
-    
-    <h2 class="hasAnchor" id="purpose"><a class="anchor" href="#purpose"></a>purpose</h2>
-
-    
-    <p>This function sets up a call to PEcAn.assim.sequential::sda.enkf()</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#purpose">purpose</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>prep.data.assim</h1>
+
+            <div class="hidden name"><code>prep.data.assim.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>prep.data.assim</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>prep.data.assim</span>(<span class='no'>settings</span>, <span class='no'>numvals</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>settings</th>
+              <td>
+                <p>the PEcAn settings object (a collection of nested lists)</p>
+              </td>
+            </tr>
+            <tr>
+              <th>numvals</th>
+              <td>
+                <p>number of simulated data points for each time point</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>None</p>
+
+          <h2 class="hasAnchor" id="purpose">
+            <a class="anchor" href="#purpose"></a>purpose
+          </h2>
+
+          <p>
+            This function sets up a call to PEcAn.assim.sequential::sda.enkf()
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#purpose">purpose</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Luke Dramko
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Luke Dramko
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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+    </div>
   </body>
 </html>
-
diff --git a/modules/uncertainty/docs/reference/read.ameriflux.L2.html b/modules/uncertainty/docs/reference/read.ameriflux.L2.html
index 3fada79..590a59e 100644
--- a/modules/uncertainty/docs/reference/read.ameriflux.L2.html
+++ b/modules/uncertainty/docs/reference/read.ameriflux.L2.html
@@ -2,143 +2,173 @@
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+
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
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+    />
+
+    <!-- clipboard.js -->
+    <script
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+
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+                  >PEcAn.uncertainty</a
+                >
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-    <h1>Read Ameriflux L2 Data</h1>
-    
-    <div class="hidden name"><code>read.ameriflux.L2.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read Ameriflux L2 Data</h1>
 
-    <div class="ref-description">
-    
-    <p>Read Ameriflux L2 Data</p>
-    
-    </div>
+            <div class="hidden name"><code>read.ameriflux.L2.Rd</code></div>
+          </div>
 
-    <pre class="usage"><span class='fu'>read.ameriflux.L2</span>(<span class='no'>file.name</span>, <span class='no'>year</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+          <div class="ref-description">
+            <p>Read Ameriflux L2 Data</p>
+          </div>
 
-    <p>Ameriflux L2 data read from file</p>
-    
+          <pre
+            class="usage"
+          ><span class='fu'>read.ameriflux.L2</span>(<span class='no'>file.name</span>, <span class='no'>year</span>)</pre>
 
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>Ameriflux L2 data read from file</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Mike Dietze, Carl Davidson
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Mike Dietze, Carl Davidson
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
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+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/uncertainty/docs/reference/read.ensemble.output.html b/modules/uncertainty/docs/reference/read.ensemble.output.html
index 49cc670..cbc3769 100644
--- a/modules/uncertainty/docs/reference/read.ensemble.output.html
+++ b/modules/uncertainty/docs/reference/read.ensemble.output.html
@@ -2,186 +2,239 @@
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
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+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+    ></script>
+
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+    />
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+    <!-- clipboard.js -->
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+    ></script>
+
+    <!-- sticky kit -->
+    <script
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+    <![endif]-->
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     <div class="container template-reference-topic">
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+                >
+                <span
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+            </div>
+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Read ensemble output</h1>
-    
-    <div class="hidden name"><code>read.ensemble.output.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Read ensemble output</h1>
 
-    <div class="ref-description">
-    
-    <p>Reads output from model ensemble</p>
-    
-    </div>
+            <div class="hidden name"><code>read.ensemble.output.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Reads output from model ensemble</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>read.ensemble.output</span>(<span class='no'>ensemble.size</span>, <span class='no'>pecandir</span>, <span class='no'>outdir</span>, <span class='no'>start.year</span>, <span class='no'>end.year</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>read.ensemble.output</span>(<span class='no'>ensemble.size</span>, <span class='no'>pecandir</span>, <span class='no'>outdir</span>, <span class='no'>start.year</span>, <span class='no'>end.year</span>,
   <span class='no'>variable</span>, <span class='kw'>ens.run.ids</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>ensemble.size</th>
-      <td><p>the number of ensemble members run</p></td>
-    </tr>
-    <tr>
-      <th>pecandir</th>
-      <td><p>specifies where pecan writes its configuration files</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>directory with model output to use in ensemble analysis</p></td>
-    </tr>
-    <tr>
-      <th>start.year</th>
-      <td><p>first year to include in ensemble analysis</p></td>
-    </tr>
-    <tr>
-      <th>end.year</th>
-      <td><p>last year to include in ensemble analysis</p></td>
-    </tr>
-    <tr>
-      <th>variable</th>
-      <td><p>target variables for ensemble analysis</p></td>
-    </tr>
-    <tr>
-      <th>ens.run.ids</th>
-      <td><p>dataframe. Must contain a column named "id" giving the run IDs to be read.
-If NULL, will attempt to read IDs from a file named "samples.Rdata" in <code>pecandir</code></p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>a list of ensemble model output</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Reads output for an ensemble of length specified by <code>ensemble.size</code> and bounded by <code>start.year</code> 
-and <code>end.year</code></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>ensemble.size</th>
+              <td><p>the number of ensemble members run</p></td>
+            </tr>
+            <tr>
+              <th>pecandir</th>
+              <td>
+                <p>specifies where pecan writes its configuration files</p>
+              </td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td>
+                <p>directory with model output to use in ensemble analysis</p>
+              </td>
+            </tr>
+            <tr>
+              <th>start.year</th>
+              <td><p>first year to include in ensemble analysis</p></td>
+            </tr>
+            <tr>
+              <th>end.year</th>
+              <td><p>last year to include in ensemble analysis</p></td>
+            </tr>
+            <tr>
+              <th>variable</th>
+              <td><p>target variables for ensemble analysis</p></td>
+            </tr>
+            <tr>
+              <th>ens.run.ids</th>
+              <td>
+                <p>
+                  dataframe. Must contain a column named "id" giving the run IDs
+                  to be read. If NULL, will attempt to read IDs from a file
+                  named "samples.Rdata" in <code>pecandir</code>
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>a list of ensemble model output</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Reads output for an ensemble of length specified by
+            <code>ensemble.size</code> and bounded by
+            <code>start.year</code> and <code>end.year</code>
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Ryan Kelly, David LeBauer, Rob Kooper
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Ryan Kelly, David LeBauer, Rob Kooper
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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diff --git a/modules/uncertainty/docs/reference/read.ensemble.ts.html b/modules/uncertainty/docs/reference/read.ensemble.ts.html
index d3731df..c36c36c 100644
--- a/modules/uncertainty/docs/reference/read.ensemble.ts.html
+++ b/modules/uncertainty/docs/reference/read.ensemble.ts.html
@@ -2,144 +2,184 @@
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+      — read.ensemble.ts • PEcAn.uncertainty
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Reads an ensemble time-series from PEcAn for the selected target variable</h1>
-    
-    <div class="hidden name"><code>read.ensemble.ts.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>
+              Reads an ensemble time-series from PEcAn for the selected target
+              variable
+            </h1>
+
+            <div class="hidden name"><code>read.ensemble.ts.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Reads ensemble time-series from PEcAn for the selected target
+              variable
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>read.ensemble.ts</span>(<span class='no'>settings</span>, <span class='kw'>ensemble.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>variable</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+  <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
 
-    <div class="ref-description">
-    
-    <p>Reads ensemble time-series from PEcAn for the selected target variable</p>
-    
-    </div>
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
 
-    <pre class="usage"><span class='fu'>read.ensemble.ts</span>(<span class='no'>settings</span>, <span class='kw'>ensemble.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>variable</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
-  <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-        
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      
-      <li><a href="#value">Value</a></li>
+          <p>list</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-Michael Dietze, Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          Michael Dietze, Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
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-<div class="pkgdown">
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-</div>
-
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+          <p>Developed by .</p>
+        </div>
+
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diff --git a/modules/uncertainty/docs/reference/run.ensemble.analysis.html b/modules/uncertainty/docs/reference/run.ensemble.analysis.html
index 1d4737b..895f756 100644
--- a/modules/uncertainty/docs/reference/run.ensemble.analysis.html
+++ b/modules/uncertainty/docs/reference/run.ensemble.analysis.html
@@ -2,155 +2,196 @@
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+                type="button"
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+                  >PEcAn.uncertainty</a
+                >
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+                  class="label label-default"
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+                  title="Released package"
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+            </div>
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+                  <a href="../index.html">
+                    <span class="fa fa-home fa-lg"></span>
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+                  <a href="../reference/index.html">Reference</a>
+                </li>
+              </ul>
+
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+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>run ensemble.analysis</h1>
-    
-    <div class="hidden name"><code>run.ensemble.analysis.Rd</code></div>
-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>run ensemble.analysis</h1>
 
-    <div class="ref-description">
-    
-    <p>run ensemble.analysis</p>
-    
-    </div>
+            <div class="hidden name"><code>run.ensemble.analysis.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>run ensemble.analysis</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>run.ensemble.analysis</span>(<span class='no'>settings</span>, <span class='kw'>plot.timeseries</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>run.ensemble.analysis</span>(<span class='no'>settings</span>, <span class='kw'>plot.timeseries</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
   <span class='kw'>ensemble.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>variable</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>plot.timeseries</th>
-      <td><p>if TRUE plots a modeled timeseries of target variable(s) with CIs</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing, creates ensemble plots as ensemble.analysis.pdf</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>plot.timeseries</th>
+              <td>
+                <p>
+                  if TRUE plots a modeled timeseries of target variable(s) with
+                  CIs
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>nothing, creates ensemble plots as ensemble.analysis.pdf</p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin, Ryan Kelly
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/modules/uncertainty/docs/reference/run.sensitivity.analysis.html b/modules/uncertainty/docs/reference/run.sensitivity.analysis.html
index 8ce5102..b27d0f3 100644
--- a/modules/uncertainty/docs/reference/run.sensitivity.analysis.html
+++ b/modules/uncertainty/docs/reference/run.sensitivity.analysis.html
@@ -2,157 +2,203 @@
 <!DOCTYPE html>
 <html>
   <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
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-
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-<!-- Bootstrap -->
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-    
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-    </div>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>run sensitivity.analysis</h1>
 
-    <div class="ref-description">
-    
-    <p>run sensitivity.analysis</p>
-    
-    </div>
+            <div class="hidden name">
+              <code>run.sensitivity.analysis.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>run sensitivity.analysis</p>
+          </div>
 
-    <pre class="usage"><span class='fu'>run.sensitivity.analysis</span>(<span class='no'>settings</span>, <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>ensemble.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+          <pre
+            class="usage"
+          ><span class='fu'>run.sensitivity.analysis</span>(<span class='no'>settings</span>, <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>ensemble.id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>variable</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>start.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>end.year</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>plot</th>
-      <td><p>logical. Option to generate sensitivity analysis and variance
-decomposition plots (plot=TRUE) or to turn these plots off (plot=FALSE).</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>nothing, saves <code>sensitivity.results</code> as sensitivity.results.Rdata,
-sensitivity plots as sensitivityanalysis.pdf, and variance decomposition 'popsicle plot'
-as variancedecomposition.pdf a side effect (OPTIONAL)</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>plot</th>
+              <td>
+                <p>
+                  logical. Option to generate sensitivity analysis and variance
+                  decomposition plots (plot=TRUE) or to turn these plots off
+                  (plot=FALSE).
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            nothing, saves <code>sensitivity.results</code> as
+            sensitivity.results.Rdata, sensitivity plots as
+            sensitivityanalysis.pdf, and variance decomposition 'popsicle plot'
+            as variancedecomposition.pdf a side effect (OPTIONAL)
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Shawn Serbin, Ryan Kelly
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Shawn Serbin, Ryan Kelly
+        </div>
+      </div>
 
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diff --git a/modules/uncertainty/docs/reference/sa.splinefun.html b/modules/uncertainty/docs/reference/sa.splinefun.html
index bfd048b..2e8afd4 100644
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Sensitivity spline function</h1>
-    
-    <div class="hidden name"><code>sa.splinefun.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Spline estimate of univariate relationship between parameter value and model output</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sa.splinefun</span>(<span class='no'>quantiles.input</span>, <span class='no'>quantiles.output</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>quantiles.input</th>
-      <td></td>
-    </tr>
-    <tr>
-      <th>quantiles.output</th>
-      <td></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>function</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Creates a spline function using the splinefun function that estimates univariate response of parameter input to model output</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Sensitivity spline function</h1>
+
+            <div class="hidden name"><code>sa.splinefun.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Spline estimate of univariate relationship between parameter value
+              and model output
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sa.splinefun</span>(<span class='no'>quantiles.input</span>, <span class='no'>quantiles.output</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>quantiles.input</th>
+              <td></td>
+            </tr>
+            <tr>
+              <th>quantiles.output</th>
+              <td></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>function</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Creates a spline function using the splinefun function that
+            estimates univariate response of parameter input to model output
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
-
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+        </div>
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index b2890e9..56602e2 100644
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Standard deviation of sample variance</h1>
-    
-    <div class="hidden name"><code>sd.var.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Calculates the standard deviation of the variance estimate</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sd.var</span>(<span class='no'>x</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>sample</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>estimate of standard deviation of the sample variance</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Uses the equation ^4(2n-1+n)</p>
-    
-    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
-    <p>Mood, Graybill, Boes 1974 'Introduction to the Theory of Statistics' 3rd ed. p 229; Casella and Berger 'Statistical Inference' p 364 ex. 7.45; 'Reference for Var(s^2)' CrossValidated <a href='http://stats.stackexchange.com/q/29905/1381'>http://stats.stackexchange.com/q/29905/1381</a>, 'Calculating required sample size, precision of variance estimate' CrossValidated <a href='http://stats.stackexchange.com/q/7004/1381'>http://stats.stackexchange.com/q/7004/1381</a>, 'Variance of Sample Variance?' Mathematics - Stack Exchange <a href='http://math.stackexchange.com/q/72975/3733'>http://math.stackexchange.com/q/72975/3733</a></p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-
-      <li><a href="#references">References</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Standard deviation of sample variance</h1>
+
+            <div class="hidden name"><code>sd.var.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Calculates the standard deviation of the variance estimate</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sd.var</span>(<span class='no'>x</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>sample</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>estimate of standard deviation of the sample variance</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>Uses the equation ^4(2n-1+n)</p>
+
+          <h2 class="hasAnchor" id="references">
+            <a class="anchor" href="#references"></a>References
+          </h2>
+
+          <p>
+            Mood, Graybill, Boes 1974 'Introduction to the Theory of Statistics'
+            3rd ed. p 229; Casella and Berger 'Statistical Inference' p 364 ex.
+            7.45; 'Reference for Var(s^2)' CrossValidated
+            <a href="http://stats.stackexchange.com/q/29905/1381"
+              >http://stats.stackexchange.com/q/29905/1381</a
+            >, 'Calculating required sample size, precision of variance
+            estimate' CrossValidated
+            <a href="http://stats.stackexchange.com/q/7004/1381"
+              >http://stats.stackexchange.com/q/7004/1381</a
+            >, 'Variance of Sample Variance?' Mathematics - Stack Exchange
+            <a href="http://math.stackexchange.com/q/72975/3733"
+              >http://math.stackexchange.com/q/72975/3733</a
+            >
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
+
+            <li><a href="#references">References</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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diff --git a/modules/uncertainty/docs/reference/sensitivity.analysis.html b/modules/uncertainty/docs/reference/sensitivity.analysis.html
index a225143..c4195ea 100644
--- a/modules/uncertainty/docs/reference/sensitivity.analysis.html
+++ b/modules/uncertainty/docs/reference/sensitivity.analysis.html
@@ -2,177 +2,249 @@
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Sensitivity Analysis</h1>
-    
-    <div class="hidden name"><code>sensitivity.analysis.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Performs univariate sensitivity analysis and variance decomposition</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>sensitivity.analysis</span>(<span class='no'>trait.samples</span>, <span class='no'>sa.samples</span>, <span class='no'>sa.output</span>, <span class='no'>outdir</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>trait.samples</th>
-      <td><p>list of vectors, one per trait, representing samples of the trait value, with length equal to the mcmc chain length. Samples are taken from either the prior distribution or meta-analysis results</p></td>
-    </tr>
-    <tr>
-      <th>sa.samples</th>
-      <td><p>data.frame with one column per trait and one row for the set of quantiles used in sensitivity analysis. Each cell contains the value of the trait at the given quantile.</p></td>
-    </tr>
-    <tr>
-      <th>sa.output</th>
-      <td><p>list of data.frames, similar to sa.samples, except cells contain the results of a model run with that trait x quantile combination and all other traits held at their median value</p></td>
-    </tr>
-    <tr>
-      <th>outdir</th>
-      <td><p>directory to which plots are written</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>results of sensitivity analysis</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>This function estimates the univariate responses of a model to a parameter for a set of traits, calculates the model sensitivity at the median, and performs a variance decomposition. This function results in a set of sensitivity plots (one per variable) and plot_variance_decomposition.</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Sensitivity Analysis</h1>
+
+            <div class="hidden name"><code>sensitivity.analysis.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Performs univariate sensitivity analysis and variance
+              decomposition
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>sensitivity.analysis</span>(<span class='no'>trait.samples</span>, <span class='no'>sa.samples</span>, <span class='no'>sa.output</span>, <span class='no'>outdir</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>trait.samples</th>
+              <td>
+                <p>
+                  list of vectors, one per trait, representing samples of the
+                  trait value, with length equal to the mcmc chain length.
+                  Samples are taken from either the prior distribution or
+                  meta-analysis results
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sa.samples</th>
+              <td>
+                <p>
+                  data.frame with one column per trait and one row for the set
+                  of quantiles used in sensitivity analysis. Each cell contains
+                  the value of the trait at the given quantile.
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>sa.output</th>
+              <td>
+                <p>
+                  list of data.frames, similar to sa.samples, except cells
+                  contain the results of a model run with that trait x quantile
+                  combination and all other traits held at their median value
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>outdir</th>
+              <td><p>directory to which plots are written</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>results of sensitivity analysis</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            This function estimates the univariate responses of a model to a
+            parameter for a set of traits, calculates the model sensitivity at
+            the median, and performs a variance decomposition. This function
+            results in a set of sensitivity plots (one per variable) and
+            plot_variance_decomposition.
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>sensitivity.analysis</span>(<span class='no'>trait.samples</span><span class='kw'>[[</span><span class='no'>pft</span>$<span class='no'>name</span>]], <span class='no'>sa.samples</span><span class='kw'>[[</span><span class='no'>pft</span>$<span class='no'>name</span>]], <span class='no'>sa.agb</span><span class='kw'>[[</span><span class='no'>pft</span>$<span class='no'>name</span>]], <span class='no'>pft</span>$<span class='no'>outdir</span>)
 <span class='co'># }</span></pre>
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-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
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+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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+            <li><a href="#details">Details</a></li>
 
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+            <li><a href="#examples">Examples</a></li>
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+          <h2>Author</h2>
 
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index e3a88be..536a953 100644
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       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Spline Ensemble</h1>
-    
-    <div class="hidden name"><code>spline.ensemble.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Estimate model output based on univariate splines</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>spline.ensemble</span>(<span class='no'>gi.phii</span>, <span class='no'>median</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>gi.phii</th>
-      <td><p>matrix given as output from <code><a href='get.gi.phii.html'>get.gi.phii</a></code></p></td>
-    </tr>
-    <tr>
-      <th>median</th>
-      <td><p>median value around which variance will be calculated</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Accepts output from get.gi.phii (the matrix $g(_i)$) and produces
-spline estimate of $f(phi)$ for use in estimating closure term associated with
-spline approximation</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Spline Ensemble</h1>
+
+            <div class="hidden name"><code>spline.ensemble.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Estimate model output based on univariate splines</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>spline.ensemble</span>(<span class='no'>gi.phii</span>, <span class='no'>median</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>gi.phii</th>
+              <td>
+                <p>
+                  matrix given as output from
+                  <code><a href="get.gi.phii.html">get.gi.phii</a></code>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>median</th>
+              <td>
+                <p>median value around which variance will be calculated</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Accepts output from get.gi.phii (the matrix $g(_i)$) and produces
+            spline estimate of $f(phi)$ for use in estimating closure term
+            associated with spline approximation
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-David LeBauer
-
-  </div>
-</div>
+          David LeBauer David LeBauer
+        </div>
+      </div>
 
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-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
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 </html>
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diff --git a/modules/uncertainty/docs/reference/spline.truncate.html b/modules/uncertainty/docs/reference/spline.truncate.html
index 3ed888f..d0b360a 100644
--- a/modules/uncertainty/docs/reference/spline.truncate.html
+++ b/modules/uncertainty/docs/reference/spline.truncate.html
@@ -2,177 +2,216 @@
 <!DOCTYPE html>
 <html>
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-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
-
-<!-- sticky kit -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
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+    <meta charset="utf-8" />
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
+    <link
+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+      crossorigin="anonymous"
+    />
+    <script
+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
+      integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa"
+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
+    <link
+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+    />
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
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+      src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js"
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+      crossorigin="anonymous"
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+    <script src="../pkgdown.js"></script>
+
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+    <![endif]-->
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+          <div class="container">
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+                type="button"
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.uncertainty</a
+                >
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+                  class="label label-default"
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+
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+            <!--/.nav-collapse -->
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+          <!--/.container -->
+        </div>
+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Truncate spline</h1>
-    
-    <div class="hidden name"><code>spline.truncate.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Truncate spline at zero if..</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>spline.truncate</span>(<span class='no'>x</span>, <span class='kw'>min.quantile</span> <span class='kw'>=</span> <span class='fu'>pnorm</span>(-<span class='fl'>3</span>))</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>vector</p></td>
-    </tr>
-    <tr>
-      <th>min.quantile</th>
-      <td><p>threshold quantile for testing lower bound on variable</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>either x or a vector with values &lt; 0 converted to zero</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>Truncate spline at zero if P[x&lt;0] &lt; pnorm(-3)
-pnorm(-3) chosen as default value for min quantile
-because this is the default low end of range for the
-sensitivity analysis.
-This parameter could be determined based on minimum value in
-settings$sensitivity.analysis$quantiles</p>
-    
-
-    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><span class='co'># NOT RUN {</span>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Truncate spline</h1>
+
+            <div class="hidden name"><code>spline.truncate.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Truncate spline at zero if..</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>spline.truncate</span>(<span class='no'>x</span>, <span class='kw'>min.quantile</span> <span class='kw'>=</span> <span class='fu'>pnorm</span>(-<span class='fl'>3</span>))</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>vector</p></td>
+            </tr>
+            <tr>
+              <th>min.quantile</th>
+              <td>
+                <p>threshold quantile for testing lower bound on variable</p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>either x or a vector with values &lt; 0 converted to zero</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            Truncate spline at zero if P[x&lt;0] &lt; pnorm(-3) pnorm(-3) chosen
+            as default value for min quantile because this is the default low
+            end of range for the sensitivity analysis. This parameter could be
+            determined based on minimum value in
+            settings$sensitivity.analysis$quantiles
+          </p>
+
+          <h2 class="hasAnchor" id="examples">
+            <a class="anchor" href="#examples"></a>Examples
+          </h2>
+          <pre class="examples"><span class='co'># NOT RUN {</span>
 <span class='fu'>set.seed</span>(<span class='fl'>0</span>)
 <span class='no'>x</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='fu'>rgamma</span>(<span class='fl'>998</span>,<span class='fl'>1</span>,<span class='fl'>1</span>), <span class='fu'>rnorm</span>(<span class='fl'>10</span>))
 <span class='fu'>min</span>(<span class='no'>x</span>) <span class='co'># -0.5238</span>
 <span class='fu'>min</span>(<span class='kw pkg'>PEcAn.uncertainty</span><span class='kw ns'>::</span><span class='fu'><a href='http://www.rdocumentation.org/packages/PEcAn.uncertainty/topics/spline.truncate'>spline.truncate</a></span>(<span class='no'>x</span>))
 <span class='co'># }</span></pre>
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
-      
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
-    <h2>Author</h2>
-    
-David LeBauer
-
-  </div>
-</div>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
+            <li><a href="#value">Value</a></li>
 
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
+            <li><a href="#details">Details</a></li>
 
-      </footer>
-   </div>
+            <li><a href="#examples">Examples</a></li>
+          </ul>
 
-  
+          <h2>Author</h2>
 
+          David LeBauer
+        </div>
+      </div>
+
+      <footer>
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
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-
diff --git a/modules/uncertainty/docs/reference/variance.stats.html b/modules/uncertainty/docs/reference/variance.stats.html
index df190d1..945f127 100644
--- a/modules/uncertainty/docs/reference/variance.stats.html
+++ b/modules/uncertainty/docs/reference/variance.stats.html
@@ -2,159 +2,196 @@
 <!DOCTYPE html>
 <html>
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-<!-- Bootstrap -->
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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+
+    <!-- jquery -->
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+      src="https://code.jquery.com/jquery-3.1.0.min.js"
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+      crossorigin="anonymous"
+    ></script>
+    <!-- Bootstrap -->
+
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+      href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"
+      rel="stylesheet"
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+    />
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+      src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- Font Awesome icons -->
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+      href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css"
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+      crossorigin="anonymous"
+    ></script>
+
+    <!-- sticky kit -->
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+      crossorigin="anonymous"
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+
+    <!-- pkgdown -->
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+    <script src="../pkgdown.js"></script>
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+
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+              <span class="navbar-brand">
+                <a class="navbar-link" href="../index.html"
+                  >PEcAn.uncertainty</a
+                >
+                <span
+                  class="label label-default"
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+                  data-placement="bottom"
+                  title="Released package"
+                  >1.6.0</span
+                >
+              </span>
+            </div>
+
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+              <ul class="nav navbar-nav">
+                <li>
+                  <a href="../index.html">
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>variance statistics</h1>
-    
-    <div class="hidden name"><code>variance.stats.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Variance and SD(variance)</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>variance.stats</span>(<span class='no'>x</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>x</th>
-      <td><p>numeric vector</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list with variance and sd of variance</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>calculates variance and sd of variance using the <code>var</code> from base R and <code><a href='sd.var.html'>sd.var</a></code> from PEcAn.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>variance statistics</h1>
+
+            <div class="hidden name"><code>variance.stats.Rd</code></div>
+          </div>
+
+          <div class="ref-description">
+            <p>Variance and SD(variance)</p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>variance.stats</span>(<span class='no'>x</span>)</pre>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>x</th>
+              <td><p>numeric vector</p></td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>list with variance and sd of variance</p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            calculates variance and sd of variance using the
+            <code>var</code> from base R and
+            <code><a href="sd.var.html">sd.var</a></code> from PEcAn.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer
+        </div>
+      </div>
 
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diff --git a/modules/uncertainty/docs/reference/write.ensemble.configs.html b/modules/uncertainty/docs/reference/write.ensemble.configs.html
index 7b5bcbe..c430700 100644
--- a/modules/uncertainty/docs/reference/write.ensemble.configs.html
+++ b/modules/uncertainty/docs/reference/write.ensemble.configs.html
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 Given a pft.xml object, a list of lists as supplied by get.sa.samples, 
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+        <!--/.navbar -->
       </header>
 
-<div class="row">
-  <div class="col-md-9 contents">
-    <div class="page-header">
-    <h1>Write ensemble config files</h1>
-    
-    <div class="hidden name"><code>write.ensemble.configs.Rd</code></div>
-    </div>
-
-    <div class="ref-description">
-    
-    <p>Writes config files for use in meta-analysis and returns a list of run ids.
-Given a pft.xml object, a list of lists as supplied by get.sa.samples, 
-a name to distinguish the output files, and the directory to place the files.</p>
-    
-    </div>
-
-    <pre class="usage"><span class='fu'>write.ensemble.configs</span>(<span class='no'>defaults</span>, <span class='no'>ensemble.samples</span>, <span class='no'>settings</span>, <span class='no'>model</span>,
+      <div class="row">
+        <div class="col-md-9 contents">
+          <div class="page-header">
+            <h1>Write ensemble config files</h1>
+
+            <div class="hidden name">
+              <code>write.ensemble.configs.Rd</code>
+            </div>
+          </div>
+
+          <div class="ref-description">
+            <p>
+              Writes config files for use in meta-analysis and returns a list of
+              run ids. Given a pft.xml object, a list of lists as supplied by
+              get.sa.samples, a name to distinguish the output files, and the
+              directory to place the files.
+            </p>
+          </div>
+
+          <pre
+            class="usage"
+          ><span class='fu'>write.ensemble.configs</span>(<span class='no'>defaults</span>, <span class='no'>ensemble.samples</span>, <span class='no'>settings</span>, <span class='no'>model</span>,
   <span class='kw'>clean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>write.to.db</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>restart</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
-    <table class="ref-arguments">
-    <colgroup><col class="name" /><col class="desc" /></colgroup>
-    <tr>
-      <th>defaults</th>
-      <td><p>pft</p></td>
-    </tr>
-    <tr>
-      <th>ensemble.samples</th>
-      <td><p>list of lists supplied by <a href='get.ensemble.samples.html'>get.ensemble.samples</a></p></td>
-    </tr>
-    <tr>
-      <th>settings</th>
-      <td><p>list of PEcAn settings</p></td>
-    </tr>
-    <tr>
-      <th>model</th>
-      <td><p>name of model to be run, e.g. "ED2" or "SIPNET"</p></td>
-    </tr>
-    <tr>
-      <th>clean</th>
-      <td><p>remove old output first?</p></td>
-    </tr>
-    <tr>
-      <th>write.to.db</th>
-      <td><p>logical: Record this run in BETY?</p></td>
-    </tr>
-    <tr>
-      <th>restart</th>
-      <td><p>In case this is a continuation of an old simulation. restart needs to be a list with name tags of runid, inputs, new.params (parameters), new.state (initial condition), ensemble.id (ensemble id), start.time and stop.time.See Details.</p></td>
-    </tr>
-    </table>
-    
-    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-    <p>list, containing $runs = data frame of runids, $ensemble.id = the ensemble ID for these runs and $samples with ids and samples used for each tag.  Also writes sensitivity analysis configuration files as a side effect</p>
-    
-    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
-    <p>The restart functionality is developed using model specific functions by calling write_restart.modelname function. First, you need to make sure that this function is already exist for your desired model.See here <a href='https://pecanproject.github.io/pecan-documentation/master/pecan-models.html'>https://pecanproject.github.io/pecan-documentation/master/pecan-models.html</a>
-new state is a dataframe with a different column for each state variable. The number of the rows in this dataframe needs to be the same as the ensemble size.
-State variables that you can use for setting up the intial conditions differs for different models. You may check the documentation of the write_restart.modelname your model.
-The units for the state variables need to be in the PEcAn standard units which can be found in standard_vars.
-new.params also has similar structure to ensemble.samples which is sent as an argument.</p>
-    
-
-  </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      
-      <li><a href="#value">Value</a></li>
-
-      <li><a href="#details">Details</a></li>
+
+          <h2 class="hasAnchor" id="arguments">
+            <a class="anchor" href="#arguments"></a>Arguments
+          </h2>
+          <table class="ref-arguments">
+            <colgroup>
+              <col class="name" />
+              <col class="desc" />
+            </colgroup>
+            <tr>
+              <th>defaults</th>
+              <td><p>pft</p></td>
+            </tr>
+            <tr>
+              <th>ensemble.samples</th>
+              <td>
+                <p>
+                  list of lists supplied by
+                  <a href="get.ensemble.samples.html">get.ensemble.samples</a>
+                </p>
+              </td>
+            </tr>
+            <tr>
+              <th>settings</th>
+              <td><p>list of PEcAn settings</p></td>
+            </tr>
+            <tr>
+              <th>model</th>
+              <td><p>name of model to be run, e.g. "ED2" or "SIPNET"</p></td>
+            </tr>
+            <tr>
+              <th>clean</th>
+              <td><p>remove old output first?</p></td>
+            </tr>
+            <tr>
+              <th>write.to.db</th>
+              <td><p>logical: Record this run in BETY?</p></td>
+            </tr>
+            <tr>
+              <th>restart</th>
+              <td>
+                <p>
+                  In case this is a continuation of an old simulation. restart
+                  needs to be a list with name tags of runid, inputs, new.params
+                  (parameters), new.state (initial condition), ensemble.id
+                  (ensemble id), start.time and stop.time.See Details.
+                </p>
+              </td>
+            </tr>
+          </table>
+
+          <h2 class="hasAnchor" id="value">
+            <a class="anchor" href="#value"></a>Value
+          </h2>
+
+          <p>
+            list, containing $runs = data frame of runids, $ensemble.id = the
+            ensemble ID for these runs and $samples with ids and samples used
+            for each tag. Also writes sensitivity analysis configuration files
+            as a side effect
+          </p>
+
+          <h2 class="hasAnchor" id="details">
+            <a class="anchor" href="#details"></a>Details
+          </h2>
+
+          <p>
+            The restart functionality is developed using model specific
+            functions by calling write_restart.modelname function. First, you
+            need to make sure that this function is already exist for your
+            desired model.See here
+            <a
+              href="https://pecanproject.github.io/pecan-documentation/master/pecan-models.html"
+              >https://pecanproject.github.io/pecan-documentation/master/pecan-models.html</a
+            >
+            new state is a dataframe with a different column for each state
+            variable. The number of the rows in this dataframe needs to be the
+            same as the ensemble size. State variables that you can use for
+            setting up the intial conditions differs for different models. You
+            may check the documentation of the write_restart.modelname your
+            model. The units for the state variables need to be in the PEcAn
+            standard units which can be found in standard_vars. new.params also
+            has similar structure to ensemble.samples which is sent as an
+            argument.
+          </p>
+        </div>
+        <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+          <h2>Contents</h2>
+          <ul class="nav nav-pills nav-stacked">
+            <li><a href="#arguments">Arguments</a></li>
+
+            <li><a href="#value">Value</a></li>
+
+            <li><a href="#details">Details</a></li>
           </ul>
 
-    <h2>Author</h2>
-    
-David LeBauer, Carl Davidson, Hamze Dokoohaki
+          <h2>Author</h2>
 
-  </div>
-</div>
+          David LeBauer, Carl Davidson, Hamze Dokoohaki
+        </div>
+      </div>
 
       <footer>
-      <div class="copyright">
-  <p>Developed by .</p>
-</div>
-
-<div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
-</div>
-
+        <div class="copyright">
+          <p>Developed by .</p>
+        </div>
+
+        <div class="pkgdown">
+          <p>
+            Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.
+          </p>
+        </div>
       </footer>
-   </div>
-
-  
-
+    </div>
   </body>
 </html>
-
diff --git a/owl-carousel/owl.carousel.css b/owl-carousel/owl.carousel.css
index 9197373..f9b6031 100644
--- a/owl-carousel/owl.carousel.css
+++ b/owl-carousel/owl.carousel.css
@@ -12,118 +12,146 @@
   -webkit-tap-highlight-color: transparent;
   /* position relative and z-index fix webkit rendering fonts issue */
   position: relative;
-  z-index: 1; }
-  .owl-carousel .owl-stage {
-    position: relative;
-    -ms-touch-action: pan-Y;
-    -moz-backface-visibility: hidden;
-    /* fix firefox animation glitch */ }
-  .owl-carousel .owl-stage:after {
-    content: ".";
-    display: block;
-    clear: both;
-    visibility: hidden;
-    line-height: 0;
-    height: 0; }
-  .owl-carousel .owl-stage-outer {
-    position: relative;
-    overflow: hidden;
-    /* fix for flashing background */
-    -webkit-transform: translate3d(0px, 0px, 0px); }
-  .owl-carousel .owl-wrapper,
-  .owl-carousel .owl-item {
-    -webkit-backface-visibility: hidden;
-    -moz-backface-visibility: hidden;
-    -ms-backface-visibility: hidden;
-    -webkit-transform: translate3d(0, 0, 0);
-    -moz-transform: translate3d(0, 0, 0);
-    -ms-transform: translate3d(0, 0, 0); }
-  .owl-carousel .owl-item {
-    position: relative;
-    min-height: 1px;
-    float: left;
-    -webkit-backface-visibility: hidden;
-    -webkit-tap-highlight-color: transparent;
-    -webkit-touch-callout: none; }
-  .owl-carousel .owl-item img {
-    display: block;
-    width: 100%; }
-  .owl-carousel .owl-nav.disabled,
-  .owl-carousel .owl-dots.disabled {
-    display: none; }
-  .owl-carousel .owl-nav .owl-prev,
-  .owl-carousel .owl-nav .owl-next,
-  .owl-carousel .owl-dot {
-    cursor: pointer;
-    cursor: hand;
-    -webkit-user-select: none;
-    -khtml-user-select: none;
-    -moz-user-select: none;
-    -ms-user-select: none;
-    user-select: none; }
-  .owl-carousel.owl-loaded {
-    display: block; }
-  .owl-carousel.owl-loading {
-    opacity: 0;
-    display: block; }
-  .owl-carousel.owl-hidden {
-    opacity: 0; }
-  .owl-carousel.owl-refresh .owl-item {
-    visibility: hidden; }
-  .owl-carousel.owl-drag .owl-item {
-    -webkit-user-select: none;
-    -moz-user-select: none;
-    -ms-user-select: none;
-    user-select: none; }
-  .owl-carousel.owl-grab {
-    cursor: move;
-    cursor: grab; }
-  .owl-carousel.owl-rtl {
-    direction: rtl; }
-  .owl-carousel.owl-rtl .owl-item {
-    float: right; }
+  z-index: 1;
+}
+.owl-carousel .owl-stage {
+  position: relative;
+  -ms-touch-action: pan-Y;
+  -moz-backface-visibility: hidden;
+  /* fix firefox animation glitch */
+}
+.owl-carousel .owl-stage:after {
+  content: ".";
+  display: block;
+  clear: both;
+  visibility: hidden;
+  line-height: 0;
+  height: 0;
+}
+.owl-carousel .owl-stage-outer {
+  position: relative;
+  overflow: hidden;
+  /* fix for flashing background */
+  -webkit-transform: translate3d(0px, 0px, 0px);
+}
+.owl-carousel .owl-wrapper,
+.owl-carousel .owl-item {
+  -webkit-backface-visibility: hidden;
+  -moz-backface-visibility: hidden;
+  -ms-backface-visibility: hidden;
+  -webkit-transform: translate3d(0, 0, 0);
+  -moz-transform: translate3d(0, 0, 0);
+  -ms-transform: translate3d(0, 0, 0);
+}
+.owl-carousel .owl-item {
+  position: relative;
+  min-height: 1px;
+  float: left;
+  -webkit-backface-visibility: hidden;
+  -webkit-tap-highlight-color: transparent;
+  -webkit-touch-callout: none;
+}
+.owl-carousel .owl-item img {
+  display: block;
+  width: 100%;
+}
+.owl-carousel .owl-nav.disabled,
+.owl-carousel .owl-dots.disabled {
+  display: none;
+}
+.owl-carousel .owl-nav .owl-prev,
+.owl-carousel .owl-nav .owl-next,
+.owl-carousel .owl-dot {
+  cursor: pointer;
+  cursor: hand;
+  -webkit-user-select: none;
+  -khtml-user-select: none;
+  -moz-user-select: none;
+  -ms-user-select: none;
+  user-select: none;
+}
+.owl-carousel.owl-loaded {
+  display: block;
+}
+.owl-carousel.owl-loading {
+  opacity: 0;
+  display: block;
+}
+.owl-carousel.owl-hidden {
+  opacity: 0;
+}
+.owl-carousel.owl-refresh .owl-item {
+  visibility: hidden;
+}
+.owl-carousel.owl-drag .owl-item {
+  -webkit-user-select: none;
+  -moz-user-select: none;
+  -ms-user-select: none;
+  user-select: none;
+}
+.owl-carousel.owl-grab {
+  cursor: move;
+  cursor: grab;
+}
+.owl-carousel.owl-rtl {
+  direction: rtl;
+}
+.owl-carousel.owl-rtl .owl-item {
+  float: right;
+}
 
 /* No Js */
 .no-js .owl-carousel {
-  display: block; }
+  display: block;
+}
 
 /*
  *  Owl Carousel - Animate Plugin
  */
 .owl-carousel .animated {
   animation-duration: 1000ms;
-  animation-fill-mode: both; }
+  animation-fill-mode: both;
+}
 
 .owl-carousel .owl-animated-in {
-  z-index: 0; }
+  z-index: 0;
+}
 
 .owl-carousel .owl-animated-out {
-  z-index: 1; }
+  z-index: 1;
+}
 
 .owl-carousel .fadeOut {
-  animation-name: fadeOut; }
+  animation-name: fadeOut;
+}
 
 @keyframes fadeOut {
   0% {
-    opacity: 1; }
+    opacity: 1;
+  }
   100% {
-    opacity: 0; } }
+    opacity: 0;
+  }
+}
 
 /*
  * 	Owl Carousel - Auto Height Plugin
  */
 .owl-height {
-  transition: height 500ms ease-in-out; }
+  transition: height 500ms ease-in-out;
+}
 
 /*
  * 	Owl Carousel - Lazy Load Plugin
  */
 .owl-carousel .owl-item .owl-lazy {
   opacity: 0;
-  transition: opacity 400ms ease; }
+  transition: opacity 400ms ease;
+}
 
 .owl-carousel .owl-item img.owl-lazy {
-  transform-style: preserve-3d; }
+  transform-style: preserve-3d;
+}
 
 /*
  * 	Owl Carousel - Video Plugin
@@ -131,7 +159,8 @@
 .owl-carousel .owl-video-wrapper {
   position: relative;
   height: 100%;
-  background: #000; }
+  background: #000;
+}
 
 .owl-carousel .owl-video-play-icon {
   position: absolute;
@@ -145,15 +174,18 @@
   cursor: pointer;
   z-index: 1;
   -webkit-backface-visibility: hidden;
-  transition: transform 100ms ease; }
+  transition: transform 100ms ease;
+}
 
 .owl-carousel .owl-video-play-icon:hover {
   -ms-transform: scale(1.3, 1.3);
-      transform: scale(1.3, 1.3); }
+  transform: scale(1.3, 1.3);
+}
 
 .owl-carousel .owl-video-playing .owl-video-tn,
 .owl-carousel .owl-video-playing .owl-video-play-icon {
-  display: none; }
+  display: none;
+}
 
 .owl-carousel .owl-video-tn {
   opacity: 0;
@@ -161,10 +193,12 @@
   background-position: center center;
   background-repeat: no-repeat;
   background-size: contain;
-  transition: opacity 400ms ease; }
+  transition: opacity 400ms ease;
+}
 
 .owl-carousel .owl-video-frame {
   position: relative;
   z-index: 1;
   height: 100%;
-  width: 100%; }
+  width: 100%;
+}
diff --git a/owl-carousel/owl.carousel.js b/owl-carousel/owl.carousel.js
index c1d3ea7..ab14587 100644
--- a/owl-carousel/owl.carousel.js
+++ b/owl-carousel/owl.carousel.js
@@ -15,1685 +15,1950 @@
  * @todo Test Zepto
  * @todo stagePadding calculate wrong active classes
  */
-;(function($, window, document, undefined) {
-
-	/**
-	 * Creates a carousel.
-	 * @class The Owl Carousel.
-	 * @public
-	 * @param {HTMLElement|jQuery} element - The element to create the carousel for.
-	 * @param {Object} [options] - The options
-	 */
-	function Owl(element, options) {
-
-		/**
-		 * Current settings for the carousel.
-		 * @public
-		 */
-		this.settings = null;
-
-		/**
-		 * Current options set by the caller including defaults.
-		 * @public
-		 */
-		this.options = $.extend({}, Owl.Defaults, options);
-
-		/**
-		 * Plugin element.
-		 * @public
-		 */
-		this.$element = $(element);
-
-		/**
-		 * Proxied event handlers.
-		 * @protected
-		 */
-		this._handlers = {};
-
-		/**
-		 * References to the running plugins of this carousel.
-		 * @protected
-		 */
-		this._plugins = {};
-
-		/**
-		 * Currently suppressed events to prevent them from beeing retriggered.
-		 * @protected
-		 */
-		this._supress = {};
-
-		/**
-		 * Absolute current position.
-		 * @protected
-		 */
-		this._current = null;
-
-		/**
-		 * Animation speed in milliseconds.
-		 * @protected
-		 */
-		this._speed = null;
-
-		/**
-		 * Coordinates of all items in pixel.
-		 * @todo The name of this member is missleading.
-		 * @protected
-		 */
-		this._coordinates = [];
-
-		/**
-		 * Current breakpoint.
-		 * @todo Real media queries would be nice.
-		 * @protected
-		 */
-		this._breakpoint = null;
-
-		/**
-		 * Current width of the plugin element.
-		 */
-		this._width = null;
-
-		/**
-		 * All real items.
-		 * @protected
-		 */
-		this._items = [];
-
-		/**
-		 * All cloned items.
-		 * @protected
-		 */
-		this._clones = [];
-
-		/**
-		 * Merge values of all items.
-		 * @todo Maybe this could be part of a plugin.
-		 * @protected
-		 */
-		this._mergers = [];
-
-		/**
-		 * Widths of all items.
-		 */
-		this._widths = [];
-
-		/**
-		 * Invalidated parts within the update process.
-		 * @protected
-		 */
-		this._invalidated = {};
-
-		/**
-		 * Ordered list of workers for the update process.
-		 * @protected
-		 */
-		this._pipe = [];
-
-		/**
-		 * Current state information for the drag operation.
-		 * @todo #261
-		 * @protected
-		 */
-		this._drag = {
-			time: null,
-			target: null,
-			pointer: null,
-			stage: {
-				start: null,
-				current: null
-			},
-			direction: null
-		};
-
-		/**
-		 * Current state information and their tags.
-		 * @type {Object}
-		 * @protected
-		 */
-		this._states = {
-			current: {},
-			tags: {
-				'initializing': [ 'busy' ],
-				'animating': [ 'busy' ],
-				'dragging': [ 'interacting' ]
-			}
-		};
-
-		$.each([ 'onResize', 'onThrottledResize' ], $.proxy(function(i, handler) {
-			this._handlers[handler] = $.proxy(this[handler], this);
-		}, this));
-
-		$.each(Owl.Plugins, $.proxy(function(key, plugin) {
-			this._plugins[key.charAt(0).toLowerCase() + key.slice(1)]
-				= new plugin(this);
-		}, this));
-
-		$.each(Owl.Workers, $.proxy(function(priority, worker) {
-			this._pipe.push({
-				'filter': worker.filter,
-				'run': $.proxy(worker.run, this)
-			});
-		}, this));
-
-		this.setup();
-		this.initialize();
-	}
-
-	/**
-	 * Default options for the carousel.
-	 * @public
-	 */
-	Owl.Defaults = {
-		items: 3,
-		loop: false,
-		center: false,
-		rewind: false,
-
-		mouseDrag: true,
-		touchDrag: true,
-		pullDrag: true,
-		freeDrag: false,
-
-		margin: 0,
-		stagePadding: 0,
-
-		merge: false,
-		mergeFit: true,
-		autoWidth: false,
-
-		startPosition: 0,
-		rtl: false,
-
-		smartSpeed: 250,
-		fluidSpeed: false,
-		dragEndSpeed: false,
-
-		responsive: {},
-		responsiveRefreshRate: 200,
-		responsiveBaseElement: window,
-
-		fallbackEasing: 'swing',
-
-		info: false,
-
-		nestedItemSelector: false,
-		itemElement: 'div',
-		stageElement: 'div',
-
-		refreshClass: 'owl-refresh',
-		loadedClass: 'owl-loaded',
-		loadingClass: 'owl-loading',
-		rtlClass: 'owl-rtl',
-		responsiveClass: 'owl-responsive',
-		dragClass: 'owl-drag',
-		itemClass: 'owl-item',
-		stageClass: 'owl-stage',
-		stageOuterClass: 'owl-stage-outer',
-		grabClass: 'owl-grab'
-	};
-
-	/**
-	 * Enumeration for width.
-	 * @public
-	 * @readonly
-	 * @enum {String}
-	 */
-	Owl.Width = {
-		Default: 'default',
-		Inner: 'inner',
-		Outer: 'outer'
-	};
-
-	/**
-	 * Enumeration for types.
-	 * @public
-	 * @readonly
-	 * @enum {String}
-	 */
-	Owl.Type = {
-		Event: 'event',
-		State: 'state'
-	};
-
-	/**
-	 * Contains all registered plugins.
-	 * @public
-	 */
-	Owl.Plugins = {};
-
-	/**
-	 * List of workers involved in the update process.
-	 */
-	Owl.Workers = [ {
-		filter: [ 'width', 'settings' ],
-		run: function() {
-			this._width = this.$element.width();
-		}
-	}, {
-		filter: [ 'width', 'items', 'settings' ],
-		run: function(cache) {
-			cache.current = this._items && this._items[this.relative(this._current)];
-		}
-	}, {
-		filter: [ 'items', 'settings' ],
-		run: function() {
-			this.$stage.children('.cloned').remove();
-		}
-	}, {
-		filter: [ 'width', 'items', 'settings' ],
-		run: function(cache) {
-			var margin = this.settings.margin || '',
-				grid = !this.settings.autoWidth,
-				rtl = this.settings.rtl,
-				css = {
-					'width': 'auto',
-					'margin-left': rtl ? margin : '',
-					'margin-right': rtl ? '' : margin
-				};
-
-			!grid && this.$stage.children().css(css);
-
-			cache.css = css;
-		}
-	}, {
-		filter: [ 'width', 'items', 'settings' ],
-		run: function(cache) {
-			var width = (this.width() / this.settings.items).toFixed(3) - this.settings.margin,
-				merge = null,
-				iterator = this._items.length,
-				grid = !this.settings.autoWidth,
-				widths = [];
-
-			cache.items = {
-				merge: false,
-				width: width
-			};
-
-			while (iterator--) {
-				merge = this._mergers[iterator];
-				merge = this.settings.mergeFit && Math.min(merge, this.settings.items) || merge;
-
-				cache.items.merge = merge > 1 || cache.items.merge;
-
-				widths[iterator] = !grid ? this._items[iterator].width() : width * merge;
-			}
-
-			this._widths = widths;
-		}
-	}, {
-		filter: [ 'items', 'settings' ],
-		run: function() {
-			var clones = [],
-				items = this._items,
-				settings = this.settings,
-				// TODO: Should be computed from number of min width items in stage
-				view = Math.max(settings.items * 2, 4),
-				size = Math.ceil(items.length / 2) * 2,
-				repeat = settings.loop && items.length ? settings.rewind ? view : Math.max(view, size) : 0,
-				append = '',
-				prepend = '';
-
-			repeat /= 2;
-
-			while (repeat--) {
-				// Switch to only using appended clones
-				clones.push(this.normalize(clones.length / 2, true));
-				append = append + items[clones[clones.length - 1]][0].outerHTML;
-				clones.push(this.normalize(items.length - 1 - (clones.length - 1) / 2, true));
-				prepend = items[clones[clones.length - 1]][0].outerHTML + prepend;
-			}
-
-			this._clones = clones;
-
-			$(append).addClass('cloned').appendTo(this.$stage);
-			$(prepend).addClass('cloned').prependTo(this.$stage);
-		}
-	}, {
-		filter: [ 'width', 'items', 'settings' ],
-		run: function() {
-			var rtl = this.settings.rtl ? 1 : -1,
-				size = this._clones.length + this._items.length,
-				iterator = -1,
-				previous = 0,
-				current = 0,
-				coordinates = [];
-
-			while (++iterator < size) {
-				previous = coordinates[iterator - 1] || 0;
-				current = this._widths[this.relative(iterator)] + this.settings.margin;
-				coordinates.push(previous + current * rtl);
-			}
-
-			this._coordinates = coordinates;
-		}
-	}, {
-		filter: [ 'width', 'items', 'settings' ],
-		run: function() {
-			var padding = this.settings.stagePadding,
-				coordinates = this._coordinates,
-				css = {
-					'width': Math.ceil(Math.abs(coordinates[coordinates.length - 1])) + padding * 2,
-					'padding-left': padding || '',
-					'padding-right': padding || ''
-				};
-
-			this.$stage.css(css);
-		}
-	}, {
-		filter: [ 'width', 'items', 'settings' ],
-		run: function(cache) {
-			var iterator = this._coordinates.length,
-				grid = !this.settings.autoWidth,
-				items = this.$stage.children();
-
-			if (grid && cache.items.merge) {
-				while (iterator--) {
-					cache.css.width = this._widths[this.relative(iterator)];
-					items.eq(iterator).css(cache.css);
-				}
-			} else if (grid) {
-				cache.css.width = cache.items.width;
-				items.css(cache.css);
-			}
-		}
-	}, {
-		filter: [ 'items' ],
-		run: function() {
-			this._coordinates.length < 1 && this.$stage.removeAttr('style');
-		}
-	}, {
-		filter: [ 'width', 'items', 'settings' ],
-		run: function(cache) {
-			cache.current = cache.current ? this.$stage.children().index(cache.current) : 0;
-			cache.current = Math.max(this.minimum(), Math.min(this.maximum(), cache.current));
-			this.reset(cache.current);
-		}
-	}, {
-		filter: [ 'position' ],
-		run: function() {
-			this.animate(this.coordinates(this._current));
-		}
-	}, {
-		filter: [ 'width', 'position', 'items', 'settings' ],
-		run: function() {
-			var rtl = this.settings.rtl ? 1 : -1,
-				padding = this.settings.stagePadding * 2,
-				begin = this.coordinates(this.current()) + padding,
-				end = begin + this.width() * rtl,
-				inner, outer, matches = [], i, n;
-
-			for (i = 0, n = this._coordinates.length; i < n; i++) {
-				inner = this._coordinates[i - 1] || 0;
-				outer = Math.abs(this._coordinates[i]) + padding * rtl;
-
-				if ((this.op(inner, '<=', begin) && (this.op(inner, '>', end)))
-					|| (this.op(outer, '<', begin) && this.op(outer, '>', end))) {
-					matches.push(i);
-				}
-			}
-
-			this.$stage.children('.active').removeClass('active');
-			this.$stage.children(':eq(' + matches.join('), :eq(') + ')').addClass('active');
-
-			if (this.settings.center) {
-				this.$stage.children('.center').removeClass('center');
-				this.$stage.children().eq(this.current()).addClass('center');
-			}
-		}
-	} ];
-
-	/**
-	 * Initializes the carousel.
-	 * @protected
-	 */
-	Owl.prototype.initialize = function() {
-		this.enter('initializing');
-		this.trigger('initialize');
-
-		this.$element.toggleClass(this.settings.rtlClass, this.settings.rtl);
-
-		if (this.settings.autoWidth && !this.is('pre-loading')) {
-			var imgs, nestedSelector, width;
-			imgs = this.$element.find('img');
-			nestedSelector = this.settings.nestedItemSelector ? '.' + this.settings.nestedItemSelector : undefined;
-			width = this.$element.children(nestedSelector).width();
-
-			if (imgs.length && width <= 0) {
-				this.preloadAutoWidthImages(imgs);
-			}
-		}
-
-		this.$element.addClass(this.options.loadingClass);
-
-		// create stage
-		this.$stage = $('<' + this.settings.stageElement + ' class="' + this.settings.stageClass + '"/>')
-			.wrap('<div class="' + this.settings.stageOuterClass + '"/>');
-
-		// append stage
-		this.$element.append(this.$stage.parent());
-
-		// append content
-		this.replace(this.$element.children().not(this.$stage.parent()));
-
-		// check visibility
-		if (this.$element.is(':visible')) {
-			// update view
-			this.refresh();
-		} else {
-			// invalidate width
-			this.invalidate('width');
-		}
-
-		this.$element
-			.removeClass(this.options.loadingClass)
-			.addClass(this.options.loadedClass);
-
-		// register event handlers
-		this.registerEventHandlers();
-
-		this.leave('initializing');
-		this.trigger('initialized');
-	};
-
-	/**
-	 * Setups the current settings.
-	 * @todo Remove responsive classes. Why should adaptive designs be brought into IE8?
-	 * @todo Support for media queries by using `matchMedia` would be nice.
-	 * @public
-	 */
-	Owl.prototype.setup = function() {
-		var viewport = this.viewport(),
-			overwrites = this.options.responsive,
-			match = -1,
-			settings = null;
-
-		if (!overwrites) {
-			settings = $.extend({}, this.options);
-		} else {
-			$.each(overwrites, function(breakpoint) {
-				if (breakpoint <= viewport && breakpoint > match) {
-					match = Number(breakpoint);
-				}
-			});
-
-			settings = $.extend({}, this.options, overwrites[match]);
-			if (typeof settings.stagePadding === 'function') {
-				settings.stagePadding = settings.stagePadding();
-			}
-			delete settings.responsive;
-
-			// responsive class
-			if (settings.responsiveClass) {
-				this.$element.attr('class',
-					this.$element.attr('class').replace(new RegExp('(' + this.options.responsiveClass + '-)\\S+\\s', 'g'), '$1' + match)
-				);
-			}
-		}
-
-		this.trigger('change', { property: { name: 'settings', value: settings } });
-		this._breakpoint = match;
-		this.settings = settings;
-		this.invalidate('settings');
-		this.trigger('changed', { property: { name: 'settings', value: this.settings } });
-	};
-
-	/**
-	 * Updates option logic if necessery.
-	 * @protected
-	 */
-	Owl.prototype.optionsLogic = function() {
-		if (this.settings.autoWidth) {
-			this.settings.stagePadding = false;
-			this.settings.merge = false;
-		}
-	};
-
-	/**
-	 * Prepares an item before add.
-	 * @todo Rename event parameter `content` to `item`.
-	 * @protected
-	 * @returns {jQuery|HTMLElement} - The item container.
-	 */
-	Owl.prototype.prepare = function(item) {
-		var event = this.trigger('prepare', { content: item });
-
-		if (!event.data) {
-			event.data = $('<' + this.settings.itemElement + '/>')
-				.addClass(this.options.itemClass).append(item)
-		}
-
-		this.trigger('prepared', { content: event.data });
-
-		return event.data;
-	};
-
-	/**
-	 * Updates the view.
-	 * @public
-	 */
-	Owl.prototype.update = function() {
-		var i = 0,
-			n = this._pipe.length,
-			filter = $.proxy(function(p) { return this[p] }, this._invalidated),
-			cache = {};
-
-		while (i < n) {
-			if (this._invalidated.all || $.grep(this._pipe[i].filter, filter).length > 0) {
-				this._pipe[i].run(cache);
-			}
-			i++;
-		}
-
-		this._invalidated = {};
-
-		!this.is('valid') && this.enter('valid');
-	};
-
-	/**
-	 * Gets the width of the view.
-	 * @public
-	 * @param {Owl.Width} [dimension=Owl.Width.Default] - The dimension to return.
-	 * @returns {Number} - The width of the view in pixel.
-	 */
-	Owl.prototype.width = function(dimension) {
-		dimension = dimension || Owl.Width.Default;
-		switch (dimension) {
-			case Owl.Width.Inner:
-			case Owl.Width.Outer:
-				return this._width;
-			default:
-				return this._width - this.settings.stagePadding * 2 + this.settings.margin;
-		}
-	};
-
-	/**
-	 * Refreshes the carousel primarily for adaptive purposes.
-	 * @public
-	 */
-	Owl.prototype.refresh = function() {
-		this.enter('refreshing');
-		this.trigger('refresh');
-
-		this.setup();
-
-		this.optionsLogic();
-
-		this.$element.addClass(this.options.refreshClass);
-
-		this.update();
-
-		this.$element.removeClass(this.options.refreshClass);
-
-		this.leave('refreshing');
-		this.trigger('refreshed');
-	};
-
-	/**
-	 * Checks window `resize` event.
-	 * @protected
-	 */
-	Owl.prototype.onThrottledResize = function() {
-		window.clearTimeout(this.resizeTimer);
-		this.resizeTimer = window.setTimeout(this._handlers.onResize, this.settings.responsiveRefreshRate);
-	};
-
-	/**
-	 * Checks window `resize` event.
-	 * @protected
-	 */
-	Owl.prototype.onResize = function() {
-		if (!this._items.length) {
-			return false;
-		}
-
-		if (this._width === this.$element.width()) {
-			return false;
-		}
-
-		if (!this.$element.is(':visible')) {
-			return false;
-		}
-
-		this.enter('resizing');
-
-		if (this.trigger('resize').isDefaultPrevented()) {
-			this.leave('resizing');
-			return false;
-		}
-
-		this.invalidate('width');
-
-		this.refresh();
-
-		this.leave('resizing');
-		this.trigger('resized');
-	};
-
-	/**
-	 * Registers event handlers.
-	 * @todo Check `msPointerEnabled`
-	 * @todo #261
-	 * @protected
-	 */
-	Owl.prototype.registerEventHandlers = function() {
-		if ($.support.transition) {
-			this.$stage.on($.support.transition.end + '.owl.core', $.proxy(this.onTransitionEnd, this));
-		}
-
-		if (this.settings.responsive !== false) {
-			this.on(window, 'resize', this._handlers.onThrottledResize);
-		}
-
-		if (this.settings.mouseDrag) {
-			this.$element.addClass(this.options.dragClass);
-			this.$stage.on('mousedown.owl.core', $.proxy(this.onDragStart, this));
-			this.$stage.on('dragstart.owl.core selectstart.owl.core', function() { return false });
-		}
-
-		if (this.settings.touchDrag){
-			this.$stage.on('touchstart.owl.core', $.proxy(this.onDragStart, this));
-			this.$stage.on('touchcancel.owl.core', $.proxy(this.onDragEnd, this));
-		}
-	};
-
-	/**
-	 * Handles `touchstart` and `mousedown` events.
-	 * @todo Horizontal swipe threshold as option
-	 * @todo #261
-	 * @protected
-	 * @param {Event} event - The event arguments.
-	 */
-	Owl.prototype.onDragStart = function(event) {
-		var stage = null;
-
-		if (event.which === 3) {
-			return;
-		}
-
-		if ($.support.transform) {
-			stage = this.$stage.css('transform').replace(/.*\(|\)| /g, '').split(',');
-			stage = {
-				x: stage[stage.length === 16 ? 12 : 4],
-				y: stage[stage.length === 16 ? 13 : 5]
-			};
-		} else {
-			stage = this.$stage.position();
-			stage = {
-				x: this.settings.rtl ?
-					stage.left + this.$stage.width() - this.width() + this.settings.margin :
-					stage.left,
-				y: stage.top
-			};
-		}
-
-		if (this.is('animating')) {
-			$.support.transform ? this.animate(stage.x) : this.$stage.stop()
-			this.invalidate('position');
-		}
-
-		this.$element.toggleClass(this.options.grabClass, event.type === 'mousedown');
-
-		this.speed(0);
-
-		this._drag.time = new Date().getTime();
-		this._drag.target = $(event.target);
-		this._drag.stage.start = stage;
-		this._drag.stage.current = stage;
-		this._drag.pointer = this.pointer(event);
-
-		$(document).on('mouseup.owl.core touchend.owl.core', $.proxy(this.onDragEnd, this));
-
-		$(document).one('mousemove.owl.core touchmove.owl.core', $.proxy(function(event) {
-			var delta = this.difference(this._drag.pointer, this.pointer(event));
-
-			$(document).on('mousemove.owl.core touchmove.owl.core', $.proxy(this.onDragMove, this));
-
-			if (Math.abs(delta.x) < Math.abs(delta.y) && this.is('valid')) {
-				return;
-			}
-
-			event.preventDefault();
-
-			this.enter('dragging');
-			this.trigger('drag');
-		}, this));
-	};
-
-	/**
-	 * Handles the `touchmove` and `mousemove` events.
-	 * @todo #261
-	 * @protected
-	 * @param {Event} event - The event arguments.
-	 */
-	Owl.prototype.onDragMove = function(event) {
-		var minimum = null,
-			maximum = null,
-			pull = null,
-			delta = this.difference(this._drag.pointer, this.pointer(event)),
-			stage = this.difference(this._drag.stage.start, delta);
-
-		if (!this.is('dragging')) {
-			return;
-		}
-
-		event.preventDefault();
-
-		if (this.settings.loop) {
-			minimum = this.coordinates(this.minimum());
-			maximum = this.coordinates(this.maximum() + 1) - minimum;
-			stage.x = (((stage.x - minimum) % maximum + maximum) % maximum) + minimum;
-		} else {
-			minimum = this.settings.rtl ? this.coordinates(this.maximum()) : this.coordinates(this.minimum());
-			maximum = this.settings.rtl ? this.coordinates(this.minimum()) : this.coordinates(this.maximum());
-			pull = this.settings.pullDrag ? -1 * delta.x / 5 : 0;
-			stage.x = Math.max(Math.min(stage.x, minimum + pull), maximum + pull);
-		}
-
-		this._drag.stage.current = stage;
-
-		this.animate(stage.x);
-	};
-
-	/**
-	 * Handles the `touchend` and `mouseup` events.
-	 * @todo #261
-	 * @todo Threshold for click event
-	 * @protected
-	 * @param {Event} event - The event arguments.
-	 */
-	Owl.prototype.onDragEnd = function(event) {
-		var delta = this.difference(this._drag.pointer, this.pointer(event)),
-			stage = this._drag.stage.current,
-			direction = delta.x > 0 ^ this.settings.rtl ? 'left' : 'right';
-
-		$(document).off('.owl.core');
-
-		this.$element.removeClass(this.options.grabClass);
-
-		if (delta.x !== 0 && this.is('dragging') || !this.is('valid')) {
-			this.speed(this.settings.dragEndSpeed || this.settings.smartSpeed);
-			this.current(this.closest(stage.x, delta.x !== 0 ? direction : this._drag.direction));
-			this.invalidate('position');
-			this.update();
-
-			this._drag.direction = direction;
-
-			if (Math.abs(delta.x) > 3 || new Date().getTime() - this._drag.time > 300) {
-				this._drag.target.one('click.owl.core', function() { return false; });
-			}
-		}
-
-		if (!this.is('dragging')) {
-			return;
-		}
-
-		this.leave('dragging');
-		this.trigger('dragged');
-	};
-
-	/**
-	 * Gets absolute position of the closest item for a coordinate.
-	 * @todo Setting `freeDrag` makes `closest` not reusable. See #165.
-	 * @protected
-	 * @param {Number} coordinate - The coordinate in pixel.
-	 * @param {String} direction - The direction to check for the closest item. Ether `left` or `right`.
-	 * @return {Number} - The absolute position of the closest item.
-	 */
-	Owl.prototype.closest = function(coordinate, direction) {
-		var position = -1,
-			pull = 30,
-			width = this.width(),
-			coordinates = this.coordinates();
-
-		if (!this.settings.freeDrag) {
-			// check closest item
-			$.each(coordinates, $.proxy(function(index, value) {
-				// on a left pull, check on current index
-				if (direction === 'left' && coordinate > value - pull && coordinate < value + pull) {
-					position = index;
-				// on a right pull, check on previous index
-				// to do so, subtract width from value and set position = index + 1
-				} else if (direction === 'right' && coordinate > value - width - pull && coordinate < value - width + pull) {
-					position = index + 1;
-				} else if (this.op(coordinate, '<', value)
-					&& this.op(coordinate, '>', coordinates[index + 1] || value - width)) {
-					position = direction === 'left' ? index + 1 : index;
-				}
-				return position === -1;
-			}, this));
-		}
-
-		if (!this.settings.loop) {
-			// non loop boundries
-			if (this.op(coordinate, '>', coordinates[this.minimum()])) {
-				position = coordinate = this.minimum();
-			} else if (this.op(coordinate, '<', coordinates[this.maximum()])) {
-				position = coordinate = this.maximum();
-			}
-		}
-
-		return position;
-	};
-
-	/**
-	 * Animates the stage.
-	 * @todo #270
-	 * @public
-	 * @param {Number} coordinate - The coordinate in pixels.
-	 */
-	Owl.prototype.animate = function(coordinate) {
-		var animate = this.speed() > 0;
-
-		this.is('animating') && this.onTransitionEnd();
-
-		if (animate) {
-			this.enter('animating');
-			this.trigger('translate');
-		}
-
-		if ($.support.transform3d && $.support.transition) {
-			this.$stage.css({
-				transform: 'translate3d(' + coordinate + 'px,0px,0px)',
-				transition: (this.speed() / 1000) + 's'
-			});
-		} else if (animate) {
-			this.$stage.animate({
-				left: coordinate + 'px'
-			}, this.speed(), this.settings.fallbackEasing, $.proxy(this.onTransitionEnd, this));
-		} else {
-			this.$stage.css({
-				left: coordinate + 'px'
-			});
-		}
-	};
-
-	/**
-	 * Checks whether the carousel is in a specific state or not.
-	 * @param {String} state - The state to check.
-	 * @returns {Boolean} - The flag which indicates if the carousel is busy.
-	 */
-	Owl.prototype.is = function(state) {
-		return this._states.current[state] && this._states.current[state] > 0;
-	};
-
-	/**
-	 * Sets the absolute position of the current item.
-	 * @public
-	 * @param {Number} [position] - The new absolute position or nothing to leave it unchanged.
-	 * @returns {Number} - The absolute position of the current item.
-	 */
-	Owl.prototype.current = function(position) {
-		if (position === undefined) {
-			return this._current;
-		}
-
-		if (this._items.length === 0) {
-			return undefined;
-		}
-
-		position = this.normalize(position);
-
-		if (this._current !== position) {
-			var event = this.trigger('change', { property: { name: 'position', value: position } });
-
-			if (event.data !== undefined) {
-				position = this.normalize(event.data);
-			}
-
-			this._current = position;
-
-			this.invalidate('position');
-
-			this.trigger('changed', { property: { name: 'position', value: this._current } });
-		}
-
-		return this._current;
-	};
-
-	/**
-	 * Invalidates the given part of the update routine.
-	 * @param {String} [part] - The part to invalidate.
-	 * @returns {Array.<String>} - The invalidated parts.
-	 */
-	Owl.prototype.invalidate = function(part) {
-		if ($.type(part) === 'string') {
-			this._invalidated[part] = true;
-			this.is('valid') && this.leave('valid');
-		}
-		return $.map(this._invalidated, function(v, i) { return i });
-	};
-
-	/**
-	 * Resets the absolute position of the current item.
-	 * @public
-	 * @param {Number} position - The absolute position of the new item.
-	 */
-	Owl.prototype.reset = function(position) {
-		position = this.normalize(position);
-
-		if (position === undefined) {
-			return;
-		}
-
-		this._speed = 0;
-		this._current = position;
-
-		this.suppress([ 'translate', 'translated' ]);
-
-		this.animate(this.coordinates(position));
-
-		this.release([ 'translate', 'translated' ]);
-	};
-
-	/**
-	 * Normalizes an absolute or a relative position of an item.
-	 * @public
-	 * @param {Number} position - The absolute or relative position to normalize.
-	 * @param {Boolean} [relative=false] - Whether the given position is relative or not.
-	 * @returns {Number} - The normalized position.
-	 */
-	Owl.prototype.normalize = function(position, relative) {
-		var n = this._items.length,
-			m = relative ? 0 : this._clones.length;
-
-		if (!this.isNumeric(position) || n < 1) {
-			position = undefined;
-		} else if (position < 0 || position >= n + m) {
-			position = ((position - m / 2) % n + n) % n + m / 2;
-		}
-
-		return position;
-	};
-
-	/**
-	 * Converts an absolute position of an item into a relative one.
-	 * @public
-	 * @param {Number} position - The absolute position to convert.
-	 * @returns {Number} - The converted position.
-	 */
-	Owl.prototype.relative = function(position) {
-		position -= this._clones.length / 2;
-		return this.normalize(position, true);
-	};
-
-	/**
-	 * Gets the maximum position for the current item.
-	 * @public
-	 * @param {Boolean} [relative=false] - Whether to return an absolute position or a relative position.
-	 * @returns {Number}
-	 */
-	Owl.prototype.maximum = function(relative) {
-		var settings = this.settings,
-			maximum = this._coordinates.length,
-			iterator,
-			reciprocalItemsWidth,
-			elementWidth;
-
-		if (settings.loop) {
-			maximum = this._clones.length / 2 + this._items.length - 1;
-		} else if (settings.autoWidth || settings.merge) {
-			iterator = this._items.length;
-			reciprocalItemsWidth = this._items[--iterator].width();
-			elementWidth = this.$element.width();
-			while (iterator--) {
-				reciprocalItemsWidth += this._items[iterator].width() + this.settings.margin;
-				if (reciprocalItemsWidth > elementWidth) {
-					break;
-				}
-			}
-			maximum = iterator + 1;
-		} else if (settings.center) {
-			maximum = this._items.length - 1;
-		} else {
-			maximum = this._items.length - settings.items;
-		}
-
-		if (relative) {
-			maximum -= this._clones.length / 2;
-		}
-
-		return Math.max(maximum, 0);
-	};
-
-	/**
-	 * Gets the minimum position for the current item.
-	 * @public
-	 * @param {Boolean} [relative=false] - Whether to return an absolute position or a relative position.
-	 * @returns {Number}
-	 */
-	Owl.prototype.minimum = function(relative) {
-		return relative ? 0 : this._clones.length / 2;
-	};
-
-	/**
-	 * Gets an item at the specified relative position.
-	 * @public
-	 * @param {Number} [position] - The relative position of the item.
-	 * @return {jQuery|Array.<jQuery>} - The item at the given position or all items if no position was given.
-	 */
-	Owl.prototype.items = function(position) {
-		if (position === undefined) {
-			return this._items.slice();
-		}
-
-		position = this.normalize(position, true);
-		return this._items[position];
-	};
-
-	/**
-	 * Gets an item at the specified relative position.
-	 * @public
-	 * @param {Number} [position] - The relative position of the item.
-	 * @return {jQuery|Array.<jQuery>} - The item at the given position or all items if no position was given.
-	 */
-	Owl.prototype.mergers = function(position) {
-		if (position === undefined) {
-			return this._mergers.slice();
-		}
-
-		position = this.normalize(position, true);
-		return this._mergers[position];
-	};
-
-	/**
-	 * Gets the absolute positions of clones for an item.
-	 * @public
-	 * @param {Number} [position] - The relative position of the item.
-	 * @returns {Array.<Number>} - The absolute positions of clones for the item or all if no position was given.
-	 */
-	Owl.prototype.clones = function(position) {
-		var odd = this._clones.length / 2,
-			even = odd + this._items.length,
-			map = function(index) { return index % 2 === 0 ? even + index / 2 : odd - (index + 1) / 2 };
-
-		if (position === undefined) {
-			return $.map(this._clones, function(v, i) { return map(i) });
-		}
-
-		return $.map(this._clones, function(v, i) { return v === position ? map(i) : null });
-	};
-
-	/**
-	 * Sets the current animation speed.
-	 * @public
-	 * @param {Number} [speed] - The animation speed in milliseconds or nothing to leave it unchanged.
-	 * @returns {Number} - The current animation speed in milliseconds.
-	 */
-	Owl.prototype.speed = function(speed) {
-		if (speed !== undefined) {
-			this._speed = speed;
-		}
-
-		return this._speed;
-	};
-
-	/**
-	 * Gets the coordinate of an item.
-	 * @todo The name of this method is missleanding.
-	 * @public
-	 * @param {Number} position - The absolute position of the item within `minimum()` and `maximum()`.
-	 * @returns {Number|Array.<Number>} - The coordinate of the item in pixel or all coordinates.
-	 */
-	Owl.prototype.coordinates = function(position) {
-		var multiplier = 1,
-			newPosition = position - 1,
-			coordinate;
-
-		if (position === undefined) {
-			return $.map(this._coordinates, $.proxy(function(coordinate, index) {
-				return this.coordinates(index);
-			}, this));
-		}
-
-		if (this.settings.center) {
-			if (this.settings.rtl) {
-				multiplier = -1;
-				newPosition = position + 1;
-			}
-
-			coordinate = this._coordinates[position];
-			coordinate += (this.width() - coordinate + (this._coordinates[newPosition] || 0)) / 2 * multiplier;
-		} else {
-			coordinate = this._coordinates[newPosition] || 0;
-		}
-
-		coordinate = Math.ceil(coordinate);
-
-		return coordinate;
-	};
-
-	/**
-	 * Calculates the speed for a translation.
-	 * @protected
-	 * @param {Number} from - The absolute position of the start item.
-	 * @param {Number} to - The absolute position of the target item.
-	 * @param {Number} [factor=undefined] - The time factor in milliseconds.
-	 * @returns {Number} - The time in milliseconds for the translation.
-	 */
-	Owl.prototype.duration = function(from, to, factor) {
-		if (factor === 0) {
-			return 0;
-		}
-
-		return Math.min(Math.max(Math.abs(to - from), 1), 6) * Math.abs((factor || this.settings.smartSpeed));
-	};
-
-	/**
-	 * Slides to the specified item.
-	 * @public
-	 * @param {Number} position - The position of the item.
-	 * @param {Number} [speed] - The time in milliseconds for the transition.
-	 */
-	Owl.prototype.to = function(position, speed) {
-		var current = this.current(),
-			revert = null,
-			distance = position - this.relative(current),
-			direction = (distance > 0) - (distance < 0),
-			items = this._items.length,
-			minimum = this.minimum(),
-			maximum = this.maximum();
-
-		if (this.settings.loop) {
-			if (!this.settings.rewind && Math.abs(distance) > items / 2) {
-				distance += direction * -1 * items;
-			}
-
-			position = current + distance;
-			revert = ((position - minimum) % items + items) % items + minimum;
-
-			if (revert !== position && revert - distance <= maximum && revert - distance > 0) {
-				current = revert - distance;
-				position = revert;
-				this.reset(current);
-			}
-		} else if (this.settings.rewind) {
-			maximum += 1;
-			position = (position % maximum + maximum) % maximum;
-		} else {
-			position = Math.max(minimum, Math.min(maximum, position));
-		}
-
-		this.speed(this.duration(current, position, speed));
-		this.current(position);
-
-		if (this.$element.is(':visible')) {
-			this.update();
-		}
-	};
-
-	/**
-	 * Slides to the next item.
-	 * @public
-	 * @param {Number} [speed] - The time in milliseconds for the transition.
-	 */
-	Owl.prototype.next = function(speed) {
-		speed = speed || false;
-		this.to(this.relative(this.current()) + 1, speed);
-	};
-
-	/**
-	 * Slides to the previous item.
-	 * @public
-	 * @param {Number} [speed] - The time in milliseconds for the transition.
-	 */
-	Owl.prototype.prev = function(speed) {
-		speed = speed || false;
-		this.to(this.relative(this.current()) - 1, speed);
-	};
-
-	/**
-	 * Handles the end of an animation.
-	 * @protected
-	 * @param {Event} event - The event arguments.
-	 */
-	Owl.prototype.onTransitionEnd = function(event) {
-
-		// if css2 animation then event object is undefined
-		if (event !== undefined) {
-			event.stopPropagation();
-
-			// Catch only owl-stage transitionEnd event
-			if ((event.target || event.srcElement || event.originalTarget) !== this.$stage.get(0)) {
-				return false;
-			}
-		}
-
-		this.leave('animating');
-		this.trigger('translated');
-	};
-
-	/**
-	 * Gets viewport width.
-	 * @protected
-	 * @return {Number} - The width in pixel.
-	 */
-	Owl.prototype.viewport = function() {
-		var width;
-		if (this.options.responsiveBaseElement !== window) {
-			width = $(this.options.responsiveBaseElement).width();
-		} else if (window.innerWidth) {
-			width = window.innerWidth;
-		} else if (document.documentElement && document.documentElement.clientWidth) {
-			width = document.documentElement.clientWidth;
-		} else {
-			console.warn('Can not detect viewport width.');
-		}
-		return width;
-	};
-
-	/**
-	 * Replaces the current content.
-	 * @public
-	 * @param {HTMLElement|jQuery|String} content - The new content.
-	 */
-	Owl.prototype.replace = function(content) {
-		this.$stage.empty();
-		this._items = [];
-
-		if (content) {
-			content = (content instanceof jQuery) ? content : $(content);
-		}
-
-		if (this.settings.nestedItemSelector) {
-			content = content.find('.' + this.settings.nestedItemSelector);
-		}
-
-		content.filter(function() {
-			return this.nodeType === 1;
-		}).each($.proxy(function(index, item) {
-			item = this.prepare(item);
-			this.$stage.append(item);
-			this._items.push(item);
-			this._mergers.push(item.find('[data-merge]').addBack('[data-merge]').attr('data-merge') * 1 || 1);
-		}, this));
-
-		this.reset(this.isNumeric(this.settings.startPosition) ? this.settings.startPosition : 0);
-
-		this.invalidate('items');
-	};
-
-	/**
-	 * Adds an item.
-	 * @todo Use `item` instead of `content` for the event arguments.
-	 * @public
-	 * @param {HTMLElement|jQuery|String} content - The item content to add.
-	 * @param {Number} [position] - The relative position at which to insert the item otherwise the item will be added to the end.
-	 */
-	Owl.prototype.add = function(content, position) {
-		var current = this.relative(this._current);
-
-		position = position === undefined ? this._items.length : this.normalize(position, true);
-		content = content instanceof jQuery ? content : $(content);
-
-		this.trigger('add', { content: content, position: position });
-
-		content = this.prepare(content);
-
-		if (this._items.length === 0 || position === this._items.length) {
-			this._items.length === 0 && this.$stage.append(content);
-			this._items.length !== 0 && this._items[position - 1].after(content);
-			this._items.push(content);
-			this._mergers.push(content.find('[data-merge]').addBack('[data-merge]').attr('data-merge') * 1 || 1);
-		} else {
-			this._items[position].before(content);
-			this._items.splice(position, 0, content);
-			this._mergers.splice(position, 0, content.find('[data-merge]').addBack('[data-merge]').attr('data-merge') * 1 || 1);
-		}
-
-		this._items[current] && this.reset(this._items[current].index());
-
-		this.invalidate('items');
-
-		this.trigger('added', { content: content, position: position });
-	};
-
-	/**
-	 * Removes an item by its position.
-	 * @todo Use `item` instead of `content` for the event arguments.
-	 * @public
-	 * @param {Number} position - The relative position of the item to remove.
-	 */
-	Owl.prototype.remove = function(position) {
-		position = this.normalize(position, true);
-
-		if (position === undefined) {
-			return;
-		}
-
-		this.trigger('remove', { content: this._items[position], position: position });
-
-		this._items[position].remove();
-		this._items.splice(position, 1);
-		this._mergers.splice(position, 1);
-
-		this.invalidate('items');
-
-		this.trigger('removed', { content: null, position: position });
-	};
-
-	/**
-	 * Preloads images with auto width.
-	 * @todo Replace by a more generic approach
-	 * @protected
-	 */
-	Owl.prototype.preloadAutoWidthImages = function(images) {
-		images.each($.proxy(function(i, element) {
-			this.enter('pre-loading');
-			element = $(element);
-			$(new Image()).one('load', $.proxy(function(e) {
-				element.attr('src', e.target.src);
-				element.css('opacity', 1);
-				this.leave('pre-loading');
-				!this.is('pre-loading') && !this.is('initializing') && this.refresh();
-			}, this)).attr('src', element.attr('src') || element.attr('data-src') || element.attr('data-src-retina'));
-		}, this));
-	};
-
-	/**
-	 * Destroys the carousel.
-	 * @public
-	 */
-	Owl.prototype.destroy = function() {
-
-		this.$element.off('.owl.core');
-		this.$stage.off('.owl.core');
-		$(document).off('.owl.core');
-
-		if (this.settings.responsive !== false) {
-			window.clearTimeout(this.resizeTimer);
-			this.off(window, 'resize', this._handlers.onThrottledResize);
-		}
-
-		for (var i in this._plugins) {
-			this._plugins[i].destroy();
-		}
-
-		this.$stage.children('.cloned').remove();
-
-		this.$stage.unwrap();
-		this.$stage.children().contents().unwrap();
-		this.$stage.children().unwrap();
-
-		this.$element
-			.removeClass(this.options.refreshClass)
-			.removeClass(this.options.loadingClass)
-			.removeClass(this.options.loadedClass)
-			.removeClass(this.options.rtlClass)
-			.removeClass(this.options.dragClass)
-			.removeClass(this.options.grabClass)
-			.attr('class', this.$element.attr('class').replace(new RegExp(this.options.responsiveClass + '-\\S+\\s', 'g'), ''))
-			.removeData('owl.carousel');
-	};
-
-	/**
-	 * Operators to calculate right-to-left and left-to-right.
-	 * @protected
-	 * @param {Number} [a] - The left side operand.
-	 * @param {String} [o] - The operator.
-	 * @param {Number} [b] - The right side operand.
-	 */
-	Owl.prototype.op = function(a, o, b) {
-		var rtl = this.settings.rtl;
-		switch (o) {
-			case '<':
-				return rtl ? a > b : a < b;
-			case '>':
-				return rtl ? a < b : a > b;
-			case '>=':
-				return rtl ? a <= b : a >= b;
-			case '<=':
-				return rtl ? a >= b : a <= b;
-			default:
-				break;
-		}
-	};
-
-	/**
-	 * Attaches to an internal event.
-	 * @protected
-	 * @param {HTMLElement} element - The event source.
-	 * @param {String} event - The event name.
-	 * @param {Function} listener - The event handler to attach.
-	 * @param {Boolean} capture - Wether the event should be handled at the capturing phase or not.
-	 */
-	Owl.prototype.on = function(element, event, listener, capture) {
-		if (element.addEventListener) {
-			element.addEventListener(event, listener, capture);
-		} else if (element.attachEvent) {
-			element.attachEvent('on' + event, listener);
-		}
-	};
-
-	/**
-	 * Detaches from an internal event.
-	 * @protected
-	 * @param {HTMLElement} element - The event source.
-	 * @param {String} event - The event name.
-	 * @param {Function} listener - The attached event handler to detach.
-	 * @param {Boolean} capture - Wether the attached event handler was registered as a capturing listener or not.
-	 */
-	Owl.prototype.off = function(element, event, listener, capture) {
-		if (element.removeEventListener) {
-			element.removeEventListener(event, listener, capture);
-		} else if (element.detachEvent) {
-			element.detachEvent('on' + event, listener);
-		}
-	};
-
-	/**
-	 * Triggers a public event.
-	 * @todo Remove `status`, `relatedTarget` should be used instead.
-	 * @protected
-	 * @param {String} name - The event name.
-	 * @param {*} [data=null] - The event data.
-	 * @param {String} [namespace=carousel] - The event namespace.
-	 * @param {String} [state] - The state which is associated with the event.
-	 * @param {Boolean} [enter=false] - Indicates if the call enters the specified state or not.
-	 * @returns {Event} - The event arguments.
-	 */
-	Owl.prototype.trigger = function(name, data, namespace, state, enter) {
-		var status = {
-			item: { count: this._items.length, index: this.current() }
-		}, handler = $.camelCase(
-			$.grep([ 'on', name, namespace ], function(v) { return v })
-				.join('-').toLowerCase()
-		), event = $.Event(
-			[ name, 'owl', namespace || 'carousel' ].join('.').toLowerCase(),
-			$.extend({ relatedTarget: this }, status, data)
-		);
-
-		if (!this._supress[name]) {
-			$.each(this._plugins, function(name, plugin) {
-				if (plugin.onTrigger) {
-					plugin.onTrigger(event);
-				}
-			});
-
-			this.register({ type: Owl.Type.Event, name: name });
-			this.$element.trigger(event);
-
-			if (this.settings && typeof this.settings[handler] === 'function') {
-				this.settings[handler].call(this, event);
-			}
-		}
-
-		return event;
-	};
-
-	/**
-	 * Enters a state.
-	 * @param name - The state name.
-	 */
-	Owl.prototype.enter = function(name) {
-		$.each([ name ].concat(this._states.tags[name] || []), $.proxy(function(i, name) {
-			if (this._states.current[name] === undefined) {
-				this._states.current[name] = 0;
-			}
-
-			this._states.current[name]++;
-		}, this));
-	};
-
-	/**
-	 * Leaves a state.
-	 * @param name - The state name.
-	 */
-	Owl.prototype.leave = function(name) {
-		$.each([ name ].concat(this._states.tags[name] || []), $.proxy(function(i, name) {
-			this._states.current[name]--;
-		}, this));
-	};
-
-	/**
-	 * Registers an event or state.
-	 * @public
-	 * @param {Object} object - The event or state to register.
-	 */
-	Owl.prototype.register = function(object) {
-		if (object.type === Owl.Type.Event) {
-			if (!$.event.special[object.name]) {
-				$.event.special[object.name] = {};
-			}
-
-			if (!$.event.special[object.name].owl) {
-				var _default = $.event.special[object.name]._default;
-				$.event.special[object.name]._default = function(e) {
-					if (_default && _default.apply && (!e.namespace || e.namespace.indexOf('owl') === -1)) {
-						return _default.apply(this, arguments);
-					}
-					return e.namespace && e.namespace.indexOf('owl') > -1;
-				};
-				$.event.special[object.name].owl = true;
-			}
-		} else if (object.type === Owl.Type.State) {
-			if (!this._states.tags[object.name]) {
-				this._states.tags[object.name] = object.tags;
-			} else {
-				this._states.tags[object.name] = this._states.tags[object.name].concat(object.tags);
-			}
-
-			this._states.tags[object.name] = $.grep(this._states.tags[object.name], $.proxy(function(tag, i) {
-				return $.inArray(tag, this._states.tags[object.name]) === i;
-			}, this));
-		}
-	};
-
-	/**
-	 * Suppresses events.
-	 * @protected
-	 * @param {Array.<String>} events - The events to suppress.
-	 */
-	Owl.prototype.suppress = function(events) {
-		$.each(events, $.proxy(function(index, event) {
-			this._supress[event] = true;
-		}, this));
-	};
-
-	/**
-	 * Releases suppressed events.
-	 * @protected
-	 * @param {Array.<String>} events - The events to release.
-	 */
-	Owl.prototype.release = function(events) {
-		$.each(events, $.proxy(function(index, event) {
-			delete this._supress[event];
-		}, this));
-	};
-
-	/**
-	 * Gets unified pointer coordinates from event.
-	 * @todo #261
-	 * @protected
-	 * @param {Event} - The `mousedown` or `touchstart` event.
-	 * @returns {Object} - Contains `x` and `y` coordinates of current pointer position.
-	 */
-	Owl.prototype.pointer = function(event) {
-		var result = { x: null, y: null };
-
-		event = event.originalEvent || event || window.event;
-
-		event = event.touches && event.touches.length ?
-			event.touches[0] : event.changedTouches && event.changedTouches.length ?
-				event.changedTouches[0] : event;
-
-		if (event.pageX) {
-			result.x = event.pageX;
-			result.y = event.pageY;
-		} else {
-			result.x = event.clientX;
-			result.y = event.clientY;
-		}
-
-		return result;
-	};
-
-	/**
-	 * Determines if the input is a Number or something that can be coerced to a Number
-	 * @protected
-	 * @param {Number|String|Object|Array|Boolean|RegExp|Function|Symbol} - The input to be tested
-	 * @returns {Boolean} - An indication if the input is a Number or can be coerced to a Number
-	 */
-	Owl.prototype.isNumeric = function(number) {
-		return !isNaN(parseFloat(number));
-	};
-
-	/**
-	 * Gets the difference of two vectors.
-	 * @todo #261
-	 * @protected
-	 * @param {Object} - The first vector.
-	 * @param {Object} - The second vector.
-	 * @returns {Object} - The difference.
-	 */
-	Owl.prototype.difference = function(first, second) {
-		return {
-			x: first.x - second.x,
-			y: first.y - second.y
-		};
-	};
-
-	/**
-	 * The jQuery Plugin for the Owl Carousel
-	 * @todo Navigation plugin `next` and `prev`
-	 * @public
-	 */
-	$.fn.owlCarousel = function(option) {
-		var args = Array.prototype.slice.call(arguments, 1);
-
-		return this.each(function() {
-			var $this = $(this),
-				data = $this.data('owl.carousel');
-
-			if (!data) {
-				data = new Owl(this, typeof option == 'object' && option);
-				$this.data('owl.carousel', data);
-
-				$.each([
-					'next', 'prev', 'to', 'destroy', 'refresh', 'replace', 'add', 'remove'
-				], function(i, event) {
-					data.register({ type: Owl.Type.Event, name: event });
-					data.$element.on(event + '.owl.carousel.core', $.proxy(function(e) {
-						if (e.namespace && e.relatedTarget !== this) {
-							this.suppress([ event ]);
-							data[event].apply(this, [].slice.call(arguments, 1));
-							this.release([ event ]);
-						}
-					}, data));
-				});
-			}
-
-			if (typeof option == 'string' && option.charAt(0) !== '_') {
-				data[option].apply(data, args);
-			}
-		});
-	};
-
-	/**
-	 * The constructor for the jQuery Plugin
-	 * @public
-	 */
-	$.fn.owlCarousel.Constructor = Owl;
-
+(function($, window, document, undefined) {
+  /**
+   * Creates a carousel.
+   * @class The Owl Carousel.
+   * @public
+   * @param {HTMLElement|jQuery} element - The element to create the carousel for.
+   * @param {Object} [options] - The options
+   */
+  function Owl(element, options) {
+    /**
+     * Current settings for the carousel.
+     * @public
+     */
+    this.settings = null;
+
+    /**
+     * Current options set by the caller including defaults.
+     * @public
+     */
+    this.options = $.extend({}, Owl.Defaults, options);
+
+    /**
+     * Plugin element.
+     * @public
+     */
+    this.$element = $(element);
+
+    /**
+     * Proxied event handlers.
+     * @protected
+     */
+    this._handlers = {};
+
+    /**
+     * References to the running plugins of this carousel.
+     * @protected
+     */
+    this._plugins = {};
+
+    /**
+     * Currently suppressed events to prevent them from beeing retriggered.
+     * @protected
+     */
+    this._supress = {};
+
+    /**
+     * Absolute current position.
+     * @protected
+     */
+    this._current = null;
+
+    /**
+     * Animation speed in milliseconds.
+     * @protected
+     */
+    this._speed = null;
+
+    /**
+     * Coordinates of all items in pixel.
+     * @todo The name of this member is missleading.
+     * @protected
+     */
+    this._coordinates = [];
+
+    /**
+     * Current breakpoint.
+     * @todo Real media queries would be nice.
+     * @protected
+     */
+    this._breakpoint = null;
+
+    /**
+     * Current width of the plugin element.
+     */
+    this._width = null;
+
+    /**
+     * All real items.
+     * @protected
+     */
+    this._items = [];
+
+    /**
+     * All cloned items.
+     * @protected
+     */
+    this._clones = [];
+
+    /**
+     * Merge values of all items.
+     * @todo Maybe this could be part of a plugin.
+     * @protected
+     */
+    this._mergers = [];
+
+    /**
+     * Widths of all items.
+     */
+    this._widths = [];
+
+    /**
+     * Invalidated parts within the update process.
+     * @protected
+     */
+    this._invalidated = {};
+
+    /**
+     * Ordered list of workers for the update process.
+     * @protected
+     */
+    this._pipe = [];
+
+    /**
+     * Current state information for the drag operation.
+     * @todo #261
+     * @protected
+     */
+    this._drag = {
+      time: null,
+      target: null,
+      pointer: null,
+      stage: {
+        start: null,
+        current: null
+      },
+      direction: null
+    };
+
+    /**
+     * Current state information and their tags.
+     * @type {Object}
+     * @protected
+     */
+    this._states = {
+      current: {},
+      tags: {
+        initializing: ["busy"],
+        animating: ["busy"],
+        dragging: ["interacting"]
+      }
+    };
+
+    $.each(
+      ["onResize", "onThrottledResize"],
+      $.proxy(function(i, handler) {
+        this._handlers[handler] = $.proxy(this[handler], this);
+      }, this)
+    );
+
+    $.each(
+      Owl.Plugins,
+      $.proxy(function(key, plugin) {
+        this._plugins[key.charAt(0).toLowerCase() + key.slice(1)] = new plugin(
+          this
+        );
+      }, this)
+    );
+
+    $.each(
+      Owl.Workers,
+      $.proxy(function(priority, worker) {
+        this._pipe.push({
+          filter: worker.filter,
+          run: $.proxy(worker.run, this)
+        });
+      }, this)
+    );
+
+    this.setup();
+    this.initialize();
+  }
+
+  /**
+   * Default options for the carousel.
+   * @public
+   */
+  Owl.Defaults = {
+    items: 3,
+    loop: false,
+    center: false,
+    rewind: false,
+
+    mouseDrag: true,
+    touchDrag: true,
+    pullDrag: true,
+    freeDrag: false,
+
+    margin: 0,
+    stagePadding: 0,
+
+    merge: false,
+    mergeFit: true,
+    autoWidth: false,
+
+    startPosition: 0,
+    rtl: false,
+
+    smartSpeed: 250,
+    fluidSpeed: false,
+    dragEndSpeed: false,
+
+    responsive: {},
+    responsiveRefreshRate: 200,
+    responsiveBaseElement: window,
+
+    fallbackEasing: "swing",
+
+    info: false,
+
+    nestedItemSelector: false,
+    itemElement: "div",
+    stageElement: "div",
+
+    refreshClass: "owl-refresh",
+    loadedClass: "owl-loaded",
+    loadingClass: "owl-loading",
+    rtlClass: "owl-rtl",
+    responsiveClass: "owl-responsive",
+    dragClass: "owl-drag",
+    itemClass: "owl-item",
+    stageClass: "owl-stage",
+    stageOuterClass: "owl-stage-outer",
+    grabClass: "owl-grab"
+  };
+
+  /**
+   * Enumeration for width.
+   * @public
+   * @readonly
+   * @enum {String}
+   */
+  Owl.Width = {
+    Default: "default",
+    Inner: "inner",
+    Outer: "outer"
+  };
+
+  /**
+   * Enumeration for types.
+   * @public
+   * @readonly
+   * @enum {String}
+   */
+  Owl.Type = {
+    Event: "event",
+    State: "state"
+  };
+
+  /**
+   * Contains all registered plugins.
+   * @public
+   */
+  Owl.Plugins = {};
+
+  /**
+   * List of workers involved in the update process.
+   */
+  Owl.Workers = [
+    {
+      filter: ["width", "settings"],
+      run: function() {
+        this._width = this.$element.width();
+      }
+    },
+    {
+      filter: ["width", "items", "settings"],
+      run: function(cache) {
+        cache.current =
+          this._items && this._items[this.relative(this._current)];
+      }
+    },
+    {
+      filter: ["items", "settings"],
+      run: function() {
+        this.$stage.children(".cloned").remove();
+      }
+    },
+    {
+      filter: ["width", "items", "settings"],
+      run: function(cache) {
+        var margin = this.settings.margin || "",
+          grid = !this.settings.autoWidth,
+          rtl = this.settings.rtl,
+          css = {
+            width: "auto",
+            "margin-left": rtl ? margin : "",
+            "margin-right": rtl ? "" : margin
+          };
+
+        !grid && this.$stage.children().css(css);
+
+        cache.css = css;
+      }
+    },
+    {
+      filter: ["width", "items", "settings"],
+      run: function(cache) {
+        var width =
+            (this.width() / this.settings.items).toFixed(3) -
+            this.settings.margin,
+          merge = null,
+          iterator = this._items.length,
+          grid = !this.settings.autoWidth,
+          widths = [];
+
+        cache.items = {
+          merge: false,
+          width: width
+        };
+
+        while (iterator--) {
+          merge = this._mergers[iterator];
+          merge =
+            (this.settings.mergeFit && Math.min(merge, this.settings.items)) ||
+            merge;
+
+          cache.items.merge = merge > 1 || cache.items.merge;
+
+          widths[iterator] = !grid
+            ? this._items[iterator].width()
+            : width * merge;
+        }
+
+        this._widths = widths;
+      }
+    },
+    {
+      filter: ["items", "settings"],
+      run: function() {
+        var clones = [],
+          items = this._items,
+          settings = this.settings,
+          // TODO: Should be computed from number of min width items in stage
+          view = Math.max(settings.items * 2, 4),
+          size = Math.ceil(items.length / 2) * 2,
+          repeat =
+            settings.loop && items.length
+              ? settings.rewind
+                ? view
+                : Math.max(view, size)
+              : 0,
+          append = "",
+          prepend = "";
+
+        repeat /= 2;
+
+        while (repeat--) {
+          // Switch to only using appended clones
+          clones.push(this.normalize(clones.length / 2, true));
+          append = append + items[clones[clones.length - 1]][0].outerHTML;
+          clones.push(
+            this.normalize(items.length - 1 - (clones.length - 1) / 2, true)
+          );
+          prepend = items[clones[clones.length - 1]][0].outerHTML + prepend;
+        }
+
+        this._clones = clones;
+
+        $(append)
+          .addClass("cloned")
+          .appendTo(this.$stage);
+        $(prepend)
+          .addClass("cloned")
+          .prependTo(this.$stage);
+      }
+    },
+    {
+      filter: ["width", "items", "settings"],
+      run: function() {
+        var rtl = this.settings.rtl ? 1 : -1,
+          size = this._clones.length + this._items.length,
+          iterator = -1,
+          previous = 0,
+          current = 0,
+          coordinates = [];
+
+        while (++iterator < size) {
+          previous = coordinates[iterator - 1] || 0;
+          current =
+            this._widths[this.relative(iterator)] + this.settings.margin;
+          coordinates.push(previous + current * rtl);
+        }
+
+        this._coordinates = coordinates;
+      }
+    },
+    {
+      filter: ["width", "items", "settings"],
+      run: function() {
+        var padding = this.settings.stagePadding,
+          coordinates = this._coordinates,
+          css = {
+            width:
+              Math.ceil(Math.abs(coordinates[coordinates.length - 1])) +
+              padding * 2,
+            "padding-left": padding || "",
+            "padding-right": padding || ""
+          };
+
+        this.$stage.css(css);
+      }
+    },
+    {
+      filter: ["width", "items", "settings"],
+      run: function(cache) {
+        var iterator = this._coordinates.length,
+          grid = !this.settings.autoWidth,
+          items = this.$stage.children();
+
+        if (grid && cache.items.merge) {
+          while (iterator--) {
+            cache.css.width = this._widths[this.relative(iterator)];
+            items.eq(iterator).css(cache.css);
+          }
+        } else if (grid) {
+          cache.css.width = cache.items.width;
+          items.css(cache.css);
+        }
+      }
+    },
+    {
+      filter: ["items"],
+      run: function() {
+        this._coordinates.length < 1 && this.$stage.removeAttr("style");
+      }
+    },
+    {
+      filter: ["width", "items", "settings"],
+      run: function(cache) {
+        cache.current = cache.current
+          ? this.$stage.children().index(cache.current)
+          : 0;
+        cache.current = Math.max(
+          this.minimum(),
+          Math.min(this.maximum(), cache.current)
+        );
+        this.reset(cache.current);
+      }
+    },
+    {
+      filter: ["position"],
+      run: function() {
+        this.animate(this.coordinates(this._current));
+      }
+    },
+    {
+      filter: ["width", "position", "items", "settings"],
+      run: function() {
+        var rtl = this.settings.rtl ? 1 : -1,
+          padding = this.settings.stagePadding * 2,
+          begin = this.coordinates(this.current()) + padding,
+          end = begin + this.width() * rtl,
+          inner,
+          outer,
+          matches = [],
+          i,
+          n;
+
+        for (i = 0, n = this._coordinates.length; i < n; i++) {
+          inner = this._coordinates[i - 1] || 0;
+          outer = Math.abs(this._coordinates[i]) + padding * rtl;
+
+          if (
+            (this.op(inner, "<=", begin) && this.op(inner, ">", end)) ||
+            (this.op(outer, "<", begin) && this.op(outer, ">", end))
+          ) {
+            matches.push(i);
+          }
+        }
+
+        this.$stage.children(".active").removeClass("active");
+        this.$stage
+          .children(":eq(" + matches.join("), :eq(") + ")")
+          .addClass("active");
+
+        if (this.settings.center) {
+          this.$stage.children(".center").removeClass("center");
+          this.$stage
+            .children()
+            .eq(this.current())
+            .addClass("center");
+        }
+      }
+    }
+  ];
+
+  /**
+   * Initializes the carousel.
+   * @protected
+   */
+  Owl.prototype.initialize = function() {
+    this.enter("initializing");
+    this.trigger("initialize");
+
+    this.$element.toggleClass(this.settings.rtlClass, this.settings.rtl);
+
+    if (this.settings.autoWidth && !this.is("pre-loading")) {
+      var imgs, nestedSelector, width;
+      imgs = this.$element.find("img");
+      nestedSelector = this.settings.nestedItemSelector
+        ? "." + this.settings.nestedItemSelector
+        : undefined;
+      width = this.$element.children(nestedSelector).width();
+
+      if (imgs.length && width <= 0) {
+        this.preloadAutoWidthImages(imgs);
+      }
+    }
+
+    this.$element.addClass(this.options.loadingClass);
+
+    // create stage
+    this.$stage = $(
+      "<" +
+        this.settings.stageElement +
+        ' class="' +
+        this.settings.stageClass +
+        '"/>'
+    ).wrap('<div class="' + this.settings.stageOuterClass + '"/>');
+
+    // append stage
+    this.$element.append(this.$stage.parent());
+
+    // append content
+    this.replace(this.$element.children().not(this.$stage.parent()));
+
+    // check visibility
+    if (this.$element.is(":visible")) {
+      // update view
+      this.refresh();
+    } else {
+      // invalidate width
+      this.invalidate("width");
+    }
+
+    this.$element
+      .removeClass(this.options.loadingClass)
+      .addClass(this.options.loadedClass);
+
+    // register event handlers
+    this.registerEventHandlers();
+
+    this.leave("initializing");
+    this.trigger("initialized");
+  };
+
+  /**
+   * Setups the current settings.
+   * @todo Remove responsive classes. Why should adaptive designs be brought into IE8?
+   * @todo Support for media queries by using `matchMedia` would be nice.
+   * @public
+   */
+  Owl.prototype.setup = function() {
+    var viewport = this.viewport(),
+      overwrites = this.options.responsive,
+      match = -1,
+      settings = null;
+
+    if (!overwrites) {
+      settings = $.extend({}, this.options);
+    } else {
+      $.each(overwrites, function(breakpoint) {
+        if (breakpoint <= viewport && breakpoint > match) {
+          match = Number(breakpoint);
+        }
+      });
+
+      settings = $.extend({}, this.options, overwrites[match]);
+      if (typeof settings.stagePadding === "function") {
+        settings.stagePadding = settings.stagePadding();
+      }
+      delete settings.responsive;
+
+      // responsive class
+      if (settings.responsiveClass) {
+        this.$element.attr(
+          "class",
+          this.$element
+            .attr("class")
+            .replace(
+              new RegExp("(" + this.options.responsiveClass + "-)\\S+\\s", "g"),
+              "$1" + match
+            )
+        );
+      }
+    }
+
+    this.trigger("change", { property: { name: "settings", value: settings } });
+    this._breakpoint = match;
+    this.settings = settings;
+    this.invalidate("settings");
+    this.trigger("changed", {
+      property: { name: "settings", value: this.settings }
+    });
+  };
+
+  /**
+   * Updates option logic if necessery.
+   * @protected
+   */
+  Owl.prototype.optionsLogic = function() {
+    if (this.settings.autoWidth) {
+      this.settings.stagePadding = false;
+      this.settings.merge = false;
+    }
+  };
+
+  /**
+   * Prepares an item before add.
+   * @todo Rename event parameter `content` to `item`.
+   * @protected
+   * @returns {jQuery|HTMLElement} - The item container.
+   */
+  Owl.prototype.prepare = function(item) {
+    var event = this.trigger("prepare", { content: item });
+
+    if (!event.data) {
+      event.data = $("<" + this.settings.itemElement + "/>")
+        .addClass(this.options.itemClass)
+        .append(item);
+    }
+
+    this.trigger("prepared", { content: event.data });
+
+    return event.data;
+  };
+
+  /**
+   * Updates the view.
+   * @public
+   */
+  Owl.prototype.update = function() {
+    var i = 0,
+      n = this._pipe.length,
+      filter = $.proxy(function(p) {
+        return this[p];
+      }, this._invalidated),
+      cache = {};
+
+    while (i < n) {
+      if (
+        this._invalidated.all ||
+        $.grep(this._pipe[i].filter, filter).length > 0
+      ) {
+        this._pipe[i].run(cache);
+      }
+      i++;
+    }
+
+    this._invalidated = {};
+
+    !this.is("valid") && this.enter("valid");
+  };
+
+  /**
+   * Gets the width of the view.
+   * @public
+   * @param {Owl.Width} [dimension=Owl.Width.Default] - The dimension to return.
+   * @returns {Number} - The width of the view in pixel.
+   */
+  Owl.prototype.width = function(dimension) {
+    dimension = dimension || Owl.Width.Default;
+    switch (dimension) {
+      case Owl.Width.Inner:
+      case Owl.Width.Outer:
+        return this._width;
+      default:
+        return (
+          this._width - this.settings.stagePadding * 2 + this.settings.margin
+        );
+    }
+  };
+
+  /**
+   * Refreshes the carousel primarily for adaptive purposes.
+   * @public
+   */
+  Owl.prototype.refresh = function() {
+    this.enter("refreshing");
+    this.trigger("refresh");
+
+    this.setup();
+
+    this.optionsLogic();
+
+    this.$element.addClass(this.options.refreshClass);
+
+    this.update();
+
+    this.$element.removeClass(this.options.refreshClass);
+
+    this.leave("refreshing");
+    this.trigger("refreshed");
+  };
+
+  /**
+   * Checks window `resize` event.
+   * @protected
+   */
+  Owl.prototype.onThrottledResize = function() {
+    window.clearTimeout(this.resizeTimer);
+    this.resizeTimer = window.setTimeout(
+      this._handlers.onResize,
+      this.settings.responsiveRefreshRate
+    );
+  };
+
+  /**
+   * Checks window `resize` event.
+   * @protected
+   */
+  Owl.prototype.onResize = function() {
+    if (!this._items.length) {
+      return false;
+    }
+
+    if (this._width === this.$element.width()) {
+      return false;
+    }
+
+    if (!this.$element.is(":visible")) {
+      return false;
+    }
+
+    this.enter("resizing");
+
+    if (this.trigger("resize").isDefaultPrevented()) {
+      this.leave("resizing");
+      return false;
+    }
+
+    this.invalidate("width");
+
+    this.refresh();
+
+    this.leave("resizing");
+    this.trigger("resized");
+  };
+
+  /**
+   * Registers event handlers.
+   * @todo Check `msPointerEnabled`
+   * @todo #261
+   * @protected
+   */
+  Owl.prototype.registerEventHandlers = function() {
+    if ($.support.transition) {
+      this.$stage.on(
+        $.support.transition.end + ".owl.core",
+        $.proxy(this.onTransitionEnd, this)
+      );
+    }
+
+    if (this.settings.responsive !== false) {
+      this.on(window, "resize", this._handlers.onThrottledResize);
+    }
+
+    if (this.settings.mouseDrag) {
+      this.$element.addClass(this.options.dragClass);
+      this.$stage.on("mousedown.owl.core", $.proxy(this.onDragStart, this));
+      this.$stage.on("dragstart.owl.core selectstart.owl.core", function() {
+        return false;
+      });
+    }
+
+    if (this.settings.touchDrag) {
+      this.$stage.on("touchstart.owl.core", $.proxy(this.onDragStart, this));
+      this.$stage.on("touchcancel.owl.core", $.proxy(this.onDragEnd, this));
+    }
+  };
+
+  /**
+   * Handles `touchstart` and `mousedown` events.
+   * @todo Horizontal swipe threshold as option
+   * @todo #261
+   * @protected
+   * @param {Event} event - The event arguments.
+   */
+  Owl.prototype.onDragStart = function(event) {
+    var stage = null;
+
+    if (event.which === 3) {
+      return;
+    }
+
+    if ($.support.transform) {
+      stage = this.$stage
+        .css("transform")
+        .replace(/.*\(|\)| /g, "")
+        .split(",");
+      stage = {
+        x: stage[stage.length === 16 ? 12 : 4],
+        y: stage[stage.length === 16 ? 13 : 5]
+      };
+    } else {
+      stage = this.$stage.position();
+      stage = {
+        x: this.settings.rtl
+          ? stage.left +
+            this.$stage.width() -
+            this.width() +
+            this.settings.margin
+          : stage.left,
+        y: stage.top
+      };
+    }
+
+    if (this.is("animating")) {
+      $.support.transform ? this.animate(stage.x) : this.$stage.stop();
+      this.invalidate("position");
+    }
+
+    this.$element.toggleClass(
+      this.options.grabClass,
+      event.type === "mousedown"
+    );
+
+    this.speed(0);
+
+    this._drag.time = new Date().getTime();
+    this._drag.target = $(event.target);
+    this._drag.stage.start = stage;
+    this._drag.stage.current = stage;
+    this._drag.pointer = this.pointer(event);
+
+    $(document).on(
+      "mouseup.owl.core touchend.owl.core",
+      $.proxy(this.onDragEnd, this)
+    );
+
+    $(document).one(
+      "mousemove.owl.core touchmove.owl.core",
+      $.proxy(function(event) {
+        var delta = this.difference(this._drag.pointer, this.pointer(event));
+
+        $(document).on(
+          "mousemove.owl.core touchmove.owl.core",
+          $.proxy(this.onDragMove, this)
+        );
+
+        if (Math.abs(delta.x) < Math.abs(delta.y) && this.is("valid")) {
+          return;
+        }
+
+        event.preventDefault();
+
+        this.enter("dragging");
+        this.trigger("drag");
+      }, this)
+    );
+  };
+
+  /**
+   * Handles the `touchmove` and `mousemove` events.
+   * @todo #261
+   * @protected
+   * @param {Event} event - The event arguments.
+   */
+  Owl.prototype.onDragMove = function(event) {
+    var minimum = null,
+      maximum = null,
+      pull = null,
+      delta = this.difference(this._drag.pointer, this.pointer(event)),
+      stage = this.difference(this._drag.stage.start, delta);
+
+    if (!this.is("dragging")) {
+      return;
+    }
+
+    event.preventDefault();
+
+    if (this.settings.loop) {
+      minimum = this.coordinates(this.minimum());
+      maximum = this.coordinates(this.maximum() + 1) - minimum;
+      stage.x =
+        ((((stage.x - minimum) % maximum) + maximum) % maximum) + minimum;
+    } else {
+      minimum = this.settings.rtl
+        ? this.coordinates(this.maximum())
+        : this.coordinates(this.minimum());
+      maximum = this.settings.rtl
+        ? this.coordinates(this.minimum())
+        : this.coordinates(this.maximum());
+      pull = this.settings.pullDrag ? (-1 * delta.x) / 5 : 0;
+      stage.x = Math.max(Math.min(stage.x, minimum + pull), maximum + pull);
+    }
+
+    this._drag.stage.current = stage;
+
+    this.animate(stage.x);
+  };
+
+  /**
+   * Handles the `touchend` and `mouseup` events.
+   * @todo #261
+   * @todo Threshold for click event
+   * @protected
+   * @param {Event} event - The event arguments.
+   */
+  Owl.prototype.onDragEnd = function(event) {
+    var delta = this.difference(this._drag.pointer, this.pointer(event)),
+      stage = this._drag.stage.current,
+      direction = (delta.x > 0) ^ this.settings.rtl ? "left" : "right";
+
+    $(document).off(".owl.core");
+
+    this.$element.removeClass(this.options.grabClass);
+
+    if ((delta.x !== 0 && this.is("dragging")) || !this.is("valid")) {
+      this.speed(this.settings.dragEndSpeed || this.settings.smartSpeed);
+      this.current(
+        this.closest(stage.x, delta.x !== 0 ? direction : this._drag.direction)
+      );
+      this.invalidate("position");
+      this.update();
+
+      this._drag.direction = direction;
+
+      if (
+        Math.abs(delta.x) > 3 ||
+        new Date().getTime() - this._drag.time > 300
+      ) {
+        this._drag.target.one("click.owl.core", function() {
+          return false;
+        });
+      }
+    }
+
+    if (!this.is("dragging")) {
+      return;
+    }
+
+    this.leave("dragging");
+    this.trigger("dragged");
+  };
+
+  /**
+   * Gets absolute position of the closest item for a coordinate.
+   * @todo Setting `freeDrag` makes `closest` not reusable. See #165.
+   * @protected
+   * @param {Number} coordinate - The coordinate in pixel.
+   * @param {String} direction - The direction to check for the closest item. Ether `left` or `right`.
+   * @return {Number} - The absolute position of the closest item.
+   */
+  Owl.prototype.closest = function(coordinate, direction) {
+    var position = -1,
+      pull = 30,
+      width = this.width(),
+      coordinates = this.coordinates();
+
+    if (!this.settings.freeDrag) {
+      // check closest item
+      $.each(
+        coordinates,
+        $.proxy(function(index, value) {
+          // on a left pull, check on current index
+          if (
+            direction === "left" &&
+            coordinate > value - pull &&
+            coordinate < value + pull
+          ) {
+            position = index;
+            // on a right pull, check on previous index
+            // to do so, subtract width from value and set position = index + 1
+          } else if (
+            direction === "right" &&
+            coordinate > value - width - pull &&
+            coordinate < value - width + pull
+          ) {
+            position = index + 1;
+          } else if (
+            this.op(coordinate, "<", value) &&
+            this.op(coordinate, ">", coordinates[index + 1] || value - width)
+          ) {
+            position = direction === "left" ? index + 1 : index;
+          }
+          return position === -1;
+        }, this)
+      );
+    }
+
+    if (!this.settings.loop) {
+      // non loop boundries
+      if (this.op(coordinate, ">", coordinates[this.minimum()])) {
+        position = coordinate = this.minimum();
+      } else if (this.op(coordinate, "<", coordinates[this.maximum()])) {
+        position = coordinate = this.maximum();
+      }
+    }
+
+    return position;
+  };
+
+  /**
+   * Animates the stage.
+   * @todo #270
+   * @public
+   * @param {Number} coordinate - The coordinate in pixels.
+   */
+  Owl.prototype.animate = function(coordinate) {
+    var animate = this.speed() > 0;
+
+    this.is("animating") && this.onTransitionEnd();
+
+    if (animate) {
+      this.enter("animating");
+      this.trigger("translate");
+    }
+
+    if ($.support.transform3d && $.support.transition) {
+      this.$stage.css({
+        transform: "translate3d(" + coordinate + "px,0px,0px)",
+        transition: this.speed() / 1000 + "s"
+      });
+    } else if (animate) {
+      this.$stage.animate(
+        {
+          left: coordinate + "px"
+        },
+        this.speed(),
+        this.settings.fallbackEasing,
+        $.proxy(this.onTransitionEnd, this)
+      );
+    } else {
+      this.$stage.css({
+        left: coordinate + "px"
+      });
+    }
+  };
+
+  /**
+   * Checks whether the carousel is in a specific state or not.
+   * @param {String} state - The state to check.
+   * @returns {Boolean} - The flag which indicates if the carousel is busy.
+   */
+  Owl.prototype.is = function(state) {
+    return this._states.current[state] && this._states.current[state] > 0;
+  };
+
+  /**
+   * Sets the absolute position of the current item.
+   * @public
+   * @param {Number} [position] - The new absolute position or nothing to leave it unchanged.
+   * @returns {Number} - The absolute position of the current item.
+   */
+  Owl.prototype.current = function(position) {
+    if (position === undefined) {
+      return this._current;
+    }
+
+    if (this._items.length === 0) {
+      return undefined;
+    }
+
+    position = this.normalize(position);
+
+    if (this._current !== position) {
+      var event = this.trigger("change", {
+        property: { name: "position", value: position }
+      });
+
+      if (event.data !== undefined) {
+        position = this.normalize(event.data);
+      }
+
+      this._current = position;
+
+      this.invalidate("position");
+
+      this.trigger("changed", {
+        property: { name: "position", value: this._current }
+      });
+    }
+
+    return this._current;
+  };
+
+  /**
+   * Invalidates the given part of the update routine.
+   * @param {String} [part] - The part to invalidate.
+   * @returns {Array.<String>} - The invalidated parts.
+   */
+  Owl.prototype.invalidate = function(part) {
+    if ($.type(part) === "string") {
+      this._invalidated[part] = true;
+      this.is("valid") && this.leave("valid");
+    }
+    return $.map(this._invalidated, function(v, i) {
+      return i;
+    });
+  };
+
+  /**
+   * Resets the absolute position of the current item.
+   * @public
+   * @param {Number} position - The absolute position of the new item.
+   */
+  Owl.prototype.reset = function(position) {
+    position = this.normalize(position);
+
+    if (position === undefined) {
+      return;
+    }
+
+    this._speed = 0;
+    this._current = position;
+
+    this.suppress(["translate", "translated"]);
+
+    this.animate(this.coordinates(position));
+
+    this.release(["translate", "translated"]);
+  };
+
+  /**
+   * Normalizes an absolute or a relative position of an item.
+   * @public
+   * @param {Number} position - The absolute or relative position to normalize.
+   * @param {Boolean} [relative=false] - Whether the given position is relative or not.
+   * @returns {Number} - The normalized position.
+   */
+  Owl.prototype.normalize = function(position, relative) {
+    var n = this._items.length,
+      m = relative ? 0 : this._clones.length;
+
+    if (!this.isNumeric(position) || n < 1) {
+      position = undefined;
+    } else if (position < 0 || position >= n + m) {
+      position = ((((position - m / 2) % n) + n) % n) + m / 2;
+    }
+
+    return position;
+  };
+
+  /**
+   * Converts an absolute position of an item into a relative one.
+   * @public
+   * @param {Number} position - The absolute position to convert.
+   * @returns {Number} - The converted position.
+   */
+  Owl.prototype.relative = function(position) {
+    position -= this._clones.length / 2;
+    return this.normalize(position, true);
+  };
+
+  /**
+   * Gets the maximum position for the current item.
+   * @public
+   * @param {Boolean} [relative=false] - Whether to return an absolute position or a relative position.
+   * @returns {Number}
+   */
+  Owl.prototype.maximum = function(relative) {
+    var settings = this.settings,
+      maximum = this._coordinates.length,
+      iterator,
+      reciprocalItemsWidth,
+      elementWidth;
+
+    if (settings.loop) {
+      maximum = this._clones.length / 2 + this._items.length - 1;
+    } else if (settings.autoWidth || settings.merge) {
+      iterator = this._items.length;
+      reciprocalItemsWidth = this._items[--iterator].width();
+      elementWidth = this.$element.width();
+      while (iterator--) {
+        reciprocalItemsWidth +=
+          this._items[iterator].width() + this.settings.margin;
+        if (reciprocalItemsWidth > elementWidth) {
+          break;
+        }
+      }
+      maximum = iterator + 1;
+    } else if (settings.center) {
+      maximum = this._items.length - 1;
+    } else {
+      maximum = this._items.length - settings.items;
+    }
+
+    if (relative) {
+      maximum -= this._clones.length / 2;
+    }
+
+    return Math.max(maximum, 0);
+  };
+
+  /**
+   * Gets the minimum position for the current item.
+   * @public
+   * @param {Boolean} [relative=false] - Whether to return an absolute position or a relative position.
+   * @returns {Number}
+   */
+  Owl.prototype.minimum = function(relative) {
+    return relative ? 0 : this._clones.length / 2;
+  };
+
+  /**
+   * Gets an item at the specified relative position.
+   * @public
+   * @param {Number} [position] - The relative position of the item.
+   * @return {jQuery|Array.<jQuery>} - The item at the given position or all items if no position was given.
+   */
+  Owl.prototype.items = function(position) {
+    if (position === undefined) {
+      return this._items.slice();
+    }
+
+    position = this.normalize(position, true);
+    return this._items[position];
+  };
+
+  /**
+   * Gets an item at the specified relative position.
+   * @public
+   * @param {Number} [position] - The relative position of the item.
+   * @return {jQuery|Array.<jQuery>} - The item at the given position or all items if no position was given.
+   */
+  Owl.prototype.mergers = function(position) {
+    if (position === undefined) {
+      return this._mergers.slice();
+    }
+
+    position = this.normalize(position, true);
+    return this._mergers[position];
+  };
+
+  /**
+   * Gets the absolute positions of clones for an item.
+   * @public
+   * @param {Number} [position] - The relative position of the item.
+   * @returns {Array.<Number>} - The absolute positions of clones for the item or all if no position was given.
+   */
+  Owl.prototype.clones = function(position) {
+    var odd = this._clones.length / 2,
+      even = odd + this._items.length,
+      map = function(index) {
+        return index % 2 === 0 ? even + index / 2 : odd - (index + 1) / 2;
+      };
+
+    if (position === undefined) {
+      return $.map(this._clones, function(v, i) {
+        return map(i);
+      });
+    }
+
+    return $.map(this._clones, function(v, i) {
+      return v === position ? map(i) : null;
+    });
+  };
+
+  /**
+   * Sets the current animation speed.
+   * @public
+   * @param {Number} [speed] - The animation speed in milliseconds or nothing to leave it unchanged.
+   * @returns {Number} - The current animation speed in milliseconds.
+   */
+  Owl.prototype.speed = function(speed) {
+    if (speed !== undefined) {
+      this._speed = speed;
+    }
+
+    return this._speed;
+  };
+
+  /**
+   * Gets the coordinate of an item.
+   * @todo The name of this method is missleanding.
+   * @public
+   * @param {Number} position - The absolute position of the item within `minimum()` and `maximum()`.
+   * @returns {Number|Array.<Number>} - The coordinate of the item in pixel or all coordinates.
+   */
+  Owl.prototype.coordinates = function(position) {
+    var multiplier = 1,
+      newPosition = position - 1,
+      coordinate;
+
+    if (position === undefined) {
+      return $.map(
+        this._coordinates,
+        $.proxy(function(coordinate, index) {
+          return this.coordinates(index);
+        }, this)
+      );
+    }
+
+    if (this.settings.center) {
+      if (this.settings.rtl) {
+        multiplier = -1;
+        newPosition = position + 1;
+      }
+
+      coordinate = this._coordinates[position];
+      coordinate +=
+        ((this.width() - coordinate + (this._coordinates[newPosition] || 0)) /
+          2) *
+        multiplier;
+    } else {
+      coordinate = this._coordinates[newPosition] || 0;
+    }
+
+    coordinate = Math.ceil(coordinate);
+
+    return coordinate;
+  };
+
+  /**
+   * Calculates the speed for a translation.
+   * @protected
+   * @param {Number} from - The absolute position of the start item.
+   * @param {Number} to - The absolute position of the target item.
+   * @param {Number} [factor=undefined] - The time factor in milliseconds.
+   * @returns {Number} - The time in milliseconds for the translation.
+   */
+  Owl.prototype.duration = function(from, to, factor) {
+    if (factor === 0) {
+      return 0;
+    }
+
+    return (
+      Math.min(Math.max(Math.abs(to - from), 1), 6) *
+      Math.abs(factor || this.settings.smartSpeed)
+    );
+  };
+
+  /**
+   * Slides to the specified item.
+   * @public
+   * @param {Number} position - The position of the item.
+   * @param {Number} [speed] - The time in milliseconds for the transition.
+   */
+  Owl.prototype.to = function(position, speed) {
+    var current = this.current(),
+      revert = null,
+      distance = position - this.relative(current),
+      direction = (distance > 0) - (distance < 0),
+      items = this._items.length,
+      minimum = this.minimum(),
+      maximum = this.maximum();
+
+    if (this.settings.loop) {
+      if (!this.settings.rewind && Math.abs(distance) > items / 2) {
+        distance += direction * -1 * items;
+      }
+
+      position = current + distance;
+      revert = ((((position - minimum) % items) + items) % items) + minimum;
+
+      if (
+        revert !== position &&
+        revert - distance <= maximum &&
+        revert - distance > 0
+      ) {
+        current = revert - distance;
+        position = revert;
+        this.reset(current);
+      }
+    } else if (this.settings.rewind) {
+      maximum += 1;
+      position = ((position % maximum) + maximum) % maximum;
+    } else {
+      position = Math.max(minimum, Math.min(maximum, position));
+    }
+
+    this.speed(this.duration(current, position, speed));
+    this.current(position);
+
+    if (this.$element.is(":visible")) {
+      this.update();
+    }
+  };
+
+  /**
+   * Slides to the next item.
+   * @public
+   * @param {Number} [speed] - The time in milliseconds for the transition.
+   */
+  Owl.prototype.next = function(speed) {
+    speed = speed || false;
+    this.to(this.relative(this.current()) + 1, speed);
+  };
+
+  /**
+   * Slides to the previous item.
+   * @public
+   * @param {Number} [speed] - The time in milliseconds for the transition.
+   */
+  Owl.prototype.prev = function(speed) {
+    speed = speed || false;
+    this.to(this.relative(this.current()) - 1, speed);
+  };
+
+  /**
+   * Handles the end of an animation.
+   * @protected
+   * @param {Event} event - The event arguments.
+   */
+  Owl.prototype.onTransitionEnd = function(event) {
+    // if css2 animation then event object is undefined
+    if (event !== undefined) {
+      event.stopPropagation();
+
+      // Catch only owl-stage transitionEnd event
+      if (
+        (event.target || event.srcElement || event.originalTarget) !==
+        this.$stage.get(0)
+      ) {
+        return false;
+      }
+    }
+
+    this.leave("animating");
+    this.trigger("translated");
+  };
+
+  /**
+   * Gets viewport width.
+   * @protected
+   * @return {Number} - The width in pixel.
+   */
+  Owl.prototype.viewport = function() {
+    var width;
+    if (this.options.responsiveBaseElement !== window) {
+      width = $(this.options.responsiveBaseElement).width();
+    } else if (window.innerWidth) {
+      width = window.innerWidth;
+    } else if (
+      document.documentElement &&
+      document.documentElement.clientWidth
+    ) {
+      width = document.documentElement.clientWidth;
+    } else {
+      console.warn("Can not detect viewport width.");
+    }
+    return width;
+  };
+
+  /**
+   * Replaces the current content.
+   * @public
+   * @param {HTMLElement|jQuery|String} content - The new content.
+   */
+  Owl.prototype.replace = function(content) {
+    this.$stage.empty();
+    this._items = [];
+
+    if (content) {
+      content = content instanceof jQuery ? content : $(content);
+    }
+
+    if (this.settings.nestedItemSelector) {
+      content = content.find("." + this.settings.nestedItemSelector);
+    }
+
+    content
+      .filter(function() {
+        return this.nodeType === 1;
+      })
+      .each(
+        $.proxy(function(index, item) {
+          item = this.prepare(item);
+          this.$stage.append(item);
+          this._items.push(item);
+          this._mergers.push(
+            item
+              .find("[data-merge]")
+              .addBack("[data-merge]")
+              .attr("data-merge") * 1 || 1
+          );
+        }, this)
+      );
+
+    this.reset(
+      this.isNumeric(this.settings.startPosition)
+        ? this.settings.startPosition
+        : 0
+    );
+
+    this.invalidate("items");
+  };
+
+  /**
+   * Adds an item.
+   * @todo Use `item` instead of `content` for the event arguments.
+   * @public
+   * @param {HTMLElement|jQuery|String} content - The item content to add.
+   * @param {Number} [position] - The relative position at which to insert the item otherwise the item will be added to the end.
+   */
+  Owl.prototype.add = function(content, position) {
+    var current = this.relative(this._current);
+
+    position =
+      position === undefined
+        ? this._items.length
+        : this.normalize(position, true);
+    content = content instanceof jQuery ? content : $(content);
+
+    this.trigger("add", { content: content, position: position });
+
+    content = this.prepare(content);
+
+    if (this._items.length === 0 || position === this._items.length) {
+      this._items.length === 0 && this.$stage.append(content);
+      this._items.length !== 0 && this._items[position - 1].after(content);
+      this._items.push(content);
+      this._mergers.push(
+        content
+          .find("[data-merge]")
+          .addBack("[data-merge]")
+          .attr("data-merge") * 1 || 1
+      );
+    } else {
+      this._items[position].before(content);
+      this._items.splice(position, 0, content);
+      this._mergers.splice(
+        position,
+        0,
+        content
+          .find("[data-merge]")
+          .addBack("[data-merge]")
+          .attr("data-merge") * 1 || 1
+      );
+    }
+
+    this._items[current] && this.reset(this._items[current].index());
+
+    this.invalidate("items");
+
+    this.trigger("added", { content: content, position: position });
+  };
+
+  /**
+   * Removes an item by its position.
+   * @todo Use `item` instead of `content` for the event arguments.
+   * @public
+   * @param {Number} position - The relative position of the item to remove.
+   */
+  Owl.prototype.remove = function(position) {
+    position = this.normalize(position, true);
+
+    if (position === undefined) {
+      return;
+    }
+
+    this.trigger("remove", {
+      content: this._items[position],
+      position: position
+    });
+
+    this._items[position].remove();
+    this._items.splice(position, 1);
+    this._mergers.splice(position, 1);
+
+    this.invalidate("items");
+
+    this.trigger("removed", { content: null, position: position });
+  };
+
+  /**
+   * Preloads images with auto width.
+   * @todo Replace by a more generic approach
+   * @protected
+   */
+  Owl.prototype.preloadAutoWidthImages = function(images) {
+    images.each(
+      $.proxy(function(i, element) {
+        this.enter("pre-loading");
+        element = $(element);
+        $(new Image())
+          .one(
+            "load",
+            $.proxy(function(e) {
+              element.attr("src", e.target.src);
+              element.css("opacity", 1);
+              this.leave("pre-loading");
+              !this.is("pre-loading") &&
+                !this.is("initializing") &&
+                this.refresh();
+            }, this)
+          )
+          .attr(
+            "src",
+            element.attr("src") ||
+              element.attr("data-src") ||
+              element.attr("data-src-retina")
+          );
+      }, this)
+    );
+  };
+
+  /**
+   * Destroys the carousel.
+   * @public
+   */
+  Owl.prototype.destroy = function() {
+    this.$element.off(".owl.core");
+    this.$stage.off(".owl.core");
+    $(document).off(".owl.core");
+
+    if (this.settings.responsive !== false) {
+      window.clearTimeout(this.resizeTimer);
+      this.off(window, "resize", this._handlers.onThrottledResize);
+    }
+
+    for (var i in this._plugins) {
+      this._plugins[i].destroy();
+    }
+
+    this.$stage.children(".cloned").remove();
+
+    this.$stage.unwrap();
+    this.$stage
+      .children()
+      .contents()
+      .unwrap();
+    this.$stage.children().unwrap();
+
+    this.$element
+      .removeClass(this.options.refreshClass)
+      .removeClass(this.options.loadingClass)
+      .removeClass(this.options.loadedClass)
+      .removeClass(this.options.rtlClass)
+      .removeClass(this.options.dragClass)
+      .removeClass(this.options.grabClass)
+      .attr(
+        "class",
+        this.$element
+          .attr("class")
+          .replace(
+            new RegExp(this.options.responsiveClass + "-\\S+\\s", "g"),
+            ""
+          )
+      )
+      .removeData("owl.carousel");
+  };
+
+  /**
+   * Operators to calculate right-to-left and left-to-right.
+   * @protected
+   * @param {Number} [a] - The left side operand.
+   * @param {String} [o] - The operator.
+   * @param {Number} [b] - The right side operand.
+   */
+  Owl.prototype.op = function(a, o, b) {
+    var rtl = this.settings.rtl;
+    switch (o) {
+      case "<":
+        return rtl ? a > b : a < b;
+      case ">":
+        return rtl ? a < b : a > b;
+      case ">=":
+        return rtl ? a <= b : a >= b;
+      case "<=":
+        return rtl ? a >= b : a <= b;
+      default:
+        break;
+    }
+  };
+
+  /**
+   * Attaches to an internal event.
+   * @protected
+   * @param {HTMLElement} element - The event source.
+   * @param {String} event - The event name.
+   * @param {Function} listener - The event handler to attach.
+   * @param {Boolean} capture - Wether the event should be handled at the capturing phase or not.
+   */
+  Owl.prototype.on = function(element, event, listener, capture) {
+    if (element.addEventListener) {
+      element.addEventListener(event, listener, capture);
+    } else if (element.attachEvent) {
+      element.attachEvent("on" + event, listener);
+    }
+  };
+
+  /**
+   * Detaches from an internal event.
+   * @protected
+   * @param {HTMLElement} element - The event source.
+   * @param {String} event - The event name.
+   * @param {Function} listener - The attached event handler to detach.
+   * @param {Boolean} capture - Wether the attached event handler was registered as a capturing listener or not.
+   */
+  Owl.prototype.off = function(element, event, listener, capture) {
+    if (element.removeEventListener) {
+      element.removeEventListener(event, listener, capture);
+    } else if (element.detachEvent) {
+      element.detachEvent("on" + event, listener);
+    }
+  };
+
+  /**
+   * Triggers a public event.
+   * @todo Remove `status`, `relatedTarget` should be used instead.
+   * @protected
+   * @param {String} name - The event name.
+   * @param {*} [data=null] - The event data.
+   * @param {String} [namespace=carousel] - The event namespace.
+   * @param {String} [state] - The state which is associated with the event.
+   * @param {Boolean} [enter=false] - Indicates if the call enters the specified state or not.
+   * @returns {Event} - The event arguments.
+   */
+  Owl.prototype.trigger = function(name, data, namespace, state, enter) {
+    var status = {
+        item: { count: this._items.length, index: this.current() }
+      },
+      handler = $.camelCase(
+        $.grep(["on", name, namespace], function(v) {
+          return v;
+        })
+          .join("-")
+          .toLowerCase()
+      ),
+      event = $.Event(
+        [name, "owl", namespace || "carousel"].join(".").toLowerCase(),
+        $.extend({ relatedTarget: this }, status, data)
+      );
+
+    if (!this._supress[name]) {
+      $.each(this._plugins, function(name, plugin) {
+        if (plugin.onTrigger) {
+          plugin.onTrigger(event);
+        }
+      });
+
+      this.register({ type: Owl.Type.Event, name: name });
+      this.$element.trigger(event);
+
+      if (this.settings && typeof this.settings[handler] === "function") {
+        this.settings[handler].call(this, event);
+      }
+    }
+
+    return event;
+  };
+
+  /**
+   * Enters a state.
+   * @param name - The state name.
+   */
+  Owl.prototype.enter = function(name) {
+    $.each(
+      [name].concat(this._states.tags[name] || []),
+      $.proxy(function(i, name) {
+        if (this._states.current[name] === undefined) {
+          this._states.current[name] = 0;
+        }
+
+        this._states.current[name]++;
+      }, this)
+    );
+  };
+
+  /**
+   * Leaves a state.
+   * @param name - The state name.
+   */
+  Owl.prototype.leave = function(name) {
+    $.each(
+      [name].concat(this._states.tags[name] || []),
+      $.proxy(function(i, name) {
+        this._states.current[name]--;
+      }, this)
+    );
+  };
+
+  /**
+   * Registers an event or state.
+   * @public
+   * @param {Object} object - The event or state to register.
+   */
+  Owl.prototype.register = function(object) {
+    if (object.type === Owl.Type.Event) {
+      if (!$.event.special[object.name]) {
+        $.event.special[object.name] = {};
+      }
+
+      if (!$.event.special[object.name].owl) {
+        var _default = $.event.special[object.name]._default;
+        $.event.special[object.name]._default = function(e) {
+          if (
+            _default &&
+            _default.apply &&
+            (!e.namespace || e.namespace.indexOf("owl") === -1)
+          ) {
+            return _default.apply(this, arguments);
+          }
+          return e.namespace && e.namespace.indexOf("owl") > -1;
+        };
+        $.event.special[object.name].owl = true;
+      }
+    } else if (object.type === Owl.Type.State) {
+      if (!this._states.tags[object.name]) {
+        this._states.tags[object.name] = object.tags;
+      } else {
+        this._states.tags[object.name] = this._states.tags[object.name].concat(
+          object.tags
+        );
+      }
+
+      this._states.tags[object.name] = $.grep(
+        this._states.tags[object.name],
+        $.proxy(function(tag, i) {
+          return $.inArray(tag, this._states.tags[object.name]) === i;
+        }, this)
+      );
+    }
+  };
+
+  /**
+   * Suppresses events.
+   * @protected
+   * @param {Array.<String>} events - The events to suppress.
+   */
+  Owl.prototype.suppress = function(events) {
+    $.each(
+      events,
+      $.proxy(function(index, event) {
+        this._supress[event] = true;
+      }, this)
+    );
+  };
+
+  /**
+   * Releases suppressed events.
+   * @protected
+   * @param {Array.<String>} events - The events to release.
+   */
+  Owl.prototype.release = function(events) {
+    $.each(
+      events,
+      $.proxy(function(index, event) {
+        delete this._supress[event];
+      }, this)
+    );
+  };
+
+  /**
+   * Gets unified pointer coordinates from event.
+   * @todo #261
+   * @protected
+   * @param {Event} - The `mousedown` or `touchstart` event.
+   * @returns {Object} - Contains `x` and `y` coordinates of current pointer position.
+   */
+  Owl.prototype.pointer = function(event) {
+    var result = { x: null, y: null };
+
+    event = event.originalEvent || event || window.event;
+
+    event =
+      event.touches && event.touches.length
+        ? event.touches[0]
+        : event.changedTouches && event.changedTouches.length
+        ? event.changedTouches[0]
+        : event;
+
+    if (event.pageX) {
+      result.x = event.pageX;
+      result.y = event.pageY;
+    } else {
+      result.x = event.clientX;
+      result.y = event.clientY;
+    }
+
+    return result;
+  };
+
+  /**
+   * Determines if the input is a Number or something that can be coerced to a Number
+   * @protected
+   * @param {Number|String|Object|Array|Boolean|RegExp|Function|Symbol} - The input to be tested
+   * @returns {Boolean} - An indication if the input is a Number or can be coerced to a Number
+   */
+  Owl.prototype.isNumeric = function(number) {
+    return !isNaN(parseFloat(number));
+  };
+
+  /**
+   * Gets the difference of two vectors.
+   * @todo #261
+   * @protected
+   * @param {Object} - The first vector.
+   * @param {Object} - The second vector.
+   * @returns {Object} - The difference.
+   */
+  Owl.prototype.difference = function(first, second) {
+    return {
+      x: first.x - second.x,
+      y: first.y - second.y
+    };
+  };
+
+  /**
+   * The jQuery Plugin for the Owl Carousel
+   * @todo Navigation plugin `next` and `prev`
+   * @public
+   */
+  $.fn.owlCarousel = function(option) {
+    var args = Array.prototype.slice.call(arguments, 1);
+
+    return this.each(function() {
+      var $this = $(this),
+        data = $this.data("owl.carousel");
+
+      if (!data) {
+        data = new Owl(this, typeof option == "object" && option);
+        $this.data("owl.carousel", data);
+
+        $.each(
+          [
+            "next",
+            "prev",
+            "to",
+            "destroy",
+            "refresh",
+            "replace",
+            "add",
+            "remove"
+          ],
+          function(i, event) {
+            data.register({ type: Owl.Type.Event, name: event });
+            data.$element.on(
+              event + ".owl.carousel.core",
+              $.proxy(function(e) {
+                if (e.namespace && e.relatedTarget !== this) {
+                  this.suppress([event]);
+                  data[event].apply(this, [].slice.call(arguments, 1));
+                  this.release([event]);
+                }
+              }, data)
+            );
+          }
+        );
+      }
+
+      if (typeof option == "string" && option.charAt(0) !== "_") {
+        data[option].apply(data, args);
+      }
+    });
+  };
+
+  /**
+   * The constructor for the jQuery Plugin
+   * @public
+   */
+  $.fn.owlCarousel.Constructor = Owl;
 })(window.Zepto || window.jQuery, window, document);
 
 /**
@@ -1703,109 +1968,110 @@
  * @author David Deutsch
  * @license The MIT License (MIT)
  */
-;(function($, window, document, undefined) {
-
-	/**
-	 * Creates the auto refresh plugin.
-	 * @class The Auto Refresh Plugin
-	 * @param {Owl} carousel - The Owl Carousel
-	 */
-	var AutoRefresh = function(carousel) {
-		/**
-		 * Reference to the core.
-		 * @protected
-		 * @type {Owl}
-		 */
-		this._core = carousel;
-
-		/**
-		 * Refresh interval.
-		 * @protected
-		 * @type {number}
-		 */
-		this._interval = null;
-
-		/**
-		 * Whether the element is currently visible or not.
-		 * @protected
-		 * @type {Boolean}
-		 */
-		this._visible = null;
-
-		/**
-		 * All event handlers.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._handlers = {
-			'initialized.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.autoRefresh) {
-					this.watch();
-				}
-			}, this)
-		};
-
-		// set default options
-		this._core.options = $.extend({}, AutoRefresh.Defaults, this._core.options);
-
-		// register event handlers
-		this._core.$element.on(this._handlers);
-	};
-
-	/**
-	 * Default options.
-	 * @public
-	 */
-	AutoRefresh.Defaults = {
-		autoRefresh: true,
-		autoRefreshInterval: 500
-	};
-
-	/**
-	 * Watches the element.
-	 */
-	AutoRefresh.prototype.watch = function() {
-		if (this._interval) {
-			return;
-		}
-
-		this._visible = this._core.$element.is(':visible');
-		this._interval = window.setInterval($.proxy(this.refresh, this), this._core.settings.autoRefreshInterval);
-	};
-
-	/**
-	 * Refreshes the element.
-	 */
-	AutoRefresh.prototype.refresh = function() {
-		if (this._core.$element.is(':visible') === this._visible) {
-			return;
-		}
-
-		this._visible = !this._visible;
-
-		this._core.$element.toggleClass('owl-hidden', !this._visible);
-
-		this._visible && (this._core.invalidate('width') && this._core.refresh());
-	};
-
-	/**
-	 * Destroys the plugin.
-	 */
-	AutoRefresh.prototype.destroy = function() {
-		var handler, property;
-
-		window.clearInterval(this._interval);
-
-		for (handler in this._handlers) {
-			this._core.$element.off(handler, this._handlers[handler]);
-		}
-		for (property in Object.getOwnPropertyNames(this)) {
-			typeof this[property] != 'function' && (this[property] = null);
-		}
-	};
-
-	$.fn.owlCarousel.Constructor.Plugins.AutoRefresh = AutoRefresh;
-
+(function($, window, document, undefined) {
+  /**
+   * Creates the auto refresh plugin.
+   * @class The Auto Refresh Plugin
+   * @param {Owl} carousel - The Owl Carousel
+   */
+  var AutoRefresh = function(carousel) {
+    /**
+     * Reference to the core.
+     * @protected
+     * @type {Owl}
+     */
+    this._core = carousel;
+
+    /**
+     * Refresh interval.
+     * @protected
+     * @type {number}
+     */
+    this._interval = null;
+
+    /**
+     * Whether the element is currently visible or not.
+     * @protected
+     * @type {Boolean}
+     */
+    this._visible = null;
+
+    /**
+     * All event handlers.
+     * @protected
+     * @type {Object}
+     */
+    this._handlers = {
+      "initialized.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._core.settings.autoRefresh) {
+          this.watch();
+        }
+      }, this)
+    };
+
+    // set default options
+    this._core.options = $.extend({}, AutoRefresh.Defaults, this._core.options);
+
+    // register event handlers
+    this._core.$element.on(this._handlers);
+  };
+
+  /**
+   * Default options.
+   * @public
+   */
+  AutoRefresh.Defaults = {
+    autoRefresh: true,
+    autoRefreshInterval: 500
+  };
+
+  /**
+   * Watches the element.
+   */
+  AutoRefresh.prototype.watch = function() {
+    if (this._interval) {
+      return;
+    }
+
+    this._visible = this._core.$element.is(":visible");
+    this._interval = window.setInterval(
+      $.proxy(this.refresh, this),
+      this._core.settings.autoRefreshInterval
+    );
+  };
+
+  /**
+   * Refreshes the element.
+   */
+  AutoRefresh.prototype.refresh = function() {
+    if (this._core.$element.is(":visible") === this._visible) {
+      return;
+    }
+
+    this._visible = !this._visible;
+
+    this._core.$element.toggleClass("owl-hidden", !this._visible);
+
+    this._visible && this._core.invalidate("width") && this._core.refresh();
+  };
+
+  /**
+   * Destroys the plugin.
+   */
+  AutoRefresh.prototype.destroy = function() {
+    var handler, property;
+
+    window.clearInterval(this._interval);
+
+    for (handler in this._handlers) {
+      this._core.$element.off(handler, this._handlers[handler]);
+    }
+    for (property in Object.getOwnPropertyNames(this)) {
+      typeof this[property] != "function" && (this[property] = null);
+    }
+  };
+
+  $.fn.owlCarousel.Constructor.Plugins.AutoRefresh = AutoRefresh;
 })(window.Zepto || window.jQuery, window, document);
 
 /**
@@ -1815,133 +2081,162 @@
  * @author David Deutsch
  * @license The MIT License (MIT)
  */
-;(function($, window, document, undefined) {
-
-	/**
-	 * Creates the lazy plugin.
-	 * @class The Lazy Plugin
-	 * @param {Owl} carousel - The Owl Carousel
-	 */
-	var Lazy = function(carousel) {
-
-		/**
-		 * Reference to the core.
-		 * @protected
-		 * @type {Owl}
-		 */
-		this._core = carousel;
-
-		/**
-		 * Already loaded items.
-		 * @protected
-		 * @type {Array.<jQuery>}
-		 */
-		this._loaded = [];
-
-		/**
-		 * Event handlers.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._handlers = {
-			'initialized.owl.carousel change.owl.carousel resized.owl.carousel': $.proxy(function(e) {
-				if (!e.namespace) {
-					return;
-				}
-
-				if (!this._core.settings || !this._core.settings.lazyLoad) {
-					return;
-				}
-
-				if ((e.property && e.property.name == 'position') || e.type == 'initialized') {
-					var settings = this._core.settings,
-						n = (settings.center && Math.ceil(settings.items / 2) || settings.items),
-						i = ((settings.center && n * -1) || 0),
-						position = (e.property && e.property.value !== undefined ? e.property.value : this._core.current()) + i,
-						clones = this._core.clones().length,
-						load = $.proxy(function(i, v) { this.load(v) }, this);
-
-					while (i++ < n) {
-						this.load(clones / 2 + this._core.relative(position));
-						clones && $.each(this._core.clones(this._core.relative(position)), load);
-						position++;
-					}
-				}
-			}, this)
-		};
-
-		// set the default options
-		this._core.options = $.extend({}, Lazy.Defaults, this._core.options);
-
-		// register event handler
-		this._core.$element.on(this._handlers);
-	};
-
-	/**
-	 * Default options.
-	 * @public
-	 */
-	Lazy.Defaults = {
-		lazyLoad: false
-	};
-
-	/**
-	 * Loads all resources of an item at the specified position.
-	 * @param {Number} position - The absolute position of the item.
-	 * @protected
-	 */
-	Lazy.prototype.load = function(position) {
-		var $item = this._core.$stage.children().eq(position),
-			$elements = $item && $item.find('.owl-lazy');
-
-		if (!$elements || $.inArray($item.get(0), this._loaded) > -1) {
-			return;
-		}
-
-		$elements.each($.proxy(function(index, element) {
-			var $element = $(element), image,
-				url = (window.devicePixelRatio > 1 && $element.attr('data-src-retina')) || $element.attr('data-src');
-
-			this._core.trigger('load', { element: $element, url: url }, 'lazy');
-
-			if ($element.is('img')) {
-				$element.one('load.owl.lazy', $.proxy(function() {
-					$element.css('opacity', 1);
-					this._core.trigger('loaded', { element: $element, url: url }, 'lazy');
-				}, this)).attr('src', url);
-			} else {
-				image = new Image();
-				image.onload = $.proxy(function() {
-					$element.css({
-						'background-image': 'url("' + url + '")',
-						'opacity': '1'
-					});
-					this._core.trigger('loaded', { element: $element, url: url }, 'lazy');
-				}, this);
-				image.src = url;
-			}
-		}, this));
-
-		this._loaded.push($item.get(0));
-	};
-
-	/**
-	 * Destroys the plugin.
-	 * @public
-	 */
-	Lazy.prototype.destroy = function() {
-		var handler, property;
-
-		for (handler in this.handlers) {
-			this._core.$element.off(handler, this.handlers[handler]);
-		}
-		for (property in Object.getOwnPropertyNames(this)) {
-			typeof this[property] != 'function' && (this[property] = null);
-		}
-	};
-
-	$.fn.owlCarousel.Constructor.Plugins.Lazy = Lazy;
-
+(function($, window, document, undefined) {
+  /**
+   * Creates the lazy plugin.
+   * @class The Lazy Plugin
+   * @param {Owl} carousel - The Owl Carousel
+   */
+  var Lazy = function(carousel) {
+    /**
+     * Reference to the core.
+     * @protected
+     * @type {Owl}
+     */
+    this._core = carousel;
+
+    /**
+     * Already loaded items.
+     * @protected
+     * @type {Array.<jQuery>}
+     */
+    this._loaded = [];
+
+    /**
+     * Event handlers.
+     * @protected
+     * @type {Object}
+     */
+    this._handlers = {
+      "initialized.owl.carousel change.owl.carousel resized.owl.carousel": $.proxy(
+        function(e) {
+          if (!e.namespace) {
+            return;
+          }
+
+          if (!this._core.settings || !this._core.settings.lazyLoad) {
+            return;
+          }
+
+          if (
+            (e.property && e.property.name == "position") ||
+            e.type == "initialized"
+          ) {
+            var settings = this._core.settings,
+              n =
+                (settings.center && Math.ceil(settings.items / 2)) ||
+                settings.items,
+              i = (settings.center && n * -1) || 0,
+              position =
+                (e.property && e.property.value !== undefined
+                  ? e.property.value
+                  : this._core.current()) + i,
+              clones = this._core.clones().length,
+              load = $.proxy(function(i, v) {
+                this.load(v);
+              }, this);
+
+            while (i++ < n) {
+              this.load(clones / 2 + this._core.relative(position));
+              clones &&
+                $.each(this._core.clones(this._core.relative(position)), load);
+              position++;
+            }
+          }
+        },
+        this
+      )
+    };
+
+    // set the default options
+    this._core.options = $.extend({}, Lazy.Defaults, this._core.options);
+
+    // register event handler
+    this._core.$element.on(this._handlers);
+  };
+
+  /**
+   * Default options.
+   * @public
+   */
+  Lazy.Defaults = {
+    lazyLoad: false
+  };
+
+  /**
+   * Loads all resources of an item at the specified position.
+   * @param {Number} position - The absolute position of the item.
+   * @protected
+   */
+  Lazy.prototype.load = function(position) {
+    var $item = this._core.$stage.children().eq(position),
+      $elements = $item && $item.find(".owl-lazy");
+
+    if (!$elements || $.inArray($item.get(0), this._loaded) > -1) {
+      return;
+    }
+
+    $elements.each(
+      $.proxy(function(index, element) {
+        var $element = $(element),
+          image,
+          url =
+            (window.devicePixelRatio > 1 && $element.attr("data-src-retina")) ||
+            $element.attr("data-src");
+
+        this._core.trigger("load", { element: $element, url: url }, "lazy");
+
+        if ($element.is("img")) {
+          $element
+            .one(
+              "load.owl.lazy",
+              $.proxy(function() {
+                $element.css("opacity", 1);
+                this._core.trigger(
+                  "loaded",
+                  { element: $element, url: url },
+                  "lazy"
+                );
+              }, this)
+            )
+            .attr("src", url);
+        } else {
+          image = new Image();
+          image.onload = $.proxy(function() {
+            $element.css({
+              "background-image": 'url("' + url + '")',
+              opacity: "1"
+            });
+            this._core.trigger(
+              "loaded",
+              { element: $element, url: url },
+              "lazy"
+            );
+          }, this);
+          image.src = url;
+        }
+      }, this)
+    );
+
+    this._loaded.push($item.get(0));
+  };
+
+  /**
+   * Destroys the plugin.
+   * @public
+   */
+  Lazy.prototype.destroy = function() {
+    var handler, property;
+
+    for (handler in this.handlers) {
+      this._core.$element.off(handler, this.handlers[handler]);
+    }
+    for (property in Object.getOwnPropertyNames(this)) {
+      typeof this[property] != "function" && (this[property] = null);
+    }
+  };
+
+  $.fn.owlCarousel.Constructor.Plugins.Lazy = Lazy;
 })(window.Zepto || window.jQuery, window, document);
 
 /**
@@ -1951,95 +2246,105 @@
  * @author David Deutsch
  * @license The MIT License (MIT)
  */
-;(function($, window, document, undefined) {
-
-	/**
-	 * Creates the auto height plugin.
-	 * @class The Auto Height Plugin
-	 * @param {Owl} carousel - The Owl Carousel
-	 */
-	var AutoHeight = function(carousel) {
-		/**
-		 * Reference to the core.
-		 * @protected
-		 * @type {Owl}
-		 */
-		this._core = carousel;
-
-		/**
-		 * All event handlers.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._handlers = {
-			'initialized.owl.carousel refreshed.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.autoHeight) {
-					this.update();
-				}
-			}, this),
-			'changed.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.autoHeight && e.property.name == 'position'){
-					this.update();
-				}
-			}, this),
-			'loaded.owl.lazy': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.autoHeight
-					&& e.element.closest('.' + this._core.settings.itemClass).index() === this._core.current()) {
-					this.update();
-				}
-			}, this)
-		};
-
-		// set default options
-		this._core.options = $.extend({}, AutoHeight.Defaults, this._core.options);
-
-		// register event handlers
-		this._core.$element.on(this._handlers);
-	};
-
-	/**
-	 * Default options.
-	 * @public
-	 */
-	AutoHeight.Defaults = {
-		autoHeight: false,
-		autoHeightClass: 'owl-height'
-	};
-
-	/**
-	 * Updates the view.
-	 */
-	AutoHeight.prototype.update = function() {
-		var start = this._core._current,
-			end = start + this._core.settings.items,
-			visible = this._core.$stage.children().toArray().slice(start, end),
-			heights = [],
-			maxheight = 0;
-
-		$.each(visible, function(index, item) {
-			heights.push($(item).height());
-		});
-
-		maxheight = Math.max.apply(null, heights);
-
-		this._core.$stage.parent()
-			.height(maxheight)
-			.addClass(this._core.settings.autoHeightClass);
-	};
-
-	AutoHeight.prototype.destroy = function() {
-		var handler, property;
-
-		for (handler in this._handlers) {
-			this._core.$element.off(handler, this._handlers[handler]);
-		}
-		for (property in Object.getOwnPropertyNames(this)) {
-			typeof this[property] != 'function' && (this[property] = null);
-		}
-	};
-
-	$.fn.owlCarousel.Constructor.Plugins.AutoHeight = AutoHeight;
-
+(function($, window, document, undefined) {
+  /**
+   * Creates the auto height plugin.
+   * @class The Auto Height Plugin
+   * @param {Owl} carousel - The Owl Carousel
+   */
+  var AutoHeight = function(carousel) {
+    /**
+     * Reference to the core.
+     * @protected
+     * @type {Owl}
+     */
+    this._core = carousel;
+
+    /**
+     * All event handlers.
+     * @protected
+     * @type {Object}
+     */
+    this._handlers = {
+      "initialized.owl.carousel refreshed.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._core.settings.autoHeight) {
+          this.update();
+        }
+      }, this),
+      "changed.owl.carousel": $.proxy(function(e) {
+        if (
+          e.namespace &&
+          this._core.settings.autoHeight &&
+          e.property.name == "position"
+        ) {
+          this.update();
+        }
+      }, this),
+      "loaded.owl.lazy": $.proxy(function(e) {
+        if (
+          e.namespace &&
+          this._core.settings.autoHeight &&
+          e.element.closest("." + this._core.settings.itemClass).index() ===
+            this._core.current()
+        ) {
+          this.update();
+        }
+      }, this)
+    };
+
+    // set default options
+    this._core.options = $.extend({}, AutoHeight.Defaults, this._core.options);
+
+    // register event handlers
+    this._core.$element.on(this._handlers);
+  };
+
+  /**
+   * Default options.
+   * @public
+   */
+  AutoHeight.Defaults = {
+    autoHeight: false,
+    autoHeightClass: "owl-height"
+  };
+
+  /**
+   * Updates the view.
+   */
+  AutoHeight.prototype.update = function() {
+    var start = this._core._current,
+      end = start + this._core.settings.items,
+      visible = this._core.$stage
+        .children()
+        .toArray()
+        .slice(start, end),
+      heights = [],
+      maxheight = 0;
+
+    $.each(visible, function(index, item) {
+      heights.push($(item).height());
+    });
+
+    maxheight = Math.max.apply(null, heights);
+
+    this._core.$stage
+      .parent()
+      .height(maxheight)
+      .addClass(this._core.settings.autoHeightClass);
+  };
+
+  AutoHeight.prototype.destroy = function() {
+    var handler, property;
+
+    for (handler in this._handlers) {
+      this._core.$element.off(handler, this._handlers[handler]);
+    }
+    for (property in Object.getOwnPropertyNames(this)) {
+      typeof this[property] != "function" && (this[property] = null);
+    }
+  };
+
+  $.fn.owlCarousel.Constructor.Plugins.AutoHeight = AutoHeight;
 })(window.Zepto || window.jQuery, window, document);
 
 /**
@@ -2049,121 +2354,130 @@
  * @author David Deutsch
  * @license The MIT License (MIT)
  */
-;(function($, window, document, undefined) {
-
-	/**
-	 * Creates the video plugin.
-	 * @class The Video Plugin
-	 * @param {Owl} carousel - The Owl Carousel
-	 */
-	var Video = function(carousel) {
-		/**
-		 * Reference to the core.
-		 * @protected
-		 * @type {Owl}
-		 */
-		this._core = carousel;
-
-		/**
-		 * Cache all video URLs.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._videos = {};
-
-		/**
-		 * Current playing item.
-		 * @protected
-		 * @type {jQuery}
-		 */
-		this._playing = null;
-
-		/**
-		 * All event handlers.
-		 * @todo The cloned content removale is too late
-		 * @protected
-		 * @type {Object}
-		 */
-		this._handlers = {
-			'initialized.owl.carousel': $.proxy(function(e) {
-				if (e.namespace) {
-					this._core.register({ type: 'state', name: 'playing', tags: [ 'interacting' ] });
-				}
-			}, this),
-			'resize.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.video && this.isInFullScreen()) {
-					e.preventDefault();
-				}
-			}, this),
-			'refreshed.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.is('resizing')) {
-					this._core.$stage.find('.cloned .owl-video-frame').remove();
-				}
-			}, this),
-			'changed.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && e.property.name === 'position' && this._playing) {
-					this.stop();
-				}
-			}, this),
-			'prepared.owl.carousel': $.proxy(function(e) {
-				if (!e.namespace) {
-					return;
-				}
-
-				var $element = $(e.content).find('.owl-video');
-
-				if ($element.length) {
-					$element.css('display', 'none');
-					this.fetch($element, $(e.content));
-				}
-			}, this)
-		};
-
-		// set default options
-		this._core.options = $.extend({}, Video.Defaults, this._core.options);
-
-		// register event handlers
-		this._core.$element.on(this._handlers);
-
-		this._core.$element.on('click.owl.video', '.owl-video-play-icon', $.proxy(function(e) {
-			this.play(e);
-		}, this));
-	};
-
-	/**
-	 * Default options.
-	 * @public
-	 */
-	Video.Defaults = {
-		video: false,
-		videoHeight: false,
-		videoWidth: false
-	};
-
-	/**
-	 * Gets the video ID and the type (YouTube/Vimeo/vzaar only).
-	 * @protected
-	 * @param {jQuery} target - The target containing the video data.
-	 * @param {jQuery} item - The item containing the video.
-	 */
-	Video.prototype.fetch = function(target, item) {
-			var type = (function() {
-					if (target.attr('data-vimeo-id')) {
-						return 'vimeo';
-					} else if (target.attr('data-vzaar-id')) {
-						return 'vzaar'
-					} else {
-						return 'youtube';
-					}
-				})(),
-				id = target.attr('data-vimeo-id') || target.attr('data-youtube-id') || target.attr('data-vzaar-id'),
-				width = target.attr('data-width') || this._core.settings.videoWidth,
-				height = target.attr('data-height') || this._core.settings.videoHeight,
-				url = target.attr('href');
-
-		if (url) {
-
-			/*
+(function($, window, document, undefined) {
+  /**
+   * Creates the video plugin.
+   * @class The Video Plugin
+   * @param {Owl} carousel - The Owl Carousel
+   */
+  var Video = function(carousel) {
+    /**
+     * Reference to the core.
+     * @protected
+     * @type {Owl}
+     */
+    this._core = carousel;
+
+    /**
+     * Cache all video URLs.
+     * @protected
+     * @type {Object}
+     */
+    this._videos = {};
+
+    /**
+     * Current playing item.
+     * @protected
+     * @type {jQuery}
+     */
+    this._playing = null;
+
+    /**
+     * All event handlers.
+     * @todo The cloned content removale is too late
+     * @protected
+     * @type {Object}
+     */
+    this._handlers = {
+      "initialized.owl.carousel": $.proxy(function(e) {
+        if (e.namespace) {
+          this._core.register({
+            type: "state",
+            name: "playing",
+            tags: ["interacting"]
+          });
+        }
+      }, this),
+      "resize.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._core.settings.video && this.isInFullScreen()) {
+          e.preventDefault();
+        }
+      }, this),
+      "refreshed.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._core.is("resizing")) {
+          this._core.$stage.find(".cloned .owl-video-frame").remove();
+        }
+      }, this),
+      "changed.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && e.property.name === "position" && this._playing) {
+          this.stop();
+        }
+      }, this),
+      "prepared.owl.carousel": $.proxy(function(e) {
+        if (!e.namespace) {
+          return;
+        }
+
+        var $element = $(e.content).find(".owl-video");
+
+        if ($element.length) {
+          $element.css("display", "none");
+          this.fetch($element, $(e.content));
+        }
+      }, this)
+    };
+
+    // set default options
+    this._core.options = $.extend({}, Video.Defaults, this._core.options);
+
+    // register event handlers
+    this._core.$element.on(this._handlers);
+
+    this._core.$element.on(
+      "click.owl.video",
+      ".owl-video-play-icon",
+      $.proxy(function(e) {
+        this.play(e);
+      }, this)
+    );
+  };
+
+  /**
+   * Default options.
+   * @public
+   */
+  Video.Defaults = {
+    video: false,
+    videoHeight: false,
+    videoWidth: false
+  };
+
+  /**
+   * Gets the video ID and the type (YouTube/Vimeo/vzaar only).
+   * @protected
+   * @param {jQuery} target - The target containing the video data.
+   * @param {jQuery} item - The item containing the video.
+   */
+  Video.prototype.fetch = function(target, item) {
+    var type = (function() {
+        if (target.attr("data-vimeo-id")) {
+          return "vimeo";
+        } else if (target.attr("data-vzaar-id")) {
+          return "vzaar";
+        } else {
+          return "youtube";
+        }
+      })(),
+      id =
+        target.attr("data-vimeo-id") ||
+        target.attr("data-youtube-id") ||
+        target.attr("data-vzaar-id"),
+      width = target.attr("data-width") || this._core.settings.videoWidth,
+      height = target.attr("data-height") || this._core.settings.videoHeight,
+      url = target.attr("href");
+
+    if (url) {
+      /*
 					Parses the id's out of the following urls (and probably more):
 					https://www.youtube.com/watch?v=:id
 					https://youtu.be/:id
@@ -2175,191 +2489,235 @@
 					Visual example: https://regexper.com/#(http%3A%7Chttps%3A%7C)%5C%2F%5C%2F(player.%7Cwww.%7Capp.)%3F(vimeo%5C.com%7Cyoutu(be%5C.com%7C%5C.be%7Cbe%5C.googleapis%5C.com)%7Cvzaar%5C.com)%5C%2F(video%5C%2F%7Cvideos%5C%2F%7Cembed%5C%2F%7Cchannels%5C%2F.%2B%5C%2F%7Cgroups%5C%2F.%2B%5C%2F%7Cwatch%5C%3Fv%3D%7Cv%5C%2F)%3F(%5BA-Za-z0-9._%25-%5D*)(%5C%26%5CS%2B)%3F
 			*/
 
-			id = url.match(/(http:|https:|)\/\/(player.|www.|app.)?(vimeo\.com|youtu(be\.com|\.be|be\.googleapis\.com)|vzaar\.com)\/(video\/|videos\/|embed\/|channels\/.+\/|groups\/.+\/|watch\?v=|v\/)?([A-Za-z0-9._%-]*)(\&\S+)?/);
-
-			if (id[3].indexOf('youtu') > -1) {
-				type = 'youtube';
-			} else if (id[3].indexOf('vimeo') > -1) {
-				type = 'vimeo';
-			} else if (id[3].indexOf('vzaar') > -1) {
-				type = 'vzaar';
-			} else {
-				throw new Error('Video URL not supported.');
-			}
-			id = id[6];
-		} else {
-			throw new Error('Missing video URL.');
-		}
-
-		this._videos[url] = {
-			type: type,
-			id: id,
-			width: width,
-			height: height
-		};
-
-		item.attr('data-video', url);
-
-		this.thumbnail(target, this._videos[url]);
-	};
-
-	/**
-	 * Creates video thumbnail.
-	 * @protected
-	 * @param {jQuery} target - The target containing the video data.
-	 * @param {Object} info - The video info object.
-	 * @see `fetch`
-	 */
-	Video.prototype.thumbnail = function(target, video) {
-		var tnLink,
-			icon,
-			path,
-			dimensions = video.width && video.height ? 'style="width:' + video.width + 'px;height:' + video.height + 'px;"' : '',
-			customTn = target.find('img'),
-			srcType = 'src',
-			lazyClass = '',
-			settings = this._core.settings,
-			create = function(path) {
-				icon = '<div class="owl-video-play-icon"></div>';
-
-				if (settings.lazyLoad) {
-					tnLink = '<div class="owl-video-tn ' + lazyClass + '" ' + srcType + '="' + path + '"></div>';
-				} else {
-					tnLink = '<div class="owl-video-tn" style="opacity:1;background-image:url(' + path + ')"></div>';
-				}
-				target.after(tnLink);
-				target.after(icon);
-			};
-
-		// wrap video content into owl-video-wrapper div
-		target.wrap('<div class="owl-video-wrapper"' + dimensions + '></div>');
-
-		if (this._core.settings.lazyLoad) {
-			srcType = 'data-src';
-			lazyClass = 'owl-lazy';
-		}
-
-		// custom thumbnail
-		if (customTn.length) {
-			create(customTn.attr(srcType));
-			customTn.remove();
-			return false;
-		}
-
-		if (video.type === 'youtube') {
-			path = "//img.youtube.com/vi/" + video.id + "/hqdefault.jpg";
-			create(path);
-		} else if (video.type === 'vimeo') {
-			$.ajax({
-				type: 'GET',
-				url: '//vimeo.com/api/v2/video/' + video.id + '.json',
-				jsonp: 'callback',
-				dataType: 'jsonp',
-				success: function(data) {
-					path = data[0].thumbnail_large;
-					create(path);
-				}
-			});
-		} else if (video.type === 'vzaar') {
-			$.ajax({
-				type: 'GET',
-				url: '//vzaar.com/api/videos/' + video.id + '.json',
-				jsonp: 'callback',
-				dataType: 'jsonp',
-				success: function(data) {
-					path = data.framegrab_url;
-					create(path);
-				}
-			});
-		}
-	};
-
-	/**
-	 * Stops the current video.
-	 * @public
-	 */
-	Video.prototype.stop = function() {
-		this._core.trigger('stop', null, 'video');
-		this._playing.find('.owl-video-frame').remove();
-		this._playing.removeClass('owl-video-playing');
-		this._playing = null;
-		this._core.leave('playing');
-		this._core.trigger('stopped', null, 'video');
-	};
-
-	/**
-	 * Starts the current video.
-	 * @public
-	 * @param {Event} event - The event arguments.
-	 */
-	Video.prototype.play = function(event) {
-		var target = $(event.target),
-			item = target.closest('.' + this._core.settings.itemClass),
-			video = this._videos[item.attr('data-video')],
-			width = video.width || '100%',
-			height = video.height || this._core.$stage.height(),
-			html;
-
-		if (this._playing) {
-			return;
-		}
-
-		this._core.enter('playing');
-		this._core.trigger('play', null, 'video');
-
-		item = this._core.items(this._core.relative(item.index()));
-
-		this._core.reset(item.index());
-
-		if (video.type === 'youtube') {
-			html = '<iframe width="' + width + '" height="' + height + '" src="//www.youtube.com/embed/' +
-				video.id + '?autoplay=1&rel=0&v=' + video.id + '" frameborder="0" allowfullscreen></iframe>';
-		} else if (video.type === 'vimeo') {
-			html = '<iframe src="//player.vimeo.com/video/' + video.id +
-				'?autoplay=1" width="' + width + '" height="' + height +
-				'" frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></iframe>';
-		} else if (video.type === 'vzaar') {
-			html = '<iframe frameborder="0"' + 'height="' + height + '"' + 'width="' + width +
-				'" allowfullscreen mozallowfullscreen webkitAllowFullScreen ' +
-				'src="//view.vzaar.com/' + video.id + '/player?autoplay=true"></iframe>';
-		}
-
-		$('<div class="owl-video-frame">' + html + '</div>').insertAfter(item.find('.owl-video'));
-
-		this._playing = item.addClass('owl-video-playing');
-	};
-
-	/**
-	 * Checks whether an video is currently in full screen mode or not.
-	 * @todo Bad style because looks like a readonly method but changes members.
-	 * @protected
-	 * @returns {Boolean}
-	 */
-	Video.prototype.isInFullScreen = function() {
-		var element = document.fullscreenElement || document.mozFullScreenElement ||
-				document.webkitFullscreenElement;
-
-		return element && $(element).parent().hasClass('owl-video-frame');
-	};
-
-	/**
-	 * Destroys the plugin.
-	 */
-	Video.prototype.destroy = function() {
-		var handler, property;
-
-		this._core.$element.off('click.owl.video');
-
-		for (handler in this._handlers) {
-			this._core.$element.off(handler, this._handlers[handler]);
-		}
-		for (property in Object.getOwnPropertyNames(this)) {
-			typeof this[property] != 'function' && (this[property] = null);
-		}
-	};
-
-	$.fn.owlCarousel.Constructor.Plugins.Video = Video;
-
+      id = url.match(
+        /(http:|https:|)\/\/(player.|www.|app.)?(vimeo\.com|youtu(be\.com|\.be|be\.googleapis\.com)|vzaar\.com)\/(video\/|videos\/|embed\/|channels\/.+\/|groups\/.+\/|watch\?v=|v\/)?([A-Za-z0-9._%-]*)(\&\S+)?/
+      );
+
+      if (id[3].indexOf("youtu") > -1) {
+        type = "youtube";
+      } else if (id[3].indexOf("vimeo") > -1) {
+        type = "vimeo";
+      } else if (id[3].indexOf("vzaar") > -1) {
+        type = "vzaar";
+      } else {
+        throw new Error("Video URL not supported.");
+      }
+      id = id[6];
+    } else {
+      throw new Error("Missing video URL.");
+    }
+
+    this._videos[url] = {
+      type: type,
+      id: id,
+      width: width,
+      height: height
+    };
+
+    item.attr("data-video", url);
+
+    this.thumbnail(target, this._videos[url]);
+  };
+
+  /**
+   * Creates video thumbnail.
+   * @protected
+   * @param {jQuery} target - The target containing the video data.
+   * @param {Object} info - The video info object.
+   * @see `fetch`
+   */
+  Video.prototype.thumbnail = function(target, video) {
+    var tnLink,
+      icon,
+      path,
+      dimensions =
+        video.width && video.height
+          ? 'style="width:' + video.width + "px;height:" + video.height + 'px;"'
+          : "",
+      customTn = target.find("img"),
+      srcType = "src",
+      lazyClass = "",
+      settings = this._core.settings,
+      create = function(path) {
+        icon = '<div class="owl-video-play-icon"></div>';
+
+        if (settings.lazyLoad) {
+          tnLink =
+            '<div class="owl-video-tn ' +
+            lazyClass +
+            '" ' +
+            srcType +
+            '="' +
+            path +
+            '"></div>';
+        } else {
+          tnLink =
+            '<div class="owl-video-tn" style="opacity:1;background-image:url(' +
+            path +
+            ')"></div>';
+        }
+        target.after(tnLink);
+        target.after(icon);
+      };
+
+    // wrap video content into owl-video-wrapper div
+    target.wrap('<div class="owl-video-wrapper"' + dimensions + "></div>");
+
+    if (this._core.settings.lazyLoad) {
+      srcType = "data-src";
+      lazyClass = "owl-lazy";
+    }
+
+    // custom thumbnail
+    if (customTn.length) {
+      create(customTn.attr(srcType));
+      customTn.remove();
+      return false;
+    }
+
+    if (video.type === "youtube") {
+      path = "//img.youtube.com/vi/" + video.id + "/hqdefault.jpg";
+      create(path);
+    } else if (video.type === "vimeo") {
+      $.ajax({
+        type: "GET",
+        url: "//vimeo.com/api/v2/video/" + video.id + ".json",
+        jsonp: "callback",
+        dataType: "jsonp",
+        success: function(data) {
+          path = data[0].thumbnail_large;
+          create(path);
+        }
+      });
+    } else if (video.type === "vzaar") {
+      $.ajax({
+        type: "GET",
+        url: "//vzaar.com/api/videos/" + video.id + ".json",
+        jsonp: "callback",
+        dataType: "jsonp",
+        success: function(data) {
+          path = data.framegrab_url;
+          create(path);
+        }
+      });
+    }
+  };
+
+  /**
+   * Stops the current video.
+   * @public
+   */
+  Video.prototype.stop = function() {
+    this._core.trigger("stop", null, "video");
+    this._playing.find(".owl-video-frame").remove();
+    this._playing.removeClass("owl-video-playing");
+    this._playing = null;
+    this._core.leave("playing");
+    this._core.trigger("stopped", null, "video");
+  };
+
+  /**
+   * Starts the current video.
+   * @public
+   * @param {Event} event - The event arguments.
+   */
+  Video.prototype.play = function(event) {
+    var target = $(event.target),
+      item = target.closest("." + this._core.settings.itemClass),
+      video = this._videos[item.attr("data-video")],
+      width = video.width || "100%",
+      height = video.height || this._core.$stage.height(),
+      html;
+
+    if (this._playing) {
+      return;
+    }
+
+    this._core.enter("playing");
+    this._core.trigger("play", null, "video");
+
+    item = this._core.items(this._core.relative(item.index()));
+
+    this._core.reset(item.index());
+
+    if (video.type === "youtube") {
+      html =
+        '<iframe width="' +
+        width +
+        '" height="' +
+        height +
+        '" src="//www.youtube.com/embed/' +
+        video.id +
+        "?autoplay=1&rel=0&v=" +
+        video.id +
+        '" frameborder="0" allowfullscreen></iframe>';
+    } else if (video.type === "vimeo") {
+      html =
+        '<iframe src="//player.vimeo.com/video/' +
+        video.id +
+        '?autoplay=1" width="' +
+        width +
+        '" height="' +
+        height +
+        '" frameborder="0" webkitallowfullscreen mozallowfullscreen allowfullscreen></iframe>';
+    } else if (video.type === "vzaar") {
+      html =
+        '<iframe frameborder="0"' +
+        'height="' +
+        height +
+        '"' +
+        'width="' +
+        width +
+        '" allowfullscreen mozallowfullscreen webkitAllowFullScreen ' +
+        'src="//view.vzaar.com/' +
+        video.id +
+        '/player?autoplay=true"></iframe>';
+    }
+
+    $('<div class="owl-video-frame">' + html + "</div>").insertAfter(
+      item.find(".owl-video")
+    );
+
+    this._playing = item.addClass("owl-video-playing");
+  };
+
+  /**
+   * Checks whether an video is currently in full screen mode or not.
+   * @todo Bad style because looks like a readonly method but changes members.
+   * @protected
+   * @returns {Boolean}
+   */
+  Video.prototype.isInFullScreen = function() {
+    var element =
+      document.fullscreenElement ||
+      document.mozFullScreenElement ||
+      document.webkitFullscreenElement;
+
+    return (
+      element &&
+      $(element)
+        .parent()
+        .hasClass("owl-video-frame")
+    );
+  };
+
+  /**
+   * Destroys the plugin.
+   */
+  Video.prototype.destroy = function() {
+    var handler, property;
+
+    this._core.$element.off("click.owl.video");
+
+    for (handler in this._handlers) {
+      this._core.$element.off(handler, this._handlers[handler]);
+    }
+    for (property in Object.getOwnPropertyNames(this)) {
+      typeof this[property] != "function" && (this[property] = null);
+    }
+  };
+
+  $.fn.owlCarousel.Constructor.Plugins.Video = Video;
 })(window.Zepto || window.jQuery, window, document);
 
 /**
@@ -2369,119 +2727,127 @@
  * @author David Deutsch
  * @license The MIT License (MIT)
  */
-;(function($, window, document, undefined) {
-
-	/**
-	 * Creates the animate plugin.
-	 * @class The Navigation Plugin
-	 * @param {Owl} scope - The Owl Carousel
-	 */
-	var Animate = function(scope) {
-		this.core = scope;
-		this.core.options = $.extend({}, Animate.Defaults, this.core.options);
-		this.swapping = true;
-		this.previous = undefined;
-		this.next = undefined;
-
-		this.handlers = {
-			'change.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && e.property.name == 'position') {
-					this.previous = this.core.current();
-					this.next = e.property.value;
-				}
-			}, this),
-			'drag.owl.carousel dragged.owl.carousel translated.owl.carousel': $.proxy(function(e) {
-				if (e.namespace) {
-					this.swapping = e.type == 'translated';
-				}
-			}, this),
-			'translate.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this.swapping && (this.core.options.animateOut || this.core.options.animateIn)) {
-					this.swap();
-				}
-			}, this)
-		};
-
-		this.core.$element.on(this.handlers);
-	};
-
-	/**
-	 * Default options.
-	 * @public
-	 */
-	Animate.Defaults = {
-		animateOut: false,
-		animateIn: false
-	};
-
-	/**
-	 * Toggles the animation classes whenever an translations starts.
-	 * @protected
-	 * @returns {Boolean|undefined}
-	 */
-	Animate.prototype.swap = function() {
-
-		if (this.core.settings.items !== 1) {
-			return;
-		}
-
-		if (!$.support.animation || !$.support.transition) {
-			return;
-		}
-
-		this.core.speed(0);
-
-		var left,
-			clear = $.proxy(this.clear, this),
-			previous = this.core.$stage.children().eq(this.previous),
-			next = this.core.$stage.children().eq(this.next),
-			incoming = this.core.settings.animateIn,
-			outgoing = this.core.settings.animateOut;
-
-		if (this.core.current() === this.previous) {
-			return;
-		}
-
-		if (outgoing) {
-			left = this.core.coordinates(this.previous) - this.core.coordinates(this.next);
-			previous.one($.support.animation.end, clear)
-				.css( { 'left': left + 'px' } )
-				.addClass('animated owl-animated-out')
-				.addClass(outgoing);
-		}
-
-		if (incoming) {
-			next.one($.support.animation.end, clear)
-				.addClass('animated owl-animated-in')
-				.addClass(incoming);
-		}
-	};
-
-	Animate.prototype.clear = function(e) {
-		$(e.target).css( { 'left': '' } )
-			.removeClass('animated owl-animated-out owl-animated-in')
-			.removeClass(this.core.settings.animateIn)
-			.removeClass(this.core.settings.animateOut);
-		this.core.onTransitionEnd();
-	};
-
-	/**
-	 * Destroys the plugin.
-	 * @public
-	 */
-	Animate.prototype.destroy = function() {
-		var handler, property;
-
-		for (handler in this.handlers) {
-			this.core.$element.off(handler, this.handlers[handler]);
-		}
-		for (property in Object.getOwnPropertyNames(this)) {
-			typeof this[property] != 'function' && (this[property] = null);
-		}
-	};
-
-	$.fn.owlCarousel.Constructor.Plugins.Animate = Animate;
-
+(function($, window, document, undefined) {
+  /**
+   * Creates the animate plugin.
+   * @class The Navigation Plugin
+   * @param {Owl} scope - The Owl Carousel
+   */
+  var Animate = function(scope) {
+    this.core = scope;
+    this.core.options = $.extend({}, Animate.Defaults, this.core.options);
+    this.swapping = true;
+    this.previous = undefined;
+    this.next = undefined;
+
+    this.handlers = {
+      "change.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && e.property.name == "position") {
+          this.previous = this.core.current();
+          this.next = e.property.value;
+        }
+      }, this),
+      "drag.owl.carousel dragged.owl.carousel translated.owl.carousel": $.proxy(
+        function(e) {
+          if (e.namespace) {
+            this.swapping = e.type == "translated";
+          }
+        },
+        this
+      ),
+      "translate.owl.carousel": $.proxy(function(e) {
+        if (
+          e.namespace &&
+          this.swapping &&
+          (this.core.options.animateOut || this.core.options.animateIn)
+        ) {
+          this.swap();
+        }
+      }, this)
+    };
+
+    this.core.$element.on(this.handlers);
+  };
+
+  /**
+   * Default options.
+   * @public
+   */
+  Animate.Defaults = {
+    animateOut: false,
+    animateIn: false
+  };
+
+  /**
+   * Toggles the animation classes whenever an translations starts.
+   * @protected
+   * @returns {Boolean|undefined}
+   */
+  Animate.prototype.swap = function() {
+    if (this.core.settings.items !== 1) {
+      return;
+    }
+
+    if (!$.support.animation || !$.support.transition) {
+      return;
+    }
+
+    this.core.speed(0);
+
+    var left,
+      clear = $.proxy(this.clear, this),
+      previous = this.core.$stage.children().eq(this.previous),
+      next = this.core.$stage.children().eq(this.next),
+      incoming = this.core.settings.animateIn,
+      outgoing = this.core.settings.animateOut;
+
+    if (this.core.current() === this.previous) {
+      return;
+    }
+
+    if (outgoing) {
+      left =
+        this.core.coordinates(this.previous) - this.core.coordinates(this.next);
+      previous
+        .one($.support.animation.end, clear)
+        .css({ left: left + "px" })
+        .addClass("animated owl-animated-out")
+        .addClass(outgoing);
+    }
+
+    if (incoming) {
+      next
+        .one($.support.animation.end, clear)
+        .addClass("animated owl-animated-in")
+        .addClass(incoming);
+    }
+  };
+
+  Animate.prototype.clear = function(e) {
+    $(e.target)
+      .css({ left: "" })
+      .removeClass("animated owl-animated-out owl-animated-in")
+      .removeClass(this.core.settings.animateIn)
+      .removeClass(this.core.settings.animateOut);
+    this.core.onTransitionEnd();
+  };
+
+  /**
+   * Destroys the plugin.
+   * @public
+   */
+  Animate.prototype.destroy = function() {
+    var handler, property;
+
+    for (handler in this.handlers) {
+      this.core.$element.off(handler, this.handlers[handler]);
+    }
+    for (property in Object.getOwnPropertyNames(this)) {
+      typeof this[property] != "function" && (this[property] = null);
+    }
+  };
+
+  $.fn.owlCarousel.Constructor.Plugins.Animate = Animate;
 })(window.Zepto || window.jQuery, window, document);
 
 /**
@@ -2492,196 +2858,211 @@
  * @author David Deutsch
  * @license The MIT License (MIT)
  */
-;(function($, window, document, undefined) {
-
-	/**
-	 * Creates the autoplay plugin.
-	 * @class The Autoplay Plugin
-	 * @param {Owl} scope - The Owl Carousel
-	 */
-	var Autoplay = function(carousel) {
-		/**
-		 * Reference to the core.
-		 * @protected
-		 * @type {Owl}
-		 */
-		this._core = carousel;
-
-		/**
-		 * The autoplay timeout.
-		 * @type {Timeout}
-		 */
-		this._timeout = null;
-
-		/**
-		 * Indicates whenever the autoplay is paused.
-		 * @type {Boolean}
-		 */
-		this._paused = false;
-
-		/**
-		 * All event handlers.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._handlers = {
-			'changed.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && e.property.name === 'settings') {
-					if (this._core.settings.autoplay) {
-						this.play();
-					} else {
-						this.stop();
-					}
-				} else if (e.namespace && e.property.name === 'position') {
-					//console.log('play?', e);
-					if (this._core.settings.autoplay) {
-						this._setAutoPlayInterval();
-					}
-				}
-			}, this),
-			'initialized.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.autoplay) {
-					this.play();
-				}
-			}, this),
-			'play.owl.autoplay': $.proxy(function(e, t, s) {
-				if (e.namespace) {
-					this.play(t, s);
-				}
-			}, this),
-			'stop.owl.autoplay': $.proxy(function(e) {
-				if (e.namespace) {
-					this.stop();
-				}
-			}, this),
-			'mouseover.owl.autoplay': $.proxy(function() {
-				if (this._core.settings.autoplayHoverPause && this._core.is('rotating')) {
-					this.pause();
-				}
-			}, this),
-			'mouseleave.owl.autoplay': $.proxy(function() {
-				if (this._core.settings.autoplayHoverPause && this._core.is('rotating')) {
-					this.play();
-				}
-			}, this),
-			'touchstart.owl.core': $.proxy(function() {
-				if (this._core.settings.autoplayHoverPause && this._core.is('rotating')) {
-					this.pause();
-				}
-			}, this),
-			'touchend.owl.core': $.proxy(function() {
-				if (this._core.settings.autoplayHoverPause) {
-					this.play();
-				}
-			}, this)
-		};
-
-		// register event handlers
-		this._core.$element.on(this._handlers);
-
-		// set default options
-		this._core.options = $.extend({}, Autoplay.Defaults, this._core.options);
-	};
-
-	/**
-	 * Default options.
-	 * @public
-	 */
-	Autoplay.Defaults = {
-		autoplay: false,
-		autoplayTimeout: 5000,
-		autoplayHoverPause: false,
-		autoplaySpeed: false
-	};
-
-	/**
-	 * Starts the autoplay.
-	 * @public
-	 * @param {Number} [timeout] - The interval before the next animation starts.
-	 * @param {Number} [speed] - The animation speed for the animations.
-	 */
-	Autoplay.prototype.play = function(timeout, speed) {
-		this._paused = false;
-
-		if (this._core.is('rotating')) {
-			return;
-		}
-
-		this._core.enter('rotating');
-
-		this._setAutoPlayInterval();
-	};
-
-	/**
-	 * Gets a new timeout
-	 * @private
-	 * @param {Number} [timeout] - The interval before the next animation starts.
-	 * @param {Number} [speed] - The animation speed for the animations.
-	 * @return {Timeout}
-	 */
-	Autoplay.prototype._getNextTimeout = function(timeout, speed) {
-		if ( this._timeout ) {
-			window.clearTimeout(this._timeout);
-		}
-		return window.setTimeout($.proxy(function() {
-			if (this._paused || this._core.is('busy') || this._core.is('interacting') || document.hidden) {
-				return;
-			}
-			this._core.next(speed || this._core.settings.autoplaySpeed);
-		}, this), timeout || this._core.settings.autoplayTimeout);
-	};
-
-	/**
-	 * Sets autoplay in motion.
-	 * @private
-	 */
-	Autoplay.prototype._setAutoPlayInterval = function() {
-		this._timeout = this._getNextTimeout();
-	};
-
-	/**
-	 * Stops the autoplay.
-	 * @public
-	 */
-	Autoplay.prototype.stop = function() {
-		if (!this._core.is('rotating')) {
-			return;
-		}
-
-		window.clearTimeout(this._timeout);
-		this._core.leave('rotating');
-	};
-
-	/**
-	 * Stops the autoplay.
-	 * @public
-	 */
-	Autoplay.prototype.pause = function() {
-		if (!this._core.is('rotating')) {
-			return;
-		}
-
-		this._paused = true;
-	};
-
-	/**
-	 * Destroys the plugin.
-	 */
-	Autoplay.prototype.destroy = function() {
-		var handler, property;
-
-		this.stop();
-
-		for (handler in this._handlers) {
-			this._core.$element.off(handler, this._handlers[handler]);
-		}
-		for (property in Object.getOwnPropertyNames(this)) {
-			typeof this[property] != 'function' && (this[property] = null);
-		}
-	};
-
-	$.fn.owlCarousel.Constructor.Plugins.autoplay = Autoplay;
-
+(function($, window, document, undefined) {
+  /**
+   * Creates the autoplay plugin.
+   * @class The Autoplay Plugin
+   * @param {Owl} scope - The Owl Carousel
+   */
+  var Autoplay = function(carousel) {
+    /**
+     * Reference to the core.
+     * @protected
+     * @type {Owl}
+     */
+    this._core = carousel;
+
+    /**
+     * The autoplay timeout.
+     * @type {Timeout}
+     */
+    this._timeout = null;
+
+    /**
+     * Indicates whenever the autoplay is paused.
+     * @type {Boolean}
+     */
+    this._paused = false;
+
+    /**
+     * All event handlers.
+     * @protected
+     * @type {Object}
+     */
+    this._handlers = {
+      "changed.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && e.property.name === "settings") {
+          if (this._core.settings.autoplay) {
+            this.play();
+          } else {
+            this.stop();
+          }
+        } else if (e.namespace && e.property.name === "position") {
+          //console.log('play?', e);
+          if (this._core.settings.autoplay) {
+            this._setAutoPlayInterval();
+          }
+        }
+      }, this),
+      "initialized.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._core.settings.autoplay) {
+          this.play();
+        }
+      }, this),
+      "play.owl.autoplay": $.proxy(function(e, t, s) {
+        if (e.namespace) {
+          this.play(t, s);
+        }
+      }, this),
+      "stop.owl.autoplay": $.proxy(function(e) {
+        if (e.namespace) {
+          this.stop();
+        }
+      }, this),
+      "mouseover.owl.autoplay": $.proxy(function() {
+        if (
+          this._core.settings.autoplayHoverPause &&
+          this._core.is("rotating")
+        ) {
+          this.pause();
+        }
+      }, this),
+      "mouseleave.owl.autoplay": $.proxy(function() {
+        if (
+          this._core.settings.autoplayHoverPause &&
+          this._core.is("rotating")
+        ) {
+          this.play();
+        }
+      }, this),
+      "touchstart.owl.core": $.proxy(function() {
+        if (
+          this._core.settings.autoplayHoverPause &&
+          this._core.is("rotating")
+        ) {
+          this.pause();
+        }
+      }, this),
+      "touchend.owl.core": $.proxy(function() {
+        if (this._core.settings.autoplayHoverPause) {
+          this.play();
+        }
+      }, this)
+    };
+
+    // register event handlers
+    this._core.$element.on(this._handlers);
+
+    // set default options
+    this._core.options = $.extend({}, Autoplay.Defaults, this._core.options);
+  };
+
+  /**
+   * Default options.
+   * @public
+   */
+  Autoplay.Defaults = {
+    autoplay: false,
+    autoplayTimeout: 5000,
+    autoplayHoverPause: false,
+    autoplaySpeed: false
+  };
+
+  /**
+   * Starts the autoplay.
+   * @public
+   * @param {Number} [timeout] - The interval before the next animation starts.
+   * @param {Number} [speed] - The animation speed for the animations.
+   */
+  Autoplay.prototype.play = function(timeout, speed) {
+    this._paused = false;
+
+    if (this._core.is("rotating")) {
+      return;
+    }
+
+    this._core.enter("rotating");
+
+    this._setAutoPlayInterval();
+  };
+
+  /**
+   * Gets a new timeout
+   * @private
+   * @param {Number} [timeout] - The interval before the next animation starts.
+   * @param {Number} [speed] - The animation speed for the animations.
+   * @return {Timeout}
+   */
+  Autoplay.prototype._getNextTimeout = function(timeout, speed) {
+    if (this._timeout) {
+      window.clearTimeout(this._timeout);
+    }
+    return window.setTimeout(
+      $.proxy(function() {
+        if (
+          this._paused ||
+          this._core.is("busy") ||
+          this._core.is("interacting") ||
+          document.hidden
+        ) {
+          return;
+        }
+        this._core.next(speed || this._core.settings.autoplaySpeed);
+      }, this),
+      timeout || this._core.settings.autoplayTimeout
+    );
+  };
+
+  /**
+   * Sets autoplay in motion.
+   * @private
+   */
+  Autoplay.prototype._setAutoPlayInterval = function() {
+    this._timeout = this._getNextTimeout();
+  };
+
+  /**
+   * Stops the autoplay.
+   * @public
+   */
+  Autoplay.prototype.stop = function() {
+    if (!this._core.is("rotating")) {
+      return;
+    }
+
+    window.clearTimeout(this._timeout);
+    this._core.leave("rotating");
+  };
+
+  /**
+   * Stops the autoplay.
+   * @public
+   */
+  Autoplay.prototype.pause = function() {
+    if (!this._core.is("rotating")) {
+      return;
+    }
+
+    this._paused = true;
+  };
+
+  /**
+   * Destroys the plugin.
+   */
+  Autoplay.prototype.destroy = function() {
+    var handler, property;
+
+    this.stop();
+
+    for (handler in this._handlers) {
+      this._core.$element.off(handler, this._handlers[handler]);
+    }
+    for (property in Object.getOwnPropertyNames(this)) {
+      typeof this[property] != "function" && (this[property] = null);
+    }
+  };
+
+  $.fn.owlCarousel.Constructor.Plugins.autoplay = Autoplay;
 })(window.Zepto || window.jQuery, window, document);
 
 /**
@@ -2691,380 +3072,446 @@
  * @author David Deutsch
  * @license The MIT License (MIT)
  */
-;(function($, window, document, undefined) {
-	'use strict';
-
-	/**
-	 * Creates the navigation plugin.
-	 * @class The Navigation Plugin
-	 * @param {Owl} carousel - The Owl Carousel.
-	 */
-	var Navigation = function(carousel) {
-		/**
-		 * Reference to the core.
-		 * @protected
-		 * @type {Owl}
-		 */
-		this._core = carousel;
-
-		/**
-		 * Indicates whether the plugin is initialized or not.
-		 * @protected
-		 * @type {Boolean}
-		 */
-		this._initialized = false;
-
-		/**
-		 * The current paging indexes.
-		 * @protected
-		 * @type {Array}
-		 */
-		this._pages = [];
-
-		/**
-		 * All DOM elements of the user interface.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._controls = {};
-
-		/**
-		 * Markup for an indicator.
-		 * @protected
-		 * @type {Array.<String>}
-		 */
-		this._templates = [];
-
-		/**
-		 * The carousel element.
-		 * @type {jQuery}
-		 */
-		this.$element = this._core.$element;
-
-		/**
-		 * Overridden methods of the carousel.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._overrides = {
-			next: this._core.next,
-			prev: this._core.prev,
-			to: this._core.to
-		};
-
-		/**
-		 * All event handlers.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._handlers = {
-			'prepared.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.dotsData) {
-					this._templates.push('<div class="' + this._core.settings.dotClass + '">' +
-						$(e.content).find('[data-dot]').addBack('[data-dot]').attr('data-dot') + '</div>');
-				}
-			}, this),
-			'added.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.dotsData) {
-					this._templates.splice(e.position, 0, this._templates.pop());
-				}
-			}, this),
-			'remove.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.dotsData) {
-					this._templates.splice(e.position, 1);
-				}
-			}, this),
-			'changed.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && e.property.name == 'position') {
-					this.draw();
-				}
-			}, this),
-			'initialized.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && !this._initialized) {
-					this._core.trigger('initialize', null, 'navigation');
-					this.initialize();
-					this.update();
-					this.draw();
-					this._initialized = true;
-					this._core.trigger('initialized', null, 'navigation');
-				}
-			}, this),
-			'refreshed.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._initialized) {
-					this._core.trigger('refresh', null, 'navigation');
-					this.update();
-					this.draw();
-					this._core.trigger('refreshed', null, 'navigation');
-				}
-			}, this)
-		};
-
-		// set default options
-		this._core.options = $.extend({}, Navigation.Defaults, this._core.options);
-
-		// register event handlers
-		this.$element.on(this._handlers);
-	};
-
-	/**
-	 * Default options.
-	 * @public
-	 * @todo Rename `slideBy` to `navBy`
-	 */
-	Navigation.Defaults = {
-		nav: false,
-		navText: [ 'prev', 'next' ],
-		navSpeed: false,
-		navElement: 'div',
-		navContainer: false,
-		navContainerClass: 'owl-nav',
-		navClass: [ 'owl-prev', 'owl-next' ],
-		slideBy: 1,
-		dotClass: 'owl-dot',
-		dotsClass: 'owl-dots',
-		dots: true,
-		dotsEach: false,
-		dotsData: false,
-		dotsSpeed: false,
-		dotsContainer: false
-	};
-
-	/**
-	 * Initializes the layout of the plugin and extends the carousel.
-	 * @protected
-	 */
-	Navigation.prototype.initialize = function() {
-		var override,
-			settings = this._core.settings;
-
-		// create DOM structure for relative navigation
-		this._controls.$relative = (settings.navContainer ? $(settings.navContainer)
-			: $('<div>').addClass(settings.navContainerClass).appendTo(this.$element)).addClass('disabled');
-
-		this._controls.$previous = $('<' + settings.navElement + '>')
-			.addClass(settings.navClass[0])
-			.html(settings.navText[0])
-			.prependTo(this._controls.$relative)
-			.on('click', $.proxy(function(e) {
-				this.prev(settings.navSpeed);
-			}, this));
-		this._controls.$next = $('<' + settings.navElement + '>')
-			.addClass(settings.navClass[1])
-			.html(settings.navText[1])
-			.appendTo(this._controls.$relative)
-			.on('click', $.proxy(function(e) {
-				this.next(settings.navSpeed);
-			}, this));
-
-		// create DOM structure for absolute navigation
-		if (!settings.dotsData) {
-			this._templates = [ $('<div>')
-				.addClass(settings.dotClass)
-				.append($('<span>'))
-				.prop('outerHTML') ];
-		}
-
-		this._controls.$absolute = (settings.dotsContainer ? $(settings.dotsContainer)
-			: $('<div>').addClass(settings.dotsClass).appendTo(this.$element)).addClass('disabled');
-
-		this._controls.$absolute.on('click', 'div', $.proxy(function(e) {
-			var index = $(e.target).parent().is(this._controls.$absolute)
-				? $(e.target).index() : $(e.target).parent().index();
-
-			e.preventDefault();
-
-			this.to(index, settings.dotsSpeed);
-		}, this));
-
-		// override public methods of the carousel
-		for (override in this._overrides) {
-			this._core[override] = $.proxy(this[override], this);
-		}
-	};
-
-	/**
-	 * Destroys the plugin.
-	 * @protected
-	 */
-	Navigation.prototype.destroy = function() {
-		var handler, control, property, override;
-
-		for (handler in this._handlers) {
-			this.$element.off(handler, this._handlers[handler]);
-		}
-		for (control in this._controls) {
-			this._controls[control].remove();
-		}
-		for (override in this.overides) {
-			this._core[override] = this._overrides[override];
-		}
-		for (property in Object.getOwnPropertyNames(this)) {
-			typeof this[property] != 'function' && (this[property] = null);
-		}
-	};
-
-	/**
-	 * Updates the internal state.
-	 * @protected
-	 */
-	Navigation.prototype.update = function() {
-		var i, j, k,
-			lower = this._core.clones().length / 2,
-			upper = lower + this._core.items().length,
-			maximum = this._core.maximum(true),
-			settings = this._core.settings,
-			size = settings.center || settings.autoWidth || settings.dotsData
-				? 1 : settings.dotsEach || settings.items;
-
-		if (settings.slideBy !== 'page') {
-			settings.slideBy = Math.min(settings.slideBy, settings.items);
-		}
-
-		if (settings.dots || settings.slideBy == 'page') {
-			this._pages = [];
-
-			for (i = lower, j = 0, k = 0; i < upper; i++) {
-				if (j >= size || j === 0) {
-					this._pages.push({
-						start: Math.min(maximum, i - lower),
-						end: i - lower + size - 1
-					});
-					if (Math.min(maximum, i - lower) === maximum) {
-						break;
-					}
-					j = 0, ++k;
-				}
-				j += this._core.mergers(this._core.relative(i));
-			}
-		}
-	};
-
-	/**
-	 * Draws the user interface.
-	 * @todo The option `dotsData` wont work.
-	 * @protected
-	 */
-	Navigation.prototype.draw = function() {
-		var difference,
-			settings = this._core.settings,
-			disabled = this._core.items().length <= settings.items,
-			index = this._core.relative(this._core.current()),
-			loop = settings.loop || settings.rewind;
-
-		this._controls.$relative.toggleClass('disabled', !settings.nav || disabled);
-
-		if (settings.nav) {
-			this._controls.$previous.toggleClass('disabled', !loop && index <= this._core.minimum(true));
-			this._controls.$next.toggleClass('disabled', !loop && index >= this._core.maximum(true));
-		}
-
-		this._controls.$absolute.toggleClass('disabled', !settings.dots || disabled);
-
-		if (settings.dots) {
-			difference = this._pages.length - this._controls.$absolute.children().length;
-
-			if (settings.dotsData && difference !== 0) {
-				this._controls.$absolute.html(this._templates.join(''));
-			} else if (difference > 0) {
-				this._controls.$absolute.append(new Array(difference + 1).join(this._templates[0]));
-			} else if (difference < 0) {
-				this._controls.$absolute.children().slice(difference).remove();
-			}
-
-			this._controls.$absolute.find('.active').removeClass('active');
-			this._controls.$absolute.children().eq($.inArray(this.current(), this._pages)).addClass('active');
-		}
-	};
-
-	/**
-	 * Extends event data.
-	 * @protected
-	 * @param {Event} event - The event object which gets thrown.
-	 */
-	Navigation.prototype.onTrigger = function(event) {
-		var settings = this._core.settings;
-
-		event.page = {
-			index: $.inArray(this.current(), this._pages),
-			count: this._pages.length,
-			size: settings && (settings.center || settings.autoWidth || settings.dotsData
-				? 1 : settings.dotsEach || settings.items)
-		};
-	};
-
-	/**
-	 * Gets the current page position of the carousel.
-	 * @protected
-	 * @returns {Number}
-	 */
-	Navigation.prototype.current = function() {
-		var current = this._core.relative(this._core.current());
-		return $.grep(this._pages, $.proxy(function(page, index) {
-			return page.start <= current && page.end >= current;
-		}, this)).pop();
-	};
-
-	/**
-	 * Gets the current succesor/predecessor position.
-	 * @protected
-	 * @returns {Number}
-	 */
-	Navigation.prototype.getPosition = function(successor) {
-		var position, length,
-			settings = this._core.settings;
-
-		if (settings.slideBy == 'page') {
-			position = $.inArray(this.current(), this._pages);
-			length = this._pages.length;
-			successor ? ++position : --position;
-			position = this._pages[((position % length) + length) % length].start;
-		} else {
-			position = this._core.relative(this._core.current());
-			length = this._core.items().length;
-			successor ? position += settings.slideBy : position -= settings.slideBy;
-		}
-
-		return position;
-	};
-
-	/**
-	 * Slides to the next item or page.
-	 * @public
-	 * @param {Number} [speed=false] - The time in milliseconds for the transition.
-	 */
-	Navigation.prototype.next = function(speed) {
-		$.proxy(this._overrides.to, this._core)(this.getPosition(true), speed);
-	};
-
-	/**
-	 * Slides to the previous item or page.
-	 * @public
-	 * @param {Number} [speed=false] - The time in milliseconds for the transition.
-	 */
-	Navigation.prototype.prev = function(speed) {
-		$.proxy(this._overrides.to, this._core)(this.getPosition(false), speed);
-	};
-
-	/**
-	 * Slides to the specified item or page.
-	 * @public
-	 * @param {Number} position - The position of the item or page.
-	 * @param {Number} [speed] - The time in milliseconds for the transition.
-	 * @param {Boolean} [standard=false] - Whether to use the standard behaviour or not.
-	 */
-	Navigation.prototype.to = function(position, speed, standard) {
-		var length;
-
-		if (!standard && this._pages.length) {
-			length = this._pages.length;
-			$.proxy(this._overrides.to, this._core)(this._pages[((position % length) + length) % length].start, speed);
-		} else {
-			$.proxy(this._overrides.to, this._core)(position, speed);
-		}
-	};
-
-	$.fn.owlCarousel.Constructor.Plugins.Navigation = Navigation;
-
+(function($, window, document, undefined) {
+  "use strict";
+
+  /**
+   * Creates the navigation plugin.
+   * @class The Navigation Plugin
+   * @param {Owl} carousel - The Owl Carousel.
+   */
+  var Navigation = function(carousel) {
+    /**
+     * Reference to the core.
+     * @protected
+     * @type {Owl}
+     */
+    this._core = carousel;
+
+    /**
+     * Indicates whether the plugin is initialized or not.
+     * @protected
+     * @type {Boolean}
+     */
+    this._initialized = false;
+
+    /**
+     * The current paging indexes.
+     * @protected
+     * @type {Array}
+     */
+    this._pages = [];
+
+    /**
+     * All DOM elements of the user interface.
+     * @protected
+     * @type {Object}
+     */
+    this._controls = {};
+
+    /**
+     * Markup for an indicator.
+     * @protected
+     * @type {Array.<String>}
+     */
+    this._templates = [];
+
+    /**
+     * The carousel element.
+     * @type {jQuery}
+     */
+    this.$element = this._core.$element;
+
+    /**
+     * Overridden methods of the carousel.
+     * @protected
+     * @type {Object}
+     */
+    this._overrides = {
+      next: this._core.next,
+      prev: this._core.prev,
+      to: this._core.to
+    };
+
+    /**
+     * All event handlers.
+     * @protected
+     * @type {Object}
+     */
+    this._handlers = {
+      "prepared.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._core.settings.dotsData) {
+          this._templates.push(
+            '<div class="' +
+              this._core.settings.dotClass +
+              '">' +
+              $(e.content)
+                .find("[data-dot]")
+                .addBack("[data-dot]")
+                .attr("data-dot") +
+              "</div>"
+          );
+        }
+      }, this),
+      "added.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._core.settings.dotsData) {
+          this._templates.splice(e.position, 0, this._templates.pop());
+        }
+      }, this),
+      "remove.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._core.settings.dotsData) {
+          this._templates.splice(e.position, 1);
+        }
+      }, this),
+      "changed.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && e.property.name == "position") {
+          this.draw();
+        }
+      }, this),
+      "initialized.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && !this._initialized) {
+          this._core.trigger("initialize", null, "navigation");
+          this.initialize();
+          this.update();
+          this.draw();
+          this._initialized = true;
+          this._core.trigger("initialized", null, "navigation");
+        }
+      }, this),
+      "refreshed.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._initialized) {
+          this._core.trigger("refresh", null, "navigation");
+          this.update();
+          this.draw();
+          this._core.trigger("refreshed", null, "navigation");
+        }
+      }, this)
+    };
+
+    // set default options
+    this._core.options = $.extend({}, Navigation.Defaults, this._core.options);
+
+    // register event handlers
+    this.$element.on(this._handlers);
+  };
+
+  /**
+   * Default options.
+   * @public
+   * @todo Rename `slideBy` to `navBy`
+   */
+  Navigation.Defaults = {
+    nav: false,
+    navText: ["prev", "next"],
+    navSpeed: false,
+    navElement: "div",
+    navContainer: false,
+    navContainerClass: "owl-nav",
+    navClass: ["owl-prev", "owl-next"],
+    slideBy: 1,
+    dotClass: "owl-dot",
+    dotsClass: "owl-dots",
+    dots: true,
+    dotsEach: false,
+    dotsData: false,
+    dotsSpeed: false,
+    dotsContainer: false
+  };
+
+  /**
+   * Initializes the layout of the plugin and extends the carousel.
+   * @protected
+   */
+  Navigation.prototype.initialize = function() {
+    var override,
+      settings = this._core.settings;
+
+    // create DOM structure for relative navigation
+    this._controls.$relative = (settings.navContainer
+      ? $(settings.navContainer)
+      : $("<div>")
+          .addClass(settings.navContainerClass)
+          .appendTo(this.$element)
+    ).addClass("disabled");
+
+    this._controls.$previous = $("<" + settings.navElement + ">")
+      .addClass(settings.navClass[0])
+      .html(settings.navText[0])
+      .prependTo(this._controls.$relative)
+      .on(
+        "click",
+        $.proxy(function(e) {
+          this.prev(settings.navSpeed);
+        }, this)
+      );
+    this._controls.$next = $("<" + settings.navElement + ">")
+      .addClass(settings.navClass[1])
+      .html(settings.navText[1])
+      .appendTo(this._controls.$relative)
+      .on(
+        "click",
+        $.proxy(function(e) {
+          this.next(settings.navSpeed);
+        }, this)
+      );
+
+    // create DOM structure for absolute navigation
+    if (!settings.dotsData) {
+      this._templates = [
+        $("<div>")
+          .addClass(settings.dotClass)
+          .append($("<span>"))
+          .prop("outerHTML")
+      ];
+    }
+
+    this._controls.$absolute = (settings.dotsContainer
+      ? $(settings.dotsContainer)
+      : $("<div>")
+          .addClass(settings.dotsClass)
+          .appendTo(this.$element)
+    ).addClass("disabled");
+
+    this._controls.$absolute.on(
+      "click",
+      "div",
+      $.proxy(function(e) {
+        var index = $(e.target)
+          .parent()
+          .is(this._controls.$absolute)
+          ? $(e.target).index()
+          : $(e.target)
+              .parent()
+              .index();
+
+        e.preventDefault();
+
+        this.to(index, settings.dotsSpeed);
+      }, this)
+    );
+
+    // override public methods of the carousel
+    for (override in this._overrides) {
+      this._core[override] = $.proxy(this[override], this);
+    }
+  };
+
+  /**
+   * Destroys the plugin.
+   * @protected
+   */
+  Navigation.prototype.destroy = function() {
+    var handler, control, property, override;
+
+    for (handler in this._handlers) {
+      this.$element.off(handler, this._handlers[handler]);
+    }
+    for (control in this._controls) {
+      this._controls[control].remove();
+    }
+    for (override in this.overides) {
+      this._core[override] = this._overrides[override];
+    }
+    for (property in Object.getOwnPropertyNames(this)) {
+      typeof this[property] != "function" && (this[property] = null);
+    }
+  };
+
+  /**
+   * Updates the internal state.
+   * @protected
+   */
+  Navigation.prototype.update = function() {
+    var i,
+      j,
+      k,
+      lower = this._core.clones().length / 2,
+      upper = lower + this._core.items().length,
+      maximum = this._core.maximum(true),
+      settings = this._core.settings,
+      size =
+        settings.center || settings.autoWidth || settings.dotsData
+          ? 1
+          : settings.dotsEach || settings.items;
+
+    if (settings.slideBy !== "page") {
+      settings.slideBy = Math.min(settings.slideBy, settings.items);
+    }
+
+    if (settings.dots || settings.slideBy == "page") {
+      this._pages = [];
+
+      for (i = lower, j = 0, k = 0; i < upper; i++) {
+        if (j >= size || j === 0) {
+          this._pages.push({
+            start: Math.min(maximum, i - lower),
+            end: i - lower + size - 1
+          });
+          if (Math.min(maximum, i - lower) === maximum) {
+            break;
+          }
+          (j = 0), ++k;
+        }
+        j += this._core.mergers(this._core.relative(i));
+      }
+    }
+  };
+
+  /**
+   * Draws the user interface.
+   * @todo The option `dotsData` wont work.
+   * @protected
+   */
+  Navigation.prototype.draw = function() {
+    var difference,
+      settings = this._core.settings,
+      disabled = this._core.items().length <= settings.items,
+      index = this._core.relative(this._core.current()),
+      loop = settings.loop || settings.rewind;
+
+    this._controls.$relative.toggleClass("disabled", !settings.nav || disabled);
+
+    if (settings.nav) {
+      this._controls.$previous.toggleClass(
+        "disabled",
+        !loop && index <= this._core.minimum(true)
+      );
+      this._controls.$next.toggleClass(
+        "disabled",
+        !loop && index >= this._core.maximum(true)
+      );
+    }
+
+    this._controls.$absolute.toggleClass(
+      "disabled",
+      !settings.dots || disabled
+    );
+
+    if (settings.dots) {
+      difference =
+        this._pages.length - this._controls.$absolute.children().length;
+
+      if (settings.dotsData && difference !== 0) {
+        this._controls.$absolute.html(this._templates.join(""));
+      } else if (difference > 0) {
+        this._controls.$absolute.append(
+          new Array(difference + 1).join(this._templates[0])
+        );
+      } else if (difference < 0) {
+        this._controls.$absolute
+          .children()
+          .slice(difference)
+          .remove();
+      }
+
+      this._controls.$absolute.find(".active").removeClass("active");
+      this._controls.$absolute
+        .children()
+        .eq($.inArray(this.current(), this._pages))
+        .addClass("active");
+    }
+  };
+
+  /**
+   * Extends event data.
+   * @protected
+   * @param {Event} event - The event object which gets thrown.
+   */
+  Navigation.prototype.onTrigger = function(event) {
+    var settings = this._core.settings;
+
+    event.page = {
+      index: $.inArray(this.current(), this._pages),
+      count: this._pages.length,
+      size:
+        settings &&
+        (settings.center || settings.autoWidth || settings.dotsData
+          ? 1
+          : settings.dotsEach || settings.items)
+    };
+  };
+
+  /**
+   * Gets the current page position of the carousel.
+   * @protected
+   * @returns {Number}
+   */
+  Navigation.prototype.current = function() {
+    var current = this._core.relative(this._core.current());
+    return $.grep(
+      this._pages,
+      $.proxy(function(page, index) {
+        return page.start <= current && page.end >= current;
+      }, this)
+    ).pop();
+  };
+
+  /**
+   * Gets the current succesor/predecessor position.
+   * @protected
+   * @returns {Number}
+   */
+  Navigation.prototype.getPosition = function(successor) {
+    var position,
+      length,
+      settings = this._core.settings;
+
+    if (settings.slideBy == "page") {
+      position = $.inArray(this.current(), this._pages);
+      length = this._pages.length;
+      successor ? ++position : --position;
+      position = this._pages[((position % length) + length) % length].start;
+    } else {
+      position = this._core.relative(this._core.current());
+      length = this._core.items().length;
+      successor
+        ? (position += settings.slideBy)
+        : (position -= settings.slideBy);
+    }
+
+    return position;
+  };
+
+  /**
+   * Slides to the next item or page.
+   * @public
+   * @param {Number} [speed=false] - The time in milliseconds for the transition.
+   */
+  Navigation.prototype.next = function(speed) {
+    $.proxy(this._overrides.to, this._core)(this.getPosition(true), speed);
+  };
+
+  /**
+   * Slides to the previous item or page.
+   * @public
+   * @param {Number} [speed=false] - The time in milliseconds for the transition.
+   */
+  Navigation.prototype.prev = function(speed) {
+    $.proxy(this._overrides.to, this._core)(this.getPosition(false), speed);
+  };
+
+  /**
+   * Slides to the specified item or page.
+   * @public
+   * @param {Number} position - The position of the item or page.
+   * @param {Number} [speed] - The time in milliseconds for the transition.
+   * @param {Boolean} [standard=false] - Whether to use the standard behaviour or not.
+   */
+  Navigation.prototype.to = function(position, speed, standard) {
+    var length;
+
+    if (!standard && this._pages.length) {
+      length = this._pages.length;
+      $.proxy(this._overrides.to, this._core)(
+        this._pages[((position % length) + length) % length].start,
+        speed
+      );
+    } else {
+      $.proxy(this._overrides.to, this._core)(position, speed);
+    }
+  };
+
+  $.fn.owlCarousel.Constructor.Plugins.Navigation = Navigation;
 })(window.Zepto || window.jQuery, window, document);
 
 /**
@@ -3074,120 +3521,127 @@
  * @author David Deutsch
  * @license The MIT License (MIT)
  */
-;(function($, window, document, undefined) {
-	'use strict';
-
-	/**
-	 * Creates the hash plugin.
-	 * @class The Hash Plugin
-	 * @param {Owl} carousel - The Owl Carousel
-	 */
-	var Hash = function(carousel) {
-		/**
-		 * Reference to the core.
-		 * @protected
-		 * @type {Owl}
-		 */
-		this._core = carousel;
-
-		/**
-		 * Hash index for the items.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._hashes = {};
-
-		/**
-		 * The carousel element.
-		 * @type {jQuery}
-		 */
-		this.$element = this._core.$element;
-
-		/**
-		 * All event handlers.
-		 * @protected
-		 * @type {Object}
-		 */
-		this._handlers = {
-			'initialized.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && this._core.settings.startPosition === 'URLHash') {
-					$(window).trigger('hashchange.owl.navigation');
-				}
-			}, this),
-			'prepared.owl.carousel': $.proxy(function(e) {
-				if (e.namespace) {
-					var hash = $(e.content).find('[data-hash]').addBack('[data-hash]').attr('data-hash');
-
-					if (!hash) {
-						return;
-					}
-
-					this._hashes[hash] = e.content;
-				}
-			}, this),
-			'changed.owl.carousel': $.proxy(function(e) {
-				if (e.namespace && e.property.name === 'position') {
-					var current = this._core.items(this._core.relative(this._core.current())),
-						hash = $.map(this._hashes, function(item, hash) {
-							return item === current ? hash : null;
-						}).join();
-
-					if (!hash || window.location.hash.slice(1) === hash) {
-						return;
-					}
-
-					window.location.hash = hash;
-				}
-			}, this)
-		};
-
-		// set default options
-		this._core.options = $.extend({}, Hash.Defaults, this._core.options);
-
-		// register the event handlers
-		this.$element.on(this._handlers);
-
-		// register event listener for hash navigation
-		$(window).on('hashchange.owl.navigation', $.proxy(function(e) {
-			var hash = window.location.hash.substring(1),
-				items = this._core.$stage.children(),
-				position = this._hashes[hash] && items.index(this._hashes[hash]);
-
-			if (position === undefined || position === this._core.current()) {
-				return;
-			}
-
-			this._core.to(this._core.relative(position), false, true);
-		}, this));
-	};
-
-	/**
-	 * Default options.
-	 * @public
-	 */
-	Hash.Defaults = {
-		URLhashListener: false
-	};
-
-	/**
-	 * Destroys the plugin.
-	 * @public
-	 */
-	Hash.prototype.destroy = function() {
-		var handler, property;
-
-		$(window).off('hashchange.owl.navigation');
-
-		for (handler in this._handlers) {
-			this._core.$element.off(handler, this._handlers[handler]);
-		}
-		for (property in Object.getOwnPropertyNames(this)) {
-			typeof this[property] != 'function' && (this[property] = null);
-		}
-	};
-
-	$.fn.owlCarousel.Constructor.Plugins.Hash = Hash;
-
+(function($, window, document, undefined) {
+  "use strict";
+
+  /**
+   * Creates the hash plugin.
+   * @class The Hash Plugin
+   * @param {Owl} carousel - The Owl Carousel
+   */
+  var Hash = function(carousel) {
+    /**
+     * Reference to the core.
+     * @protected
+     * @type {Owl}
+     */
+    this._core = carousel;
+
+    /**
+     * Hash index for the items.
+     * @protected
+     * @type {Object}
+     */
+    this._hashes = {};
+
+    /**
+     * The carousel element.
+     * @type {jQuery}
+     */
+    this.$element = this._core.$element;
+
+    /**
+     * All event handlers.
+     * @protected
+     * @type {Object}
+     */
+    this._handlers = {
+      "initialized.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && this._core.settings.startPosition === "URLHash") {
+          $(window).trigger("hashchange.owl.navigation");
+        }
+      }, this),
+      "prepared.owl.carousel": $.proxy(function(e) {
+        if (e.namespace) {
+          var hash = $(e.content)
+            .find("[data-hash]")
+            .addBack("[data-hash]")
+            .attr("data-hash");
+
+          if (!hash) {
+            return;
+          }
+
+          this._hashes[hash] = e.content;
+        }
+      }, this),
+      "changed.owl.carousel": $.proxy(function(e) {
+        if (e.namespace && e.property.name === "position") {
+          var current = this._core.items(
+              this._core.relative(this._core.current())
+            ),
+            hash = $.map(this._hashes, function(item, hash) {
+              return item === current ? hash : null;
+            }).join();
+
+          if (!hash || window.location.hash.slice(1) === hash) {
+            return;
+          }
+
+          window.location.hash = hash;
+        }
+      }, this)
+    };
+
+    // set default options
+    this._core.options = $.extend({}, Hash.Defaults, this._core.options);
+
+    // register the event handlers
+    this.$element.on(this._handlers);
+
+    // register event listener for hash navigation
+    $(window).on(
+      "hashchange.owl.navigation",
+      $.proxy(function(e) {
+        var hash = window.location.hash.substring(1),
+          items = this._core.$stage.children(),
+          position = this._hashes[hash] && items.index(this._hashes[hash]);
+
+        if (position === undefined || position === this._core.current()) {
+          return;
+        }
+
+        this._core.to(this._core.relative(position), false, true);
+      }, this)
+    );
+  };
+
+  /**
+   * Default options.
+   * @public
+   */
+  Hash.Defaults = {
+    URLhashListener: false
+  };
+
+  /**
+   * Destroys the plugin.
+   * @public
+   */
+  Hash.prototype.destroy = function() {
+    var handler, property;
+
+    $(window).off("hashchange.owl.navigation");
+
+    for (handler in this._handlers) {
+      this._core.$element.off(handler, this._handlers[handler]);
+    }
+    for (property in Object.getOwnPropertyNames(this)) {
+      typeof this[property] != "function" && (this[property] = null);
+    }
+  };
+
+  $.fn.owlCarousel.Constructor.Plugins.Hash = Hash;
 })(window.Zepto || window.jQuery, window, document);
 
 /**
@@ -3199,77 +3653,78 @@
  * @author David Deutsch
  * @license The MIT License (MIT)
  */
-;(function($, window, document, undefined) {
-
-	var style = $('<support>').get(0).style,
-		prefixes = 'Webkit Moz O ms'.split(' '),
-		events = {
-			transition: {
-				end: {
-					WebkitTransition: 'webkitTransitionEnd',
-					MozTransition: 'transitionend',
-					OTransition: 'oTransitionEnd',
-					transition: 'transitionend'
-				}
-			},
-			animation: {
-				end: {
-					WebkitAnimation: 'webkitAnimationEnd',
-					MozAnimation: 'animationend',
-					OAnimation: 'oAnimationEnd',
-					animation: 'animationend'
-				}
-			}
-		},
-		tests = {
-			csstransforms: function() {
-				return !!test('transform');
-			},
-			csstransforms3d: function() {
-				return !!test('perspective');
-			},
-			csstransitions: function() {
-				return !!test('transition');
-			},
-			cssanimations: function() {
-				return !!test('animation');
-			}
-		};
-
-	function test(property, prefixed) {
-		var result = false,
-			upper = property.charAt(0).toUpperCase() + property.slice(1);
-
-		$.each((property + ' ' + prefixes.join(upper + ' ') + upper).split(' '), function(i, property) {
-			if (style[property] !== undefined) {
-				result = prefixed ? property : true;
-				return false;
-			}
-		});
-
-		return result;
-	}
-
-	function prefixed(property) {
-		return test(property, true);
-	}
-
-	if (tests.csstransitions()) {
-		/* jshint -W053 */
-		$.support.transition = new String(prefixed('transition'))
-		$.support.transition.end = events.transition.end[ $.support.transition ];
-	}
-
-	if (tests.cssanimations()) {
-		/* jshint -W053 */
-		$.support.animation = new String(prefixed('animation'))
-		$.support.animation.end = events.animation.end[ $.support.animation ];
-	}
-
-	if (tests.csstransforms()) {
-		/* jshint -W053 */
-		$.support.transform = new String(prefixed('transform'));
-		$.support.transform3d = tests.csstransforms3d();
-	}
-
+(function($, window, document, undefined) {
+  var style = $("<support>").get(0).style,
+    prefixes = "Webkit Moz O ms".split(" "),
+    events = {
+      transition: {
+        end: {
+          WebkitTransition: "webkitTransitionEnd",
+          MozTransition: "transitionend",
+          OTransition: "oTransitionEnd",
+          transition: "transitionend"
+        }
+      },
+      animation: {
+        end: {
+          WebkitAnimation: "webkitAnimationEnd",
+          MozAnimation: "animationend",
+          OAnimation: "oAnimationEnd",
+          animation: "animationend"
+        }
+      }
+    },
+    tests = {
+      csstransforms: function() {
+        return !!test("transform");
+      },
+      csstransforms3d: function() {
+        return !!test("perspective");
+      },
+      csstransitions: function() {
+        return !!test("transition");
+      },
+      cssanimations: function() {
+        return !!test("animation");
+      }
+    };
+
+  function test(property, prefixed) {
+    var result = false,
+      upper = property.charAt(0).toUpperCase() + property.slice(1);
+
+    $.each(
+      (property + " " + prefixes.join(upper + " ") + upper).split(" "),
+      function(i, property) {
+        if (style[property] !== undefined) {
+          result = prefixed ? property : true;
+          return false;
+        }
+      }
+    );
+
+    return result;
+  }
+
+  function prefixed(property) {
+    return test(property, true);
+  }
+
+  if (tests.csstransitions()) {
+    /* jshint -W053 */
+    $.support.transition = new String(prefixed("transition"));
+    $.support.transition.end = events.transition.end[$.support.transition];
+  }
+
+  if (tests.cssanimations()) {
+    /* jshint -W053 */
+    $.support.animation = new String(prefixed("animation"));
+    $.support.animation.end = events.animation.end[$.support.animation];
+  }
+
+  if (tests.csstransforms()) {
+    /* jshint -W053 */
+    $.support.transform = new String(prefixed("transform"));
+    $.support.transform3d = tests.csstransforms3d();
+  }
 })(window.Zepto || window.jQuery, window, document);
diff --git a/owl-carousel/owl.theme.css b/owl-carousel/owl.theme.css
index 413b8a4..cc414ac 100644
--- a/owl-carousel/owl.theme.css
+++ b/owl-carousel/owl.theme.css
@@ -9,42 +9,52 @@
 .owl-theme .owl-nav {
   margin-top: 10px;
   text-align: center;
-  -webkit-tap-highlight-color: transparent; }
-  .owl-theme .owl-nav [class*='owl-'] {
-    color: #FFF;
-    font-size: 14px;
-    margin: 5px;
-    padding: 4px 7px;
-    background: #D6D6D6;
-    display: inline-block;
-    cursor: pointer;
-    border-radius: 3px; }
-    .owl-theme .owl-nav [class*='owl-']:hover {
-      background: #869791;
-      color: #FFF;
-      text-decoration: none; }
-  .owl-theme .owl-nav .disabled {
-    opacity: 0.5;
-    cursor: default; }
+  -webkit-tap-highlight-color: transparent;
+}
+.owl-theme .owl-nav [class*="owl-"] {
+  color: #fff;
+  font-size: 14px;
+  margin: 5px;
+  padding: 4px 7px;
+  background: #d6d6d6;
+  display: inline-block;
+  cursor: pointer;
+  border-radius: 3px;
+}
+.owl-theme .owl-nav [class*="owl-"]:hover {
+  background: #869791;
+  color: #fff;
+  text-decoration: none;
+}
+.owl-theme .owl-nav .disabled {
+  opacity: 0.5;
+  cursor: default;
+}
 
 .owl-theme .owl-nav.disabled + .owl-dots {
-  margin-top: 10px; }
+  margin-top: 10px;
+}
 
 .owl-theme .owl-dots {
   text-align: center;
-  -webkit-tap-highlight-color: transparent; }
-  .owl-theme .owl-dots .owl-dot {
-    display: inline-block;
-    zoom: 1;
-    *display: inline; }
-    .owl-theme .owl-dots .owl-dot span {
-      width: 10px;
-      height: 10px;
-      margin: 5px 7px;
-      background: #D6D6D6;
-      display: block;
-      -webkit-backface-visibility: visible;
-      transition: opacity 200ms ease;
-      border-radius: 30px; }
-    .owl-theme .owl-dots .owl-dot.active span, .owl-theme .owl-dots .owl-dot:hover span {
-      background: #869791; }
+  -webkit-tap-highlight-color: transparent;
+}
+.owl-theme .owl-dots .owl-dot {
+  display: inline-block;
+  zoom: 1;
+  *display: inline;
+}
+.owl-theme .owl-dots .owl-dot span {
+  width: 10px;
+  height: 10px;
+  margin: 5px 7px;
+  background: #d6d6d6;
+  display: block;
+  -webkit-backface-visibility: visible;
+  transition: opacity 200ms ease;
+  border-radius: 30px;
+}
+.owl-theme .owl-dots .owl-dot.active span,
+.owl-theme .owl-dots .owl-dot:hover span {
+  background: #869791;
+}
diff --git a/people.html b/people.html
index 022af78..d639976 100644
--- a/people.html
+++ b/people.html
@@ -1,66 +1,149 @@
 <!DOCTYPE html>
 <html lang="en-US">
   <head>
-    <meta charset="UTF-8">
+    <meta charset="UTF-8" />
     <meta http-equiv="X-UA-Compatible" content="chrome=1" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <meta name="description" content="PEcAn : The Predictive Ecosystem Analyzer" />
-    <meta name="google-site-verification" content="WiPnxPvenKX6-C6fNrwp9v64f23Q1qYw26Kapyswgms" />
-    <link rel="stylesheet" type="text/css" media="screen" href="stylesheets/stylesheet.css">
+    <meta
+      name="description"
+      content="PEcAn : The Predictive Ecosystem Analyzer"
+    />
+    <meta
+      name="google-site-verification"
+      content="WiPnxPvenKX6-C6fNrwp9v64f23Q1qYw26Kapyswgms"
+    />
+    <link
+      rel="stylesheet"
+      type="text/css"
+      media="screen"
+      href="stylesheets/stylesheet.css"
+    />
     <title>PEcAn</title>
-    <link rel="stylesheet" href="css/components.css">
-    <link rel="stylesheet" href="css/icons.css">
-    <link rel="stylesheet" href="css/responsee.css">
-    <link rel="stylesheet" href="owl-carousel/owl.carousel.css">
-    <link rel="stylesheet" href="owl-carousel/owl.theme.css">     
-    <link rel="stylesheet" href="css/template-style.css">
-    <link href='https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
-    <link href='https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
+    <link rel="stylesheet" href="css/components.css" />
+    <link rel="stylesheet" href="css/icons.css" />
+    <link rel="stylesheet" href="css/responsee.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.carousel.css" />
+    <link rel="stylesheet" href="owl-carousel/owl.theme.css" />
+    <link rel="stylesheet" href="css/template-style.css" />
+    <link
+      href="https://fonts.googleapis.com/css?family=Playfair+Display&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
+    <link
+      href="https://fonts.googleapis.com/css?family=Open+Sans:400,300,700,800&subset=latin,latin-ext"
+      rel="stylesheet"
+      type="text/css"
+    />
     <script type="text/javascript" src="js/jquery-1.8.3.min.js"></script>
-    <script type="text/javascript" src="js/jquery-ui.min.js"></script>      
+    <script type="text/javascript" src="js/jquery-ui.min.js"></script>
   </head>
-  
+
   <body class="size-1140">
-  	<a target="_blank" class="hide-s" href="https://github.com/PecanProject" style="position:fixed;top:120px;right:-14px;z-index:10;"><img src="images/view-on-github.png" alt="" style="width: 200px; padding-right: 10px;"></a>
-    
+    <a
+      target="_blank"
+      class="hide-s"
+      href="https://github.com/PecanProject"
+      style="position:fixed;top:120px;right:-14px;z-index:10;"
+      ><img
+        src="images/view-on-github.png"
+        alt=""
+        style="width: 200px; padding-right: 10px;"
+    /></a>
+
     <!-- HEADER -->
-    
-        <header role="banner" class="position-absolute">    
+
+    <header role="banner" class="position-absolute">
       <!-- Top Navigation -->
       <nav class="background-dark background-transparent-hightlight full-width">
         <div class="s-12 l-2">
           <a href="index.html" class="logo">
             <!-- Logo White Version -->
-            <img class="logo-white" src="images/logo.png" alt="">
+            <img class="logo-white" src="images/logo.png" alt="" />
             <!-- Logo Dark Version -->
-            <img class="logo-dark" src="images/logo.png" alt="">
+            <img class="logo-dark" src="images/logo.png" alt="" />
           </a>
         </div>
         <div class="top-nav s-12 l-10 background-dark">
-          
           <ul class="right chevron">
             <li><a href="index.html">Home</a></li>
-            <li><a>About</a>
+            <li>
+              <a>About</a>
               <ul>
-                <li><a href="people.html" style="color: black;font-weight: 800;">People</a></li>
-                <li><a href="news.html" style="color: black;font-weight: 800;">News</a></li>
-                <li><a href="pecan_workshop.html" style="color: black;font-weight: 800;">Workshop</a></li>
-                <li><a href="contact.html" style="color: black;font-weight: 800;">Contact Us</a></li>
+                <li>
+                  <a href="people.html" style="color: black;font-weight: 800;"
+                    >People</a
+                  >
+                </li>
+                <li>
+                  <a href="news.html" style="color: black;font-weight: 800;"
+                    >News</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="pecan_workshop.html"
+                    style="color: black;font-weight: 800;"
+                    >Workshop</a
+                  >
+                </li>
+                <li>
+                  <a href="contact.html" style="color: black;font-weight: 800;"
+                    >Contact Us</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a>Documentation</a>
+            <li>
+              <a>Documentation</a>
               <ul>
-                <li><a href="documentation.html" style="color: black;font-weight: 800;">Documentation</a></li>
-                <li><a href="pkgdocs.html" style="color: black;font-weight: 800;">Package Documentation</a></li>
-                <li><a href="tutorials.html" style="color: black;font-weight: 800;">Tutorials</a></li>
-                <li><a href="http://pecan.ncsa.illinois.edu/pecan" style="color: black;font-weight: 800;">Demo</a></li>
+                <li>
+                  <a
+                    href="documentation.html"
+                    style="color: black;font-weight: 800;"
+                    >Documentation</a
+                  >
+                </li>
+                <li>
+                  <a href="pkgdocs.html" style="color: black;font-weight: 800;"
+                    >Package Documentation</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="tutorials.html"
+                    style="color: black;font-weight: 800;"
+                    >Tutorials</a
+                  >
+                </li>
+                <li>
+                  <a
+                    href="http://pecan.ncsa.illinois.edu/pecan"
+                    style="color: black;font-weight: 800;"
+                    >Demo</a
+                  >
+                </li>
               </ul>
             </li>
-            <li><a href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN">Download</a></li>
-            <li><a>Google</a>
+            <li>
+              <a
+                href="http://opensource.ncsa.illinois.edu/projects/artifacts.php?key=PECAN"
+                >Download</a
+              >
+            </li>
+            <li>
+              <a>Google</a>
               <ul>
-                <li><a href="gsoc.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
-                <li><a href="gsod.html" style="color: black;font-weight: 800;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a></li>
+                <li>
+                  <a href="gsoc.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
+                <li>
+                  <a href="gsod.html" style="color: black;font-weight: 800;"
+                    >&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;GSoD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</a
+                  >
+                </li>
               </ul>
             </li>
             <li><a href="Report_an_issue.html">Bug Report</a></li>
@@ -77,234 +160,397 @@
             <h1 class="text-white margin-top-20  text-size-60 text-line-height-1">About Us</h1>
           </div>  
         </header> -->
-        <div class="section background-white"> 
-          <div class="line">  
+        <div class="section background-white">
+          <div class="line">
             <div class="line margin-top-30">
               <div class="margin">
                 <div class="s-12 m-6 l-6">
-                  <img src="http://people.bu.edu/dietze/images/MikePalEON.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="http://people.bu.edu/dietze/images/MikePalEON.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Dr. Michael Dietze</h3>
                   <h6>PEcAn Lead PI</h6>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Boston University<br>
-                  Associate Professor<br>
-                  Department of Earth and Environment<br>
-                  <a href="http://people.bu.edu/dietze" rel="nofollow">http://people.bu.edu/dietze</a><br>
-                  dietze at bu dot edu
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Boston University<br />
+                    Associate Professor<br />
+                    Department of Earth and Environment<br />
+                    <a href="http://people.bu.edu/dietze" rel="nofollow"
+                      >http://people.bu.edu/dietze</a
+                    ><br />
+                    dietze at bu dot edu
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="https://datascience.arizona.edu/sites/default/files/styles/large/public/images/people/david_lebauer.jpg?itok=oQHA33dc" alt="" style="height: 300px;"><br>
+                  <img
+                    src="https://datascience.arizona.edu/sites/default/files/styles/large/public/images/people/david_lebauer.jpg?itok=oQHA33dc"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Dr. David LeBauer</h3>
                   <h6>PEcAn Co-PI</h6>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  University of Arizona<br>
-                  Director of Data Science for the Arizona<br>
-                  Experiment Station<br>
-                  <a href="https://davidlebauer.com" rel="nofollow"> https://davidlebauer.com</a><br>
-                  email: dlebauer@arizona.edu
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    University of Arizona<br />
+                    Director of Data Science for the Arizona<br />
+                    Experiment Station<br />
+                    <a href="https://davidlebauer.com" rel="nofollow">
+                      https://davidlebauer.com</a
+                    ><br />
+                    email: dlebauer@arizona.edu
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="images/kenton_pic.png" alt="" style="height: 300px;"><br>
+                  <img
+                    src="images/kenton_pic.png"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Dr. Kenton McHenry</h3>
                   <h6>PEcAn Co-PI</h6>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  National Center for Supercomputing<br>
-                  Applications<br>
-                  Image, Spatial, and Data Analysis Group<br>
-                  Project Leader & Research Scientist<br>
-                  <a href="http://isda.ncsa.illinois.edu/" rel="nofollow">http://isda.ncsa.illinois.edu/</a>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    National Center for Supercomputing<br />
+                    Applications<br />
+                    Image, Spatial, and Data Analysis Group<br />
+                    Project Leader & Research Scientist<br />
+                    <a href="http://isda.ncsa.illinois.edu/" rel="nofollow"
+                      >http://isda.ncsa.illinois.edu/</a
+                    >
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="images/ankur_pic.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="images/ankur_pic.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Dr. Ankur Desai</h3>
                   <h6>PEcAn Co-PI</h6>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  University of Wisconsin<br>
-                  Department of<br> 
-                  Atmospheric and Oceanic<br>
-                  Sciences<br>
-                  <a href="http://flux.aos.wisc.edu/" rel="nofollow">http://flux.aos.wisc.edu/</a>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    University of Wisconsin<br />
+                    Department of<br />
+                    Atmospheric and Oceanic<br />
+                    Sciences<br />
+                    <a href="http://flux.aos.wisc.edu/" rel="nofollow"
+                      >http://flux.aos.wisc.edu/</a
+                    >
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="http://isda.ncsa.illinois.edu/drupal/sites/default/files/pictures/picture-18.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="http://isda.ncsa.illinois.edu/drupal/sites/default/files/pictures/picture-18.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Rob Kooper</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  National Center for Supercomputing<br>
-                  Applications<br>
-                  Image, Spatial, and Data Analysis Group<br>
-                  Project Leader & Research Scientist<br>
-                  <a href="http://isda.ncsa.illinois.edu/drupal/users/kooper" rel="nofollow">http://isda.ncsa.illinois.edu/drupal/users/kooper</a>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    National Center for Supercomputing<br />
+                    Applications<br />
+                    Image, Spatial, and Data Analysis Group<br />
+                    Project Leader & Research Scientist<br />
+                    <a
+                      href="http://isda.ncsa.illinois.edu/drupal/users/kooper"
+                      rel="nofollow"
+                      >http://isda.ncsa.illinois.edu/drupal/users/kooper</a
+                    >
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="images/shawn_pic.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="images/shawn_pic.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Shawn Serbin</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Research Scientist<br>
-                  Brookhaven National Lab<br><br><br><br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Research Scientist<br />
+                    Brookhaven National Lab<br /><br /><br /><br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="images/chris_pic.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="images/chris_pic.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Christopher Black</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Postdoctoral Scholar<br>
-                  Penn State<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Postdoctoral Scholar<br />
+                    Penn State<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="http://www.bu.edu/earth/files/2016/01/ifp_photo-426x636.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="http://www.bu.edu/earth/files/2016/01/ifp_photo-426x636.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Istem Fer</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Postdoctoral Fellow<br>
-                  Boston University<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Postdoctoral Fellow<br />
+                    Boston University<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="https://i1.rgstatic.net/ii/profile.image/687414838312962-1540903877055_Q128/Hamze_Dokoohaki.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="https://i1.rgstatic.net/ii/profile.image/687414838312962-1540903877055_Q128/Hamze_Dokoohaki.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Hamze Dokoohaki</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Postdoctoral Fellow<br>
-                  Boston University<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Postdoctoral Fellow<br />
+                    Boston University<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="images/alexey_pic.png" alt="" style="height: 300px;"><br>
+                  <img
+                    src="images/alexey_pic.png"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Alexey Shiklomanov</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Post Doctorate Researcher<br>
-                  PNNL<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Post Doctorate Researcher<br />
+                    PNNL<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="http://www.bu.edu/earth/files/2014/08/04-elizabeth.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="http://www.bu.edu/earth/files/2014/08/04-elizabeth.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Betsy Cowdery</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Graduate Student<br>
-                  Boston University<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Graduate Student<br />
+                    Boston University<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="images/tonyg_pic.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="images/tonyg_pic.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Tony Gardella</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Project Manager<br>
-                  Boston University<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Project Manager<br />
+                    Boston University<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="https://us.123rf.com/450wm/pavelstasevich/pavelstasevich1811/pavelstasevich181101028/112815904-stock-vector-no-image-available-icon-flat-vector-illustration.jpg?ver=6" alt="" style="height: 300px;"><br>
+                  <img
+                    src="https://us.123rf.com/450wm/pavelstasevich/pavelstasevich1811/pavelstasevich181101028/112815904-stock-vector-no-image-available-icon-flat-vector-illustration.jpg?ver=6"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Tempest McCabe</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Graduate Student Boston University<br>
-                  Ann Raiho - Graduate Student Notre Dame<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Graduate Student Boston University<br />
+                    Ann Raiho - Graduate Student Notre Dame<br />
                   </p>
                 </div>
               </div>
-            </div>      
+            </div>
           </div>
-        </div> 
-        <h1 class="text-dark margin-top-10  text-size-30 text-line-height-1" style="text-align: center;">Previous Contributors</h1>
-        <div class="section background-white"> 
-          <div class="line">  
+        </div>
+        <h1
+          class="text-dark margin-top-10  text-size-30 text-line-height-1"
+          style="text-align: center;"
+        >
+          Previous Contributors
+        </h1>
+        <div class="section background-white">
+          <div class="line">
             <div class="line margin-top-30">
               <div class="margin">
                 <div class="s-12 m-6 l-6">
-                  <img src="https://us.123rf.com/450wm/pavelstasevich/pavelstasevich1811/pavelstasevich181101028/112815904-stock-vector-no-image-available-icon-flat-vector-illustration.jpg?ver=6" alt="" style="height: 300px;"><br>
+                  <img
+                    src="https://us.123rf.com/450wm/pavelstasevich/pavelstasevich1811/pavelstasevich181101028/112815904-stock-vector-no-image-available-icon-flat-vector-illustration.jpg?ver=6"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>James Simkins</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Graduate Student<br>
-                  University of Wisconsin<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Graduate Student<br />
+                    University of Wisconsin<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="http://people.bu.edu/dietze/images/JoshLab_small.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="http://people.bu.edu/dietze/images/JoshLab_small.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Josh Mantooth</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Graduate Student<br>
-                  Boston University<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Graduate Student<br />
+                    Boston University<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="http://people.bu.edu/dietze/images/ToniViskari_small.JPG" alt="" style="height: 300px;"><br>
+                  <img
+                    src="http://people.bu.edu/dietze/images/ToniViskari_small.JPG"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Toni Viskari</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Postdoctoral Fellow<br>
-                  Brookhaven National Lab<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Postdoctoral Fellow<br />
+                    Brookhaven National Lab<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="http://people.bu.edu/dietze/images/Brady_crop.JPG" alt="" style="height: 300px;"><br>
+                  <img
+                    src="http://people.bu.edu/dietze/images/Brady_crop.JPG"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Brady Hardiman</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Postdoctoral Fellow<br>
-                  Boston University<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Postdoctoral Fellow<br />
+                    Boston University<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="http://www.life.illinois.edu/dietze/images/CarlDavidsonSmall.jpg" alt="" style="height: 300px;"><br>
+                  <img
+                    src="http://www.life.illinois.edu/dietze/images/CarlDavidsonSmall.jpg"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Carl Davidson</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Masters Student (2012)<br>
-                  University of Illinois<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Masters Student (2012)<br />
+                    University of Illinois<br />
                   </p>
                 </div>
                 <div class="s-12 m-6 l-6">
-                  <img src="https://us.123rf.com/450wm/pavelstasevich/pavelstasevich1811/pavelstasevich181101028/112815904-stock-vector-no-image-available-icon-flat-vector-illustration.jpg?ver=6" alt="" style="height: 300px;"><br>
+                  <img
+                    src="https://us.123rf.com/450wm/pavelstasevich/pavelstasevich1811/pavelstasevich181101028/112815904-stock-vector-no-image-available-icon-flat-vector-illustration.jpg?ver=6"
+                    alt=""
+                    style="height: 300px;"
+                  /><br />
                   <h3>Patrick Mulrooney</h3>
-                  <p class="margin-top-30" style="color: black;font-weight: 400;">
-                  Research Programmer<br>
-                  National Center for Supercomputing<br>
-                  Applications<br>
-                  University of lllinois<br>
+                  <p
+                    class="margin-top-30"
+                    style="color: black;font-weight: 400;"
+                  >
+                    Research Programmer<br />
+                    National Center for Supercomputing<br />
+                    Applications<br />
+                    University of lllinois<br />
                   </p>
                 </div>
               </div>
-            </div>      
+            </div>
           </div>
-        </div> 
+        </div>
       </article>
     </main>
 
-  <!-- scripts -->    
+    <!-- scripts -->
+
+    <script type="text/javascript" src="js/responsee.js"></script>
+    <script type="text/javascript" src="owl-carousel/owl.carousel.js"></script>
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-  <script type="text/javascript" src="js/responsee.js"></script>
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diff --git a/pkgdocs/index.html b/pkgdocs/index.html
index d886c8d..8962cd1 100644
--- a/pkgdocs/index.html
+++ b/pkgdocs/index.html
@@ -1,43 +1,65 @@
 <h2 id="documentation">Documentation:</h2>
 <ul>
-<li><a href="/base/all/docs/index.html">base/all</a></li>
-<li><a href="/base/db/docs/index.html">base/db</a></li>
-<li><a href="/base/logger/docs/index.html">base/logger</a></li>
-<li><a href="/base/qaqc/docs/index.html">base/qaqc</a></li>
-<li><a href="/base/remote/docs/index.html">base/remote</a></li>
-<li><a href="/base/settings/docs/index.html">base/settings</a></li>
-<li><a href="/base/utils/docs/index.html">base/utils</a></li>
-<li><a href="/base/visualization/docs/index.html">base/visualization</a></li>
-<li><a href="/base/workflow/docs/index.html">base/workflow</a></li>
-<li><a href="/models/biocro/docs/index.html">models/biocro</a></li>
-<li><a href="/models/cable/docs/index.html">models/cable</a></li>
-<li><a href="/models/clm45/docs/index.html">models/clm45</a></li>
-<li><a href="/models/dalec/docs/index.html">models/dalec</a></li>
-<li><a href="/models/dvmdostem/docs/index.html">models/dvmdostem</a></li>
-<li><a href="/models/ed/docs/index.html">models/ed</a></li>
-<li><a href="/models/fates/docs/index.html">models/fates</a></li>
-<li><a href="/models/gday/docs/index.html">models/gday</a></li>
-<li><a href="/models/jules/docs/index.html">models/jules</a></li>
-<li><a href="/models/linkages/docs/index.html">models/linkages</a></li>
-<li><a href="/models/lpjguess/docs/index.html">models/lpjguess</a></li>
-<li><a href="/models/maat/docs/index.html">models/maat</a></li>
-<li><a href="/models/maespa/docs/index.html">models/maespa</a></li>
-<li><a href="/models/preles/docs/index.html">models/preles</a></li>
-<li><a href="/models/sipnet/docs/index.html">models/sipnet</a></li>
-<li><a href="/models/template/docs/index.html">models/template</a></li>
-<li><a href="/modules/allometry/docs/index.html">modules/allometry</a></li>
-<li><a href="/modules/assim.batch/docs/index.html">modules/assim.batch</a></li>
-<li><a href="/modules/assim.sequential/docs/index.html">modules/assim.sequential</a></li>
-<li><a href="/modules/benchmark/docs/index.html">modules/benchmark</a></li>
-<li><a href="/modules/data.atmosphere/docs/index.html">modules/data.atmosphere</a></li>
-<li><a href="/modules/data.hydrology/docs/index.html">modules/data.hydrology</a></li>
-<li><a href="/modules/data.land/docs/index.html">modules/data.land</a></li>
-<li><a href="/modules/data.mining/docs/index.html">modules/data.mining</a></li>
-<li><a href="/modules/data.remote/docs/index.html">modules/data.remote</a></li>
-<li><a href="/modules/emulator/docs/index.html">modules/emulator</a></li>
-<li><a href="/modules/meta.analysis/docs/index.html">modules/meta.analysis</a></li>
-<li><a href="/modules/photosynthesis/docs/index.html">modules/photosynthesis</a></li>
-<li><a href="/modules/priors/docs/index.html">modules/priors</a></li>
-<li><a href="/modules/rtm/docs/index.html">modules/rtm</a></li>
-<li><a href="/modules/uncertainty/docs/index.html">modules/uncertainty</a></li>
+  <li><a href="/base/all/docs/index.html">base/all</a></li>
+  <li><a href="/base/db/docs/index.html">base/db</a></li>
+  <li><a href="/base/logger/docs/index.html">base/logger</a></li>
+  <li><a href="/base/qaqc/docs/index.html">base/qaqc</a></li>
+  <li><a href="/base/remote/docs/index.html">base/remote</a></li>
+  <li><a href="/base/settings/docs/index.html">base/settings</a></li>
+  <li><a href="/base/utils/docs/index.html">base/utils</a></li>
+  <li><a href="/base/visualization/docs/index.html">base/visualization</a></li>
+  <li><a href="/base/workflow/docs/index.html">base/workflow</a></li>
+  <li><a href="/models/biocro/docs/index.html">models/biocro</a></li>
+  <li><a href="/models/cable/docs/index.html">models/cable</a></li>
+  <li><a href="/models/clm45/docs/index.html">models/clm45</a></li>
+  <li><a href="/models/dalec/docs/index.html">models/dalec</a></li>
+  <li><a href="/models/dvmdostem/docs/index.html">models/dvmdostem</a></li>
+  <li><a href="/models/ed/docs/index.html">models/ed</a></li>
+  <li><a href="/models/fates/docs/index.html">models/fates</a></li>
+  <li><a href="/models/gday/docs/index.html">models/gday</a></li>
+  <li><a href="/models/jules/docs/index.html">models/jules</a></li>
+  <li><a href="/models/linkages/docs/index.html">models/linkages</a></li>
+  <li><a href="/models/lpjguess/docs/index.html">models/lpjguess</a></li>
+  <li><a href="/models/maat/docs/index.html">models/maat</a></li>
+  <li><a href="/models/maespa/docs/index.html">models/maespa</a></li>
+  <li><a href="/models/preles/docs/index.html">models/preles</a></li>
+  <li><a href="/models/sipnet/docs/index.html">models/sipnet</a></li>
+  <li><a href="/models/template/docs/index.html">models/template</a></li>
+  <li><a href="/modules/allometry/docs/index.html">modules/allometry</a></li>
+  <li>
+    <a href="/modules/assim.batch/docs/index.html">modules/assim.batch</a>
+  </li>
+  <li>
+    <a href="/modules/assim.sequential/docs/index.html"
+      >modules/assim.sequential</a
+    >
+  </li>
+  <li><a href="/modules/benchmark/docs/index.html">modules/benchmark</a></li>
+  <li>
+    <a href="/modules/data.atmosphere/docs/index.html"
+      >modules/data.atmosphere</a
+    >
+  </li>
+  <li>
+    <a href="/modules/data.hydrology/docs/index.html">modules/data.hydrology</a>
+  </li>
+  <li><a href="/modules/data.land/docs/index.html">modules/data.land</a></li>
+  <li>
+    <a href="/modules/data.mining/docs/index.html">modules/data.mining</a>
+  </li>
+  <li>
+    <a href="/modules/data.remote/docs/index.html">modules/data.remote</a>
+  </li>
+  <li><a href="/modules/emulator/docs/index.html">modules/emulator</a></li>
+  <li>
+    <a href="/modules/meta.analysis/docs/index.html">modules/meta.analysis</a>
+  </li>
+  <li>
+    <a href="/modules/photosynthesis/docs/index.html">modules/photosynthesis</a>
+  </li>
+  <li><a href="/modules/priors/docs/index.html">modules/priors</a></li>
+  <li><a href="/modules/rtm/docs/index.html">modules/rtm</a></li>
+  <li>
+    <a href="/modules/uncertainty/docs/index.html">modules/uncertainty</a>
+  </li>
 </ul>
diff --git a/stylesheets/pygment_trac.css b/stylesheets/pygment_trac.css
index e65cedf..dff8325 100644
--- a/stylesheets/pygment_trac.css
+++ b/stylesheets/pygment_trac.css
@@ -1,70 +1,234 @@
-.highlight .hll { background-color: #ffffcc }
-.highlight  { background: #f0f3f3; }
-.highlight .c { color: #0099FF; font-style: italic } /* Comment */
-.highlight .err { color: #AA0000; background-color: #FFAAAA } /* Error */
-.highlight .k { color: #006699; font-weight: bold } /* Keyword */
-.highlight .o { color: #555555 } /* Operator */
-.highlight .cm { color: #0099FF; font-style: italic } /* Comment.Multiline */
-.highlight .cp { color: #009999 } /* Comment.Preproc */
-.highlight .c1 { color: #0099FF; font-style: italic } /* Comment.Single */
-.highlight .cs { color: #0099FF; font-weight: bold; font-style: italic } /* Comment.Special */
-.highlight .gd { background-color: #FFCCCC; border: 1px solid #CC0000 } /* Generic.Deleted */
-.highlight .ge { font-style: italic } /* Generic.Emph */
-.highlight .gr { color: #FF0000 } /* Generic.Error */
-.highlight .gh { color: #003300; font-weight: bold } /* Generic.Heading */
-.highlight .gi { background-color: #CCFFCC; border: 1px solid #00CC00 } /* Generic.Inserted */
-.highlight .go { color: #AAAAAA } /* Generic.Output */
-.highlight .gp { color: #000099; font-weight: bold } /* Generic.Prompt */
-.highlight .gs { font-weight: bold } /* Generic.Strong */
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+}